proforma for submission of research...
TRANSCRIPT
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PROFORMA FOR SUBMISSION OF RESEARCH & DEVELOPMENT
PROJECTS UNDER BIOINFORMATICS
PART I: GENERAL INFORMATION
1. Name of the Institute/University/Organization submitting the Project Proposal:
Institute of Bioinformatics,
Unit 1, Discoverer building, 7th
Floor,
International Tech Park Bangalore
Whitefield, Bangalore - 560 066
Ph: +91 80 28416140; Fax: +91 80 28416132
Web: www.ibioinformatics.org
2. State: Karnataka
3. Status of the Institute: Private Non-Profit Institute Recognized by DSIR in 2004
4. Name and designation of the Executive Authority of the Institute/University
forwarding the application: Dr. Akhilesh Pandey
Founder and Director
Institute of Bioinformatics
Unit 1, Discoverer building, 7th
Floor,
International Tech Park Bangalore
Whitefield Road, Bangalore - 560 066
Ph: +91 80 28416140; Fax: +91 80 28416132
Email: [email protected]
5. Project Title: “Development of 1000 Human Signaling Pathway Reference Maps- A
Unique 10 Centre Collaborative Network Initiative for Human Resource Development in
Bioinformatics in India”
6. Category of the Project: R&D in Bioinformatics
7. Specific Area: Database Development
8. Duration: 4 Years
9. Total Cost (Rs.): 849.26 lakhs
10. Is the project Single Institutional or Multiple-Institutional S/M)? : M
11. If the project is multi-institutional, please furnish the following:
Project Coordinators
1) Name: Dr. Akhilesh Pandey 2) Name: Dr. Rajesh Raju
Affiliation: Institute of Bioinformatics Affiliation: Institute of Bioinformatics
Address: Discoverer building, 7th Floor, Address: Discoverer building, 7
th Floor,
International Tech Park Bangalore, International Tech Park Bangalore,
Whitefield Road, Bangalore - 560 066, Whitefield Road, Bangalore - 560 066,
Ph: +91 80 28416140; Ph: +91 80 28416140;
Fax: +91 80 28416132 Fax: +91 80 28416132
Email: [email protected] Email: [email protected]
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12. Project Summary (Not to exceed two pages) Cell signaling pathways encompass the topological network of molecular reactions which mediate response to the diverse array of signals that the cells encounter. It is established that dysregulation of signaling pathways is the cornerstone to several diseases such as cancer, diabetes, or neurological disorders. With a large number of genomes being analyzed, it is now clear that an understanding of signaling pathways hold the key to develop strategies to combat these disorders and not merely a listing of mutations and mutated genes. In fact, signaling pathways and not individual genes have already been proposed as therapeutic targets in a number of cancers including breast (Rosen et al., 2010), pancreatic (Xia et al., 2011), non-small-cell lung (Schmid et al., 2010), head and neck (Freudlsperger et al., 2010) and ovarian (Shao et al., 2012) cancers. Thus, analysis of signaling pathways is not only indispensible for understanding biological systems but is also essential to re-establish pathways that have become deregulated in disease states. Out of nearly 4000 genes that encode transmembrane proteins (Lander et al., 2001), only partial information on signaling pathways initiated by less than 200 receptors are available in different pathway resources. Many of these resources are also moving away from its open-source/free-software roots to a user-pay system. Moreover, these resources also lack the pathway information to the level of the genes which are regulated by specific signaling pathways along with their transcriptional regulators. Currently, there is no database available in the public domain that is equipped to address complex biological problems through systems biology approaches. Thus, there is an urgent need for development of a resource of signaling pathways suitable for all systems biology approaches that can be used by the entire spectrum of biomedical community. Towards this, with internal funding, Institute of Bioinformatics, Bangalore, have established a publicly-available freely-accessible resource of human signaling pathways named NetPath (www.netpath.org) (Kandasamy and Mohan et al., Genome Biology, 2010). We have already developed the tool, 'PathBuilder', to streamline pathway development (Kandasamy et al., Bioinformatics, 2010). For the first time in India, we have already initiated post-graduate student training programme in 10 universities, integrating well into curriculum, to develop signaling pathways. Thus far, this revolutionizing effort has led to training of over 200 students from bioinformatics, biochemistry and biotechnology disciplines in these universities. This has already led to the publication of 28 signaling pathways authored by 60 scientists including students and faculty members from several national Universities, research scientists from IOB, and national and international experts of specific signaling pathways. Signaling pathways developed include TGF-beta (Raju et al., Database, 2011); Prolactin signaling pathway (Radhakrishnan et al., Journal of Cell Communication and Signaling, 2012); TWEAK signaling pathway (Bhattacharjee et al., Journal of Signal Transduction, 2012); TSH pathway (Goel et al., Journal of Proteomics and Bioinformatics, 2011); FSH pathway (Telikicherla et al., BMC Research Notes, 2011); Leptin signaling pathway (Nanjappa et al., Journal of Proteomics and Bioinformatics, 2011) and RANKL signaling pathway (Raju et al., Database, 2011). Our community participation effort has already shown lot of promise as an effective and fast-track mode of human resource development in India. We have a larger vision of characterizing most of the signaling pathways in humans. The prime goal of this project is to develop 1000 signaling pathway maps with a panel of national and international experts on specific signaling pathways on board. Simultaneously, we propose to achieve human resource development in this area of biomedical science, by forging a network of Universities to impart training to the post-graduate students of biological sciences in India. To best impart this human resource development programme, we will also facilitate interaction between the students and the faculty members with the world leaders who have significantly contributed to the field of signal transduction through conferences and workshops. The coordinated outcome of this proposed project would transform NetPath into, the largest
open-source repository of human signaling pathways, well-equipped to meet the challenges
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of functional genomics and systems biology. The current data in NetPath is being used for
analysis of experimental data in the context of specific pathways, function and diseases by
the entire biomedical community. A detailed characterization of molecules and their reactions
that synchronize cellular function would accelerate research and enable identification and
attribution of function to a large number of molecules in specific pathways. High-quality
data emanating from this project will be used to develop open-source pathway data
analysis suites and also for developing heuristic methods for the prediction of novel
molecules and their relationships in signaling pathways. Such novel molecules unique to
specific cellular processes may be selectively validated for their therapeutic applications. We are confident that our 1000 signaling pathway reference map will become a worldwide
community standard even before the project is completed. The proposed model of human
resource development in this project will help envision, strengthen and reinforce
biomedical research in India. This will be a continued endeavor with involvement of
bioinformaticians and experimental biologists in India in the subsequent phases to achieve
our goals (Figure 1).
Figure 1: An outline of our goals that will be initiated with this proposal
Over 1000 students from bioscience disciplines will be trained in the period of 4 years under
this project. We are sure that the trained manpower will radiate their knowledge across
various laboratories and institutions in the future. The network and association developed
between premier educational and research organizations in India would enable technology
transfer and interventions channelizing targeted and broader scientific endeavors in the
future. Successful outcome of our vision would place India in the forefront of biomedical
research in the world.
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PART II: PARTICULARS OF INVESTIGATORS
Principal Investigator
13. Name: Dr. T. S. Keshava Prasad
Date of Birth: 08 April, 1975 Sex (M/F): M
Indicate whether Principal Investigator/Co-Investigator: Principal Investigator
Designation: Faculty Scientist
Department: Bioinformatics
Institute/University: Institute of Bioinformatics
Address: Unit 1, Discoverer building, 7th Floor,
International Tech Park Bangalore,
Whitefield, Bangalore – 560 066, Karnataka
Ph: +91 80 28416140; Fax: +91 80 28416132
Web: www.ibioinformatics.org
Email: [email protected]
No. of projects being handled at present: 05
Note: Use separate page, if more investigators are involved..
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Co-investigators from Institute of Bioinformatics
1. Name: Dr. Rajesh Raju
Date of Birth: 05 February, 1981 Sex (M/F): M
Indicate whether Principal Investigator/Co-Investigator: Co-investigator
Designation: Faculty Scientist
Department: Bioinformatics
Institute/University: Institute of Bioinformatics
Address: Unit 1, Discoverer building, 7th Floor,
International Tech Park Bangalore,
Whitefield, Bangalore – 560 066, Karnataka.
Ph: +91 80 28416140; Fax: +91 80 28416132
Web: www.ibioinformatics.org
Email: [email protected]
Number of research projects being handled at present: 0
2. Name: Dr. Aditi Chatterjee
Date of Birth: 13 September, 1971 Sex (M/F): F
Indicate whether Principal Investigator/Co-Investigator: Co- investigator
Designation: Faculty Scientist
Institute/University: Institute of Bioinformatics, Bangalore
Address: Unit 1, Discoverer building, 7th Floor,
International Tech Park Bangalore,
Whitefield Road, Bangalore-560 066, Karnataka.
Ph: +91 80 28416140; Fax: +91 80 28416132
Email: [email protected]
Number of research projects being handled at present: 01
3. Name: Dr. Sowmya Soman
Date of Birth: 17 March, 1981 Sex (M/F): F
Indicate whether Principal Investigator/Co-Investigator: Co-investigator
Designation: Faculty Scientist
Department: Bioinformatics
Institute/University: Institute of Bioinformatics
Address: Unit 1, Discoverer building, 7th Floor,
International Tech Park Bangalore,
Whitefield, Bangalore – 560 066, Karnataka.
Ph: +91 80 28416140; Fax: +91 80 28416132
Web: www.ibioinformatics.org
Email: [email protected]
Number of research projects being handled at present: 0
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4. Name: Dr. Akhilesh Pandey
Date of Birth: 26 August, 1969 Sex (M/F): M
Indicate whether Principal Investigator/Co-Investigator: Co-investigator
Designation: Founder and Director
Department: Bioinformatics
Institute/University: Institute of Bioinformatics
Address: Unit 1, Discoverer building, 7th Floor,
International Tech Park Bangalore,
Whitefield, Bangalore – 560 066, Karnataka.
Ph: +91 80 28416140; Fax: +91 80 28416132
Web: www.ibioinformatics.org
Email: [email protected]
Number of research projects being handled at present: 05
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Co-investigators and Project Leaders from Participating Research Centers
Project Leaders from Pune University
Name: Dr. Kulkarni-Kale Urmila
Date of Birth: 09 May, 1964 Sex (M/F): F
Indicate whether Principal Investigator/Co-Investigator: Co-investigator
Designation: Information scientist
Department: Department of Bioinformatics
Institute/University: University of Pune
Address: University of Pune,
Ganeshkhind Road,
Pune - 411 007, Maharashtra.
Ph: +91 20 25692039, 25690195; Fax: +91 20 25690087
Email: [email protected]
Name: Dr. Sangeeta Sawat
Date of Birth: 28 February, 1966 Sex (M/F): F
Indicate whether Principal Investigator/Co-Investigator: Co-investigator
Designation: Assistant Professor
Department: Department of Bioinformatics
Institute/University: University of Pune
Address: University of Pune,
Ganeshkhind Road,
Pune - 411 007, Maharashtra.
Ph: +91 20 25692039, 25690195; Fax: +91 20 25690087
Email: [email protected]
Name: Dr. Dattatraya V. Desai
Date of Birth: 31 October, 1974 Sex (M/F): M
Indicate whether Principal Investigator/Co-Investigator: Co-investigator
Designation: Information scientist
Department: Department of Bioinformatics
Institute/University: University of Pune
Address: University of Pune,
Ganeshkhind Road,
Pune - 411 007, Maharashtra.
Ph: +91 20 25692039, 25690195; Fax: +91 20 25690087
Email: [email protected]
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Project Leaders from Madurai Kamaraj University
Name: Dr. P. Gunasekaran
Date of Birth: 02 July, 1954 Sex (M/F): M
Indicate whether Principal Investigator/Co-Investigator: Co-investigator
Designation: Coordinator (NRCBS program and Genomics program),
Senior Professor and Head
Department: Department of Genetics
Institute/University: Madurai Kamaraj University
Address: Center for Excellence in Genomic Sciences,
School of Biological Sciences, Madurai Kamaraj University,
Madurai 625 021, Tamil Nadu.
Ph: +91 452 2458478/2458209/2459873
Email: [email protected]
Name: Dr. S. Krishnaswamy
Date of Birth: 29 July, 1959 Sex (M/F): M
Indicate whether Principal Investigator/Co-Investigator: Co-investigator
Designation: Senior Professor, Head & Chairperson
Department: Department of Genetic Engineering
Institute/University: Madurai Kamaraj University
Address: School of Biotechnology,
Madurai Kamaraj University,
Madurai 625 021, Tamil Nadu.
Ph: +91 452 2459141
Email: [email protected]
Name: Dr. G. Kumaresan
Date of Birth: 28 June, 1976 Sex (M/F): M
Indicate whether Principal Investigator/Co-Investigator: Co-investigator
Designation: Associate Professor
Department: Department of Genetics
Institute/University: Madurai Kamaraj University
Address: Center for Excellence in Genomic Sciences,
School of Biological Sciences, Madurai Kamaraj University,
Madurai 625 021, Tamil Nadu.
Ph: +91 452 2458478/2458209/2459873
Email: [email protected]
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Project Leaders from Pondicherry University
Name: Dr. Archana Pan
Date of Birth: 06 October, 1966 Sex (M/F): F
Indicate whether Principal Investigator/Co-Investigator: Co-investigator
Designation: Assistant Professor
Department: Centre for Bioinformatics
Institute/University: Pondicherry University
Address: Pondicherry University,
R.V. Nagar, Kalapet, Puducherry- 605 014.
Ph: +91 413 2655584, 2654419; Fax No: +91 413 2655211, 2655265
Email: [email protected]
Name: Dr. P. P. Mathur
Date of Birth: 02 June, 1955 Sex (M/F): M
Indicate whether Principal Investigator/Co-Investigator: Co-investigator
Designation: Professor and Head
Department: Centre for Bioinformatics
Institute/University: Pondicherry University
Address: Pondicherry University,
R.V. Nagar, Kalapet, Puducherry- 605 014.
Ph: +91 413 2655212, 2654419
Email: [email protected]
Project Leaders from Anna University
Name: Dr. P. Gautam
Date of Birth: 22 May, 1959 Sex (M/F): M
Indicate whether Principal Investigator/Co-Investigator: Co-investigator
Designation: Professor and Chairman, Faculty of Technology
Department: Centre for Biotechnology
Institute/University: Anna University
Address: Centre for Biotechnology,
Anna University, Chennai 600 025, Tamil Nadu.
Ph: +91-44-2235 8371, +91-9444179685
Email: [email protected]
Project Leaders from Armed Forces Medical College
Name: Gp Capt S Shankar M.D.
Date of Birth: 19 July, 1967 Sex (M/F): M
Indicate whether Principal Investigator/Co-Investigator: Co-investigator
Designation: Professor
Department: Internal Medicine
Institute/University: Armed Forces Medical College
Address: Department of internal medicine
Armed Forces Medical College,
Wanowrie, Pune – 411 040, Maharashtra.
Ph: +91 9373466044
Email: [email protected]
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Name: Brig Velu Nair, AVSM, VSM**
Date of Birth: 04 May, 1956 Sex (M/F): M
Indicate whether Principal Investigator/Co-Investigator: Co-investigator
Designation: Professor and Head
Department: Internal Medicine
Institute/University: Armed Forces Medical College
Address: Department of internal medicine
Armed Forces Medical College,
Wanowrie, Pune – 411 040, Maharashtra.
Ph: 020-2602601 (O)
Email: [email protected]
Project Leaders from University of Kerala
Name: Dr. Achuth Shankar
Date of Birth: 14 July, 1963 Sex (M/F): M
Indicate whether Principal Investigator/Co-Investigator: Co-investigator
Designation: Professor and Director (SIUCEB)
Department: Centre of Bioinformatics
Institute/University: University of Kerala
Address: Dept. of Computational Biology & Bioinformatics
State Inter-University Centre of Excellence in Bioinformatics (SIUCEB)
North Campus – Kariavattom, University of Kerala
Thiruvananthapuram- 695581, Kerala.
Ph:+91 471 2308759
Email: [email protected]
Project Leaders from University of Mysore
Name: Dr. H. S. Prakash
Date of Birth: 05 February, 1956 Sex (M/F): M
Indicate whether Principal Investigator/Co-Investigator: Co-investigator
Designation: Professor
Department: Applied Botany and Biotechnology
Institute/University: University of Mysore
Address: Department of Applied Botany and Biotechnology
Manasagangotri, Mysore-570006, Karnataka.
Ph: +91-821-2419877
Email: [email protected]
Name: Dr. Geetha N. Prashanth
Date of Birth: 18 January, 1972 Sex (M/F): F
Indicate whether Principal Investigator/Co-Investigator: Co-investigator
Designation: Lecturer
Department: Applied Botany and Biotechnology
Institute/University: University of Mysore
Address: Department of Applied Botany and Biotechnology
Manasagangotri, Mysore-570006, Karnataka.
Ph: +91-821-2419825
Email: [email protected]
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Name: Dr. K. Ramachandra Kini
Date of Birth: 04 April, 1971 Sex (M/F): M
Indicate whether Principal Investigator/Co-Investigator: Co-investigator
Designation: Reader
Department: Applied Botany and Biotechnology
Institute/University: University of Mysore
Address: Department of Applied Botany and Biotechnology
Manasagangotri, Mysore-570006, Karnataka.
Ph: +91-821-2419805 /+91-9448128916
Email: [email protected]
Project Leaders from Mangalore University
Name: Dr. K. K. Vijayalaxmi
Date of Birth: 20 July, 1954 Sex (M/F): F
Indicate whether Principal Investigator/Co-Investigator: Co-investigator
Designation: Professor and Head of the Department
Department: Applied Zoology
Institute/University: Mangalore University
Address: Department of Applied Zoology,
Mangalore University, Mangalagangotri - 574 199, Karnataka.
Ph: +91-824-2287373
Email: [email protected]
Name: Dr. K. Bhaskar Shenoy
Date of Birth: 10 December, 1960 Sex (M/F): M
Indicate whether Principal Investigator/Co-Investigator: Co-investigator
Designation: Associate Professor
Department: Applied Zoology
Institute/University: Mangalore University
Address: Department of Applied Zoology,
Mangalore University, Mangalagangotri - 574 199, Karnataka.
Ph: +91-824-2287373, +91-824-2284750
Email: [email protected]
Name: Dr. Prashantha Naik
Date of Birth: 10 April, 1972 Sex (M/F): M
Indicate whether Principal Investigator/Co-Investigator: Co-investigator
Designation: Associate Professor
Department: Biosciences
Institute/University: Mangalore University
Address: Department of Applied Zoology,
Mangalore University, Mangalagangotri - 574 199, Karnataka.
Ph: +91-824-2287261
Email: [email protected]
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Project Leaders from Kuvempu University
Name: Dr. Riaz Mahmood
Date of Birth: 10 June, 1961 Sex (M/F): M
Indicate whether Principal Investigator/Co-Investigator: Co-investigator
Designation: Professor and Head
Department: Post-Graduate Studies and Reseach in Biotechnology
Institute/University: Kuvempu University
Address: Department of Post-Graduate Studies and Reseach in Biotechnology
Bioscience Block, Kuvempu University, Jnanasahyadri
Shankaraghatta-577 451, Karnataka.
Phone: +91-8282-256235, 256167 Fax: 08282-256255
Email: [email protected]
Name: H. S. Santosh Kumar
Date of Birth: 20 June, 1981 Sex (M/F): M
Indicate whether Principal Investigator/Co-Investigator: Co-investigator
Designation: Assistant Professor
Department: Post-Graduate Studies and Reseach in Biotechnology
Institute/University: Kuvempu University
Address: Department of Post-Graduate Studies and Reseach in Biotechnology
Bioscience Block, Kuvempu University, Jnanasahyadri
Shankaraghatta-577 451, Karnataka.
Phone: +91-8282-256235, 256167 Fax: 08282-256255
Email: [email protected]
Project Leaders from Central University Kerala
Name: Dr. Sameer Kumar
Date of Birth: 14 August, 1980 Sex (M/F): M
Indicate whether Principal Investigator/Co-Investigator: Co-investigator
Designation: Assistant Professor
Department: Biochemistry and Molecular Biology
Institute/University: Central University of Kerala, Kasargod
Address: Dept of Biochemistry and Molecular Biology
Central University of Kerala,
Padennakkad (P.O), Nileshwar,
Kasaragod-671 328, Kerala.
Ph: +91-9447697893
Email: [email protected]
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PART III: TECHNICAL DETAILS OF PROJECT
16. Introduction
16.1 Origin of the proposal
Despite a decade after the first draft of human genome became available, elucidation of the
role of proteins and the effect of large number of sequence variations on the phenotype still
persists to be a huge challenge to the scientific community. This is largely due to the fact that
multiple gene products can arise from a single gene and that their expression could be
temporally regulated in cells/cell types at their different stages of growth and development.
Besides, post-translational modifications are one of the major determinants of localization
and regulation of activity of proteins, and hence their function. It has now become clear that
proteins exist in larger dynamic complexes forming networks and that spatiotemporal flux in
these complex networks drive cellular processes. In biological systems, cellular processes are
coordinatively regulated through autocrine, paracrine, endocrine and juxtacrine signals. The
flux in networks which mediates transduction of signals through their specific receptors to
bring about cellular response is known as signaling pathways. Thus, signaling pathways
essentially integrate functional genomics to systems biology.
The advances in genomics, transcriptomics and proteomics technology platforms have
enabled large-scale identification and quantification of transcripts, proteins and protein-
protein interactions with high sensitivity and specificity. These technology platforms have
also facilitated the identification of genes (both at the level of mRNA or protein) that are
differentially regulated in diverse disease conditions such as cancer, arthritis, or neurological
disorders. In recent years, the biomedical research community has also realized the
importance and promoted the development of resources that manually or computationally
catalog biological information such as protein-protein interactions and gene expression. Even
though many software have been developed that adds various analysis components to these
interaction or expression data sets, in most cases, they do not provide an accurate biological
premise for these data. This lack of biological premise is the result of high heterogeneity
in the experimental data, context-specificity, spatiotemporal regulation of protein
activity, post-translational modifications of proteins and the ability of proteins to
interact with multiple proteins.
Biological pathways are a well co-ordinated and regulated set of molecular events which
includes protein-protein interactions, post-translational modifications, intracellular movement
of proteins and gene expression which brings about a particular phenotypic effect in the cell.
Although a large number of proteins and their sequence variations had been associated
with diverse diseases, their participating signal transduction pathways have long been
considered as the most effective targets for therapy. At the human interface, these
pathways are elicited when the cells are subjected to diverse array of extracellular or
intracellular stimuli. These signaling pathways provide important modular framework for
studying the biological context of a set of molecular interactions or a gene/protein expression
dataset. Molecular reactions that takes place under a particular stimulus is scattered across the
literature. There have been, in the past, efforts towards the generation of pathway resources.
However, many of these efforts are not comprehensive in their coverage of molecules and
predominantly consider only components of canonical modules. Moreover, many of them do
not provide the data in community standard data exchange formats including PSI-MI,
BioPAX and SBML so that it can be used with various pathway analysis software. Hence,
generation of resources which put molecular reactions in a pathway perspective that
can be used by the entire scientific community for systems biology approaches is the
need of the hour.
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Initial effort- NetPath
Institute of Bioinformatics (IOB) has initiated the development of resource of signaling
pathways to study the relationship among proteins that mediate cellular responses. In
collaboration with the Computational Biology Center at Memorial Sloan-Kettering Cancer
Center and with Gary Bader's lab at the University of Toronto, IOB has developed a set of 10
cancer signaling pathways for 'Cancer Cell Map' (http://cancer.cellmap.org/cellmap/)
(Unpublished) (Figure 2).
Scientists at IOB have improved this initial effort (with internal funding) to develop another
set of ten human signaling pathways pertaining to immune system which includes B cell
receptor, T cell receptor, Interleukins- 1, 2, 3, 4, 5, 6, 7 and 9 pathways. Each of these
signaling pathways were reviewed and approved by experts who represented 18 international
research centres. This has led to the development of a unique resource of open access human
signaling pathways named 'NetPath' (http://www.netpath.org/). NetPath, published in
‘Genome Biology’, was one of
the most highly accessed
research articles in 2010
(Kandasamy and Mohan et al.,
2010) (Figure 3). NetPath
currently hosts 27 ligand-
receptor specific human
signaling pathways of utmost
relevance to cancer, immunity,
obesity and endocrine system,
freely accessible to the
biomedical community (Figure
4). A pathway in NetPath
contains spatiotemporal
biochemical reactions induced
by the interaction of specific
Figure 2: A screenshot of the home page of Cancer Cell Map
Figure 3: NetPath was one of the most highly assessed
articles published in Genome Biology
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ligand(s) to their receptor(s) identified from published research articles. These reactions are
characterized into protein-protein interactions, enzyme-substrate and post-translational
modification events, and protein transport events across various cellular compartments.
Along with transcriptional regulators, NetPath also documents genes transcriptionally
regulated by specific pathways.
Figure 4: A screenshot of the home page of NetPath- NetPath home page has options for
browsing the pathways and search for the molecules. It also contains the statistics on the
number of pathways and reactions available in NetPath.
Pathways in NetPath have more than ten times the amount of data than any other resource
currently available in the public domain including KEGG (Kanehisa et al., 1996, Kanehisa et
al., 2004) (moving away from its open-source/free-software roots to a user-pay system),
NCI-PID (Carl et al., 2009), BioCarta (http://www.biocarta.com/index.asp) and Reactome
(Croft et al., 2011). Taking into account the comprehensiveness, heterogeneity and
complexity, for graphical representation of NetPath data, scientists at IOB have also
developed signaling pathway maps named 'NetSlim' (Raju et al., 2011). NetSlim contains
high-confidence pathway maps generated by applying a set of confidence criteria to
individual NetPath pathway reactions. NetPath and NetSlim pathway data are available for
download in standard formats such as PSI-MI version 2.5 (Hermjakob et al., 2004), BioPAX
level 3 (Demir et al., 2010) and SBML version 2.1 (Hucka et al., 2003), while the NetSlim
pathway maps are available for download in GPML (Van Iersel et al., 2008), GenMAPP
(Salomonis et al., 2007), JPEG and PDF formats from NetSlim and WikiPathways (Pico et
al., 2008 and Kelder et al., 2012) under adaptive Creative Commons License. NetSlim model
of TGF-beta pathway in NetPath is shown in Figure 5 as a prototype.
NetPath and NetSlim data in standard formats are also available through
WikiPathways and Cancer Cellmap (http://cancer.cellmap.org/cellmap/). NetPath and
NetSlim data in these standard formats also available through WikiPathways and Cancer
Cellmap (http://cancer.cellmap.org/cellmap/).
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Figure 5: The TGF-beta NetSlim map developed using PathVisio- The nodes and edges
represent the molecules and their reactions, respectively. A key for the various symbols,
colors and abbreviations used in the pathway diagram is provided in NetSlim database
(www.netpath.org/netslim).
TGF-beta Signaling Pathway
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These incorporated into NCBI BioSystems (Geer et al., 2010), and BioGPS (Wu et al., 2009)
have been invariably used by various pathway analysis tools such as Gene Spring, Cytoscape
(Shannon et al., 2003), and Integrated Pathway Resources, Analysis and Visualization
System (iPAVS) (Sreenivasaiah et al., 2012) for data analysis. Current pathway analysis
suites integrate data from various resources in the public domain which lack consensus
among them. These commercial suites uses anonymous data (data undefined) that
generate confusion among the users on the source, connectivity of molecules, and the
quality of the results.
We have already established the resources such as Human Protein Reference Database
(HPRD) (Goel et al.,, 2012, Goel et al., 2010, Prasad et al., 2009, Mishra et al., 2006, Peri et
al., 2004, Peri et al, 2003) (cited by over 1000 research articles including those in Nature,
Science and Cell), Human Proteinpedia (Kandasamy et al., 2009, Mathivanan et al., 2008)
(published in Nature Biotechnology), Plasma Proteome Database (Muthusamy et al., 2005)
and Resource for Asian Primary Immunodeficiency Diseases (RAPID) (Keerthikumar et al.,
2009) (published in Nucleic Acids Research) as gold-standard databases for human proteome
information. To the best of our knowledge, data from HPRD, Human Proteinpedia and
RAPID databases from India that have been linked into NCBI databases such as Entrez
Gene and RefSeq.
NetPath pathways are the most used and visited pathways in WikiPathways
(www.wikipathways.org) compared to the pathways provided by others. The public
availability of NetPath and NetSlim data have enabled researchers worldwide to
analyze and represent transcriptomics and proteomics data derived from various high-
throughput experimental platforms (Ritchie et al., 2012; Jiao et al., 2011; Navab et al.,
2011; Milenković et al., 2011; Morris et al., 2011; Turner et al., 2011; Grady et al., 2011;
Yamamoto et al., 2011; Kelder et al., 2011; Yaspan and Veatch, 2011; Astsaturov et al.,
2010; Gu et al., 2010; Imamura et al., 2010; Hammond et al., 2010; Isserlin et al., 2010;
Mostaghel et al., 2010; Hoang et al., 2010; Chaussepied et al., 2010; Wasiliew et al., 2009;
Bush et al., 2009; Bouwens et al., 2009; Rutella et al., 2009; van Iersel et al., 2008; and Oler
et al., 2008).
We have also embarked upon a new social initiative wherein we trained masters’ level
students from universities and involved them in the development of signaling pathways. With
the success of this pilot social experiment, we aim to take this initiative to the next level to
generate a layer of competent students who can spread the current concepts in signal
transduction across the bioscience students’ community in India.
In parallel, considering the utmost utility and necessity to put together pathway information
required to analyze complex biological experimental data, we propose to expand the number
of pathways in NetPath to 1000 signaling pathways. Looking forward to this, we have
initially set out to develop specific pathways of clinical significance that are not provided by
other resources in the public domain. We have revolutionised the development of signaling
pathways by training post-graduate level students from different universities in India. An early exposure to the details of signal transduction has already gained many of them
employment and Ph.D. positions within and across India. There are over 100 human signaling
pathways currently under development at IOB. The current status of the signaling pathways
being developed by the participation of post-graduate students from the current participating
institutes and others is provided in Table 1.
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Participating
Institutes Project Leaders Signaling pathways Status
Pondicherry
University
Dr. Archana Pan
and
Dr. P. P. Mathur
(Centre for
Bioinformatics)
Thyroid Stimulating hormone Goel et al., Journal of Proteomics and
Bioinformatics, 2011
TNF-related weak inducer of apoptosis Bhattacharjee et al., Journal of Signal
Transduction, 2011
Growth Hormone Releasing Hormone Under Review
Parathyroid hormone Under Review
Thrombin Under Review
TNF-related apoptosis-inducing ligand Under Review
Erythropoietin Under Review
Glucagon Under Review
University of
Mysore
Dr. H. S. Prakash,
Dr. Geetha N. P. and Dr. K. R. Kini
(Applied Botany and
Biotechnology)
Fibroblast growth factor Under Review
Hepatocyte growth factor Under Review
Nerve growth factor Under Review
Thrombopoietin Under Review
University of
Pune
Dr. Urmila Kale,
Dr. Sangeetha Sawat
and Dattatraya V.
Desai (Bioinformatics
centre)
Prolactin Radhakrishnan et al, Journal of cell
communication and signaling, 2012
Interleukin-11 Under Review
Platelet Activating Factor Under Review
Armed Forces
Medical
College
Dr. Shankar S
and
Dr. Velu Nair (Haematology)
Corticotropin Releasing Hormone Under Review
fms-like tyrosine kinase receptor-3 Under Review
Melatonin Under Review
Oncostatin-M Under Review
Neurotensin Under Review
Kuvempu
University
Dr. Riaz Mahmood
and
H. S. Santosh
(Department of Post-
Graduate Studies and
Research in
Biotechnology and
Bioinformatics)
RANKL/RANK Raju et al., Database, 2011
Anexelekto (AXL) Under Review
FAS Under Review
Anti-mullerian hormone Under Review
Dr. MGR
University
Dr. Rama
Vaidyanathan
and
Dr. N. Sudhakar (Biotechnology)
Tie2/TEK Under Review
Ghrelin Under Review
Amrita
University
Dr. Bipin Nair
(Amrita School of
Biotechnology)
Leptin Nanjappa et al., Journal of
Proteomics and Bioinformatics, 2011
National
Institute for
Research in
Reproductive
Health
Dr. Srabani
Mukherjee
(Molecular
Endocrinology)
Follicle Stimulating Hormone Telikicherla et al., BMC Research
Notes, 2011
Table: 1 Current status of signaling pathways under development at IOB
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This effort has also led to the unique opportunity for publication by students at their post-
graduate level (Figure 6).
Figure 6: A screenshot of a set of specific signaling pathways published by scientists at
Institute of Bioinformatics in international peer-reviewed journals with the students,
the faculty members and the pathway authorities as co-authors.
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Integrating experimental data on molecules obtained at the level of DNA, RNA and protein
level encompasses almost all aspects of biology. The evolving technological platforms are
not being handled by students during their coursework practical sessions. Thus, training post-
graduate level students from various universities in India on the development of signaling
pathways would foster human resource development. Our social experiment has gained
broad attention and appreciation in the university bioscience community in India. This
human resource development programme in the current participating institutes and
prospectively new institutes across the country would also potentiate the development of
1000 signaling pathways for NetPath
These pathways were developed by the participation of students from currently Participating
Institutes. The students and the Project leaders from the respective Participating Centres are
authors in these publications.
Integrating protein-protein interactions, PTMs, activation/inhibition status of proteins with
reference to specific assays, spatial distribution of proteins across various subcellular
compartments coupled to transcriptional regulation of genes by specific signaling pathways,
NetPath will serve as a unique platform for heuristic approaches to global pathway analysis.
The pathway data obtained in this proposed project would form the basis for computational
analysis of data pertaining to transient behaviour of cells coupled to their biological processes
and also to devise new hypothesis driven experimental approaches in the subsequent phases
of our study. With very competent bioinformaticians in India in different universities and
research institutes, we plan to carry forward this community participation and human
resource development programme to develop open-access pathway analysis software suites in
the next phase of our research. Thus, our three-tier approach- (i) development of a
comprehensive resource of signaling pathways, (ii) development of open-access pathway
analysis suites and (iii) validation, and hypothesis- driven experimental approaches to
identify novel molecules and missing links in signaling pathways would help place India
in forefront of biomedical research.
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16.2 Definition of the problem
Physiologically, cells encounter various ligands and their coordinated outcomes are difficult
to be exactly replicated ex vivo. Such a scenario has necessitated reductionist approaches to
study and characterize biochemical events mediating response to individual ligands through
multiple receptors and vice versa. The initial human genome sequence project estimated 20%
of the genes (over 4000 genes) to code for membrane proteins (Lander et al., 2001). Based on
the signaling mechanism, cell surface receptors are mainly classified into receptor tyrosine
kinases (Robinson et al., 2000), receptor serine/ threonine kinases (Ten Dijke et al., 1994), G-
Protein coupled receptors (Harmar et al., 2009), guanylyl cyclase receptors, ionotropic
receptors (Collingridge et al., 2009) and others which depend on cytoplasmic kinases or
adaptor molecules for signal transduction. Of many intracellular receptors, nuclear receptors
form a category of bifunctional receptors which binds to their membrane-permeable ligands
and are capable of regulating expression of their target genes by directly binding to specific
responsive elements.
The reactions pertaining to signaling pathways scattered in literature can also be
characterized into those derived from experiments involving activation of (i) a specific
receptor by multiple ligands, (ii) a specific ligand-receptor combination, and (iii) multiple
receptors by a specific ligand. Thus, the identification of pathway specific reactions under
these categories to devise topology of reactions in the pathways inevitably requires human
intrusion. Classical pathway representations are not sufficient to meet the challenges of
integrating heterogeneous datasets to obtain deeper insights into signal processing and
transduction. Thus, there is an increasing need for systematic assembly of experimentally
identified biochemical reactions specific to ligands, receptors, and their specific
combinations. Moreover, such high-quality datasets should be made available in
computer-readable formats to model, integrate and analyze complex biological
processes. Such networks of molecular reactions can be used to analyse cross-talks and
dynamic behaviour of signaling networks by qualitative and quantitative
experimentation and by computational modelling approaches. Acquisition of high-quality
signaling pathway data sets from the vast published literature is a tedious time-consuming
process which involves lot of planning with heuristic feasibility, established pipeline for data
acquisition, coordinators and trainers with inevitably huge man-power, and hence is a
limitation for many in the biological research world.
Pathway data in currently available public resources differs in the number of pathways,
number of components and reactions in each of these pathways, curation criteria, reaction
types, depth and coverage. Moreover, none of these resources document transcriptionally
regulated genes and their regulators in the context of specific pathways. Signaling pathways
as a platform for drug discovery is an active area of research and rely on data integrated from
multiple resources. Hence, development of resource of signaling pathways that systematically
documents reactions based on their experimental design in the published literature with their
specificity to ligand(s) or receptor(s) for broader applications is the need of the hour.
Towards this larger vision, scientists at Institute of Bioinformatics have developed a resource
of signaling pathways named NetPath/NetSlim (Kandasamy and Mohan et al., 2010 and Raju
et al., 2011) which had been widely accepted and been used for the pathway data analysis by
various software in the public domain. Scientists at IOB has expertise in coordinating
database development and biocuration as exemplified by the success of global resources such
as HPRD (Goel et al., 2012, Goel et al., 2010, Prasad et al., 2009, Mishra et al., 2006, Peri et
al., 2004, Peri et al, 2003), Human Proteinpedia (Kandasamy et al., 2009, Mathivanan et al.,
2008), Plasma Proteome database (Muthusamy et al., 2005) and Resource for Asian Primary
Immunodeficiency Diseases (RAPID) (Keerthikumar et al., 2009).
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Here, we propose to expand the number of pathways in NetPath to host 1000 pathways with
the participation of the bioscience community in India. We also consider this a best mean to
bring about human resource development in signaling pathways in India. At the stage best
suitable for them without affecting their curriculum, involving post-graduate students would
provide them an early feel and better understanding of protein biology, advances in cellular
signaling and experimental platforms. Most importantly, the early exposure to biological
research with unique opportunity of publication would place them well above their
counterparts. The proposed effort will also lead to technology transfer across study centers
with effective capacity building for detailed understanding of signaling pathways. The
proposed community participation programme will be further extended to mathematical
modeling and development of pathway analysis suites by involving bioinformaticians from
various universities and research institutes in India. We have also initiated the experimental
validation of the currently developed signaling pathways (e.g. EGFR, TGF-beta, TSLP and
Interleukin-33) and plan to continue hypothesis-driven approaches using cutting-edge mass
spectrometry platform in the subsequent phases. We believe that data pertaining to 1000
signaling pathways in NetPath coupled to the protein information in HPRD and Human
Proteinpedia would serve as an ideal platform for the functional analysis of the human
proteome in the future.
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16.3 Objectives
Specific Objective 1. Formation of an expert panel in signaling pathways
Development of high-quality ligand-receptor specific signaling pathways requires the active
participation of the experts of each of the pathways. This will ensure to accommodate the
evolved/evolving concepts and context specific information necessary for analysis of
signaling pathways. This panel which constitutes both national and foreign experts will
contribute as the best platform for the national human resource development
programme in signal transduction associated with this project.
Specific Objective 2. Human resource development in signaling pathways
Human resource development programme in signal transduction will be implemented at the
level of post-graduate level students in different universities in India. Through orientation
programmes, hand-on training programmes and workshops, the students will be taught the
current concepts in signal transduction. Beyond the lagging generation of text books, the
participation of the peer national and foreign experts in the domain will help us introduce
students to the current concepts and developments in protein biology and signal transduction.
Guided by domain experts, transduced through orientation lectures, hands-on training
programmes and workshops leading to publication with students as co-authors (the first of its
kind with the knowledge of what they have exactly done), is the most effective system for
human resource development in any field. We believe that our unique programme
reaching out to students of different bioscience disciplines without affecting the
curriculum will transform the educational system in India.
Specific Objective 3. Development of 1000 human signaling pathways
Scientists at Institute of Bioinformatics have developed an open-access resource of signal
transduction pathways named "NetPath". NetPath currently hosts 30 signaling pathways.
Each pathway in NetPath contains molecules and reactions with almost 10 times the data
available in any other resources in the public domain. Such limited data in other resources
does not contribute to the effective analysis of signaling pathways. Moreover, these resources
contain less than 200 through specific receptors. In the light of over 4000 receptors encoded
in the human genome, we understand that the currently available resources are not equipped
to meet the challenges of functional genomics and systems biology. In order to accelerate
basic research on signal transduction mechanisms, and to identify molecules and pathways
deregulated in diverse diseases for therapeutic approaches, we propose to develop 1000
signaling pathways in NetPath. Successful outcome of our vision would place India in the
forefront of biomedical research in the world.
Specific Objective 4. Developing a software suite to convert pathway data into standard
community data formats
The pathway data along with all the parameters associated with it should be made available in
computer readable formats to facilitate data exchange, interoperability, and analysis using
different pathway analysis software. Moreover, it is also necessary to make the data available
in different community standard formats to encompass the enhanced utility by different
research groups and bioinformaticians. Hence, we propose to develop a software suite
which would facilitate conversion of pathway data into BioPAX, PSI-MI, SBML and
GPML formats, the most widely used standard formats in the bioscience community.
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17. Review of Current Status of research and development in the subject
International Status
Currently, there are over 325 resources available worldwide which catalogs empirical
reactions involving proteins, carbohydrates, lipids, nucleic acids, drugs, or small molecules.
Commercial signaling pathway resources are not freely available for the academic use. The
resources such as Protein lounge (www.proteinlounge.com) and BioCarta
(www.biocarta.com/index.asp) lounges colourful pathway images but only with limited
canonical pathway reactions. Pathway maps commercially developed by vendors such as Cell
Signaling Technology (www.cellsignal.com), Sigma-Aldrich (http://www.sigmaaldrich.com),
Invitrogen (http://www.invitrogen.com) and Millipore (http://www.millipore.com) are
intended to highlight their reagents and products. Primary resources with signaling pathways
developed by their own group include NetPath/NetSlim, Kyoto Encyclopedia of Genes and
Genomes (KEGG) (Kanehisa et al., 2000) (moving away from its open-source/free-
software roots to an user-pay system), Reactome (Matthews et al., 2009), Pathway
Interaction Database (NCI-PID) (Schaefer et al., 2009) (are dominated by private
enterprises and charge as much as $5,00,000 for institutional license), Signal
Transduction Knowledge Environment (STKE) (Gough, 2002), Integrating Network Objects
with Hierarchies (INOH) (Yamamoto et al., 2011), Panther (Thomas et al., 2003), and Cell
Signaling Networks Database (CSNDB) (Igarashi et al., 1997). These resources provide
pathway data in one or multiple standard formats and the quality of the data cannot be
evaluated. NetPath is unique from these resources as it contains: 1) transcriptionally
regulated genes 2) transcriptional regulators of genes, 3) cell name/type in which each
reaction is studied, 4) display of human-readable data for each pathway in one page, 5)
availability of confidence signaling pathway data filtered based on a set of confidence
criteria, and 6) availability of interactive high-confidence signaling pathway maps.
Salient features of NetPath compared with most popular resources are provided in Table 2.
Signaling
pathway
resources
File formats
available for data
download
Pathway map
features and data
download
Description of
molecules, PTMs,
cellular location
and reactions
Pathways
reviewed by
experts?
Transcriptional
regulatory
networks
available?
NetPath
BioPAX, PSI-MI, SBML,
Excel, Tab-delimited
High-confidence reaction network map in GPML,
GenMAPP, PDF, JPG and SVG
Yes Yes Yes
KEGG BioPAX KGML No No No
Reactome BioPAX, SBML, Protégé, MySQL database dump
PDF, SVG Yes Yes No
NCI-PID XML, BioPAX SVG, JPG No Yes No
Panther SBML SBGN, PNG No Reviewed by
Curation Coordinator
No
STKE - SVG No Yes No
BioCarta - No download option No Yes No
Protein Lounge - PowerPoint slides No Yes No
WikiPathways - GPML, GenMAPP,
PDF, PNG, SVG No
Pathways from multiple sources
including NetPath No
Table: 2 Salient features of NetPath compared with most popular resources in the
public domain
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NetPath contains around ten times more molecules and reactions available in any of
these resources. All these information are available in the context of receptor-specific,
ligand-specific and ligand/receptor-combination-specific based on the experimental reports in
research articles for 1000 signaling pathways would establish NetPath as the most reliable
resource of signaling pathways in the public domain. Even with this coverage, we
acknowledge that there is more information left out due to limited man-power and ever-
increasing deposition of pathway information that will be periodically incorporated into
NetPath. Pathway data in NetPath is peer-reviewed, publicly-available, and open-
accessible resource that can be critiqued and updated by the scientific community.
Web-based community participation efforts are ongoing for resources such as WikiPathways
(Similar in principle to Wikipedia) and Panther. These web-based curation platforms aims
researchers in the field of signal transduction and do not provide extensive training to
students who lack exposure on signal transduction pathway studies. India and Japan had been
leading the efforts in resource development in Asia. With human protein resources such as
HPRD, Human Proteinpedia, and NetPath/NetSlim in India, Institute of Bioinformatics has
led the major efforts on human proteome information in India.
2 National Status
Resources for signaling pathway related information thus far developed in India include
NetPath/NetSlim from Institute of Bioinformatics and Database of quantitative cellular
signaling (DQCS) from NCBS (Shivakumaran et al., 2003). DQCS contains reaction kinetic
models of individual reactions identified in mammalian cells. However, DQCS does not
contain pathway specific information if reaction schemes, concentrations or rate constants of
individual reactions are not available. IOB is leading the efforts in characterising ligand-
receptor specific signaling pathways in India through manual annotation, analysis of protein-
protein interaction networks and by mass spectrometry based approaches to identify novel
components in signaling pathways (Mathivanan et al., 2006; Bose et al., 2006; Gandhi et al.,
2006; Amanchy et al., 2008; Harsha et al., 2008; Kandasamy et a., 2009; andasamy et a.,
2010; Demir et al., 2010; Zhong et al., 2011; Amanchy et al., 2011; Raju et al., 2011;
Nanjappa et al., 2011; Raju et al., 2011; Telikicherla et al, 2011; Goel et al., 2011; Zhong et
al., 2012; Bhattacharjee et al., 2012). IOB has also developed unique global protein resources
such as Human Protein Reference Database, Human Proteinpedia, Plasma Proteome
Database, and Mouse Protein Reference Database repositories from India. IOB is also
involved in developing Tuberculosis Reference Database as a part of TbNet India initiative in
India.
There are several research labs in India that focus on signal transduction pathways. Dr.
Upinder S. Bhalla, Neurobiology, NCBS, is a well-known expert in neurosignaling who have
developed Database of quantitative cellular signaling (DQCS). Dr. Sudhir Krishna, Cellular
Organization and Signaling, NCBS, is a renowned expert in signal transduction pathways
from India, who has extensively studied Notch signaling pathway and its role in
tumorogenesis. Dr. Mohan R. Wani from National Centre for Cell Science, Pune is an expert
on RANKL, Interleukin-3, GM-CSF, TNF-alpha signaling pathways with major focus on
their role in bone remodeling and its associated disorders. Dr. N. Srinivasan from IISc,
Bangalore is a computational biology expert for analysis of protein structure, protein-protein
interactions and prediction of protein function. Dr. Rita Christopher from NIMHANS,
Bangalore is has expertise in clinical biochemistry and neurochemistry. Dr. Nagasuma
Chandra, Bioinformatics Centre, IISc, Bangalore, is an expert in Bioinformatics. She is
applying her expertise to understand diseases and immunological processes by systems
biology approaches. Dr. K. Sekar, Structural Biology and Bio-computing, IISC, Bangalore, is
an expert in biophysics with major focus on protein sequence and structure analysis.
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Dr. Kanury Venkata Subba Rao from International Centre for Genetic Engineering and
Biotechnology, Delhi, is a well known scientist focused in understanding the regulatory
mechanisms involved in ligand-receptor mediated signaling pathways pertaining to immune
response. Dr. Bhaskar Saha from National Centre for Cell Science, Pune, is well known for
his signal transduction research involved in T cell and dentritic cells response to infection.
Dr. Debasisa Mohanty, National Institute of Immunology, New Delhi, is a renowned scientist
primarily involved in systems biology approaches for identification of conserved network
modules and their dynamic features. Dr. G. P. S. Raghava, Institute of Microbial Technology,
Chandigarh, is a leading scientist in India known for computer Aided Protein Structure
Prediction and identification of Vaccine Candidates.
Subsequently, with the involvement of these experts in the national panel of experts on
signaling pathways, we are sure to take our community participation programme
beyond its current limits.
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17.3 Importance of the proposed project in the context of current status
Signal transduction networks have long been identified as the platform to decipher
relationship among genes and other molecules. Ever evolving, but currently available high-
sensitive proteomics technologies potentiates identification of subtle changes in the PTM
status of proteins, fluxes in protein complexes, and dynamic protein reorganization in cells.
Pathway data available in literature put together would bring to light various novel
molecules and their reactions that are not present in other resources or are not been
covered in review articles (Figure 7).
Figure 7: Cytoscape network map of TGF beta pathway data in NetPath overlaid with
the molecules in TGF-beta pathway in KEGG. The green colour nodes represent the
molecule in KEGG for the TGF-beta pathway. NetPath contains 220 molecules and 481
reactions with all the 30 molecules and their reactions available in KEGG for this pathway.
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A large number of molecules may not be connected to the core of the signaling networks due
to the lack of protein-protein interaction and substrate information to connect with molecules
in the core signaling pathways for which this information are available. Hence, they can be
called as orphan to specific pathways (Figure 8). This emphasizes the need for well-
structured signal transduction pathway resources as a platform to model, analyze, integrate
and visualize complex functional networks.
Figure 8: Orphan molecules in TGF beta pathway in NetPath- The maps shows the
interaction network generated by importing NetPath TGF-beta pathway BioPAX level 3.1
into Cytoscape. The nodes highlighted in yellow represents orphan proteins in the pathway.
This represents proteins that are identified to be activated/inhibited by activity assays or are
identified to have their PTM status modulated. They are defined as orphans due to their lack
of protein-protein interaction and substrate information to connect with molecules to the core
of the signaling pathways for which this information are available.
Like metabolic networks, signaling networks can be characterized by well-defined ligand-
receptor system and biological outputs assayed for their functional effects. Further, they can
be modeled to identify feedback loops and multi-step regulatory modules. Modeling also
enables estimation of the necessary parameters for hypothesis-driven experimental
approaches. Exploration of network architecture and biological implications from bottom-up
approaches requires reliable connection maps which can be constrained by expedite and
analyzed by computational approaches. Current methods for analysis of transcriptomics and
proteomics expression data to identify perturbations in signaling pathways using over-
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representation analysis (Draghici et al., 2003), functional class scoring approaches/gene set
enrichment analysis (Ackermann and Strimmer, 2009; Subramanian et al., 2005), and
pathway topology-based approaches (Draghici et al., 2007) are highly dependent on the
amount of pathway data. Currently, data from various resources which lacks consensus
among them are brought together for this purpose. Further to the agony, pathway resources
currently available in the public domain do not incorporate the genes regulated by specific
signaling pathways, instead, they import information on the genes from various sources such
as Gene Ontology and gene regulatory network databases to provide analysis of gene
expression data in the context of specific pathways. Our reductionist approach to generate
signaling pathway data would provide an appropriate platform to analyze the integration of
multiple signals coupled to temporal fluctuation using mathematical models. Thus, a
comprehensive documentation of molecules involved in mediating specific signaling
pathways coupled to their gene regulatory networks derived from different types of
experimental platforms with a unique curation pipeline described in this project is the
need of the hour. This proposed project would accomplish the generation of the necessary
high-quality pathway data for development of more reliable and comprehensive platform for
analysis of biological data for subsequent phases of our research.
Many years have passed since Gleevec have revolutionized the treatment of chronic myeloid
leukemia. Genomic, transcriptomics and proteomics approaches have led to the identification
of various mutants, over- and under-expressed or deregulated activity of proteins associated
with different clinical phenotypes. From cell surface receptors (e.g. Receptor tyrosine
kinases, Receptor Serine/Threonine kinases, G-Protein Coupled Receptors and Ionotropic
Receptors), to intracellular proteins (enzymes, adaptors, nuclear receptors, transporters and
transcriptional regulators) common to specific biological function, there are different
perspectives to molecular targeted therapy. Components in signal transduction networks that
are identified to cross-talk with multiple pathways are long been identified as drugable targets
(Cook and McCormick, 1993; Wu et al, 1993) (Figure 9). Thus, a detailed cataloguing of
proteins and other molecules proved in mediating specific cellular response or biological
function in published research articles would serve as a centralized analysis platform
for drug discovery.
Signaling pathway reactions are studied as discrete entities using both low-throughput and
high-throughput technologies. The pathway maps currently available in text books are the
result of collection of such studies and do not introduce how they were assembled. These
maps are often interpreted as being established and does not reach out to the concepts of
complex regulatory events associated with them. One of the critical issues in biomedical
education is the challenge of being updated with the evolving concepts and technology. At
student level these are mostly accomplished by assignments or project works. However, it
takes years of focused literature search to understand the current concepts of dynamic
signaling networks, mode of development and quality of data in pathway resources, and
pathway analysis of data from various experimental platforms.
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Figure 9: A set of research publications which highlight and discuss different signaling
pathways as therapeutic targets to combat diverse disease conditions
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17.4 Anticipated Products & Processes of Practical/Technological utility/Socio-economic
relevance expected to be evolved by pursuing the project.
1. Human resource development in India
The proposed project will help envision, strengthen and reinforce biomedical research in
India. This will be a continued endeavor with involvement of bioinformaticians and
experimental biologists in India in the subsequent phases of our research. Over 1000 students
will be trained in the period of 4 years under this project.
2. NetPath from India as premier open-access resource for signaling pathways
facilitating systems biology approaches
Coordinated outcome of this project will result in the development of 1000 signaling
pathways publicly available through NetPath. NetPath data will be used for analysis of
experimental data in the context of specific pathways, function and diseases and would
enable systems biology approaches by the entire biomedical community. High-quality data
emanating from this project will be used to develop open-source pathway data analysis suites
and also for developing heuristic methods for the prediction of novel molecules and their
relationships in signaling pathways.
3. NetPath as a platform to identify relationships among genes and their contribution to
pathological phenotypes
A detailed characterization of molecules and their reactions that synchronize cellular funct ion
would accelerate research and enable identification and attribution of function to a large
number of molecules in specific pathways. These molecules can be selectively validated for
their therapeutic applications.
4. NetPath community participation programme as a platform for collaborative efforts
The network and association developed between premier educational and research
organizations in India would enable technology transfer and interventions channelizing
targeted and broader scientific endeavors in the future.
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18. Work Plan (Incase for multi institutional projects, work plan, role & responsibility
of each institute to be given separately)
Responsibility of co-investigators in this community participation project is summarized in
Table 3.
Participating Institute Project Leaders from
Participating Institutes Responsibilities
Anna University Dr. P. Gautam
(Centre for Biotechnology)
Organization and facilitation of orientation programmes, workshops,
training and biocuration
Pondicherry University
Dr. Archana Pan and Dr. P. P. Mathur (Centre for Bioinformatics)
Organization and facilitation of
orientation programmes, workshops,
training and biocuration
Madurai Kamaraj
University
Dr. P. Gunasekaran and Dr. G
Kumaresan (Department of Genetics)
and Dr. S. Krishnaswamy
(Department of Genetic Engineering)
Organization and facilitation of orientation programmes, workshops,
training and biocuration
University of Pune
Dr. Urmila Kulkarni-Kale, Sangeeta
Sawat, and Dattatraya Desai
(Bioinformatics centre)
Organization and facilitation of
orientation programmes, workshops,
training and biocuration
University of Kerala
Dr. Achuth Shankar
(Computational Biology and Bioinformatics)
Organization and facilitation of
orientation programmes, workshops, training and biocuration
Armed Forces Medical
College
Dr. S. Shankar and Dr. Velu Nair
(Department of internal medicine)
Organization and facilitation of orientation programmes, workshops,
training and biocuration
Mangalore University
Dr. K. K. Vijayalaxmi, Dr. K.
Bhasker Shenoy (Department of
applied Zoology) and Dr. Prashantha
Naik (Department of Biosciences)
Organization and facilitation of orientation programmes, workshops,
training and biocuration
Central University of Kerala
Dr. Sameer Kumar
(Biochemistry and Molecular
Biology)
Organization and facilitation of
orientation programmes, workshops,
training and biocuration
Kuvempu University
Dr. Riaz Mahmood and H. S. Santosh Kumar (Department of Post-Graduate
Studies and Research in
Biotechnology and Bioinformatics)
Organization and facilitation of
orientation programmes, workshops, training and biocuration
University of Mysore
Dr. H. S. Prakash, Dr. K. R. Kini, and
Dr. Geetha N Prashanth,
(Applied botany and Biotechnology)
Organization and facilitation of
orientation programmes, workshops,
training and biocuration
Table 3: Role and responsibility of the co-investigators from the Participating Institutes
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18.1 Methodology
Specific Objective 1. Formation of an expert panel in signaling pathways
The first step to accomplish this project will be to identify national or international experts on
that particular signaling/ligand receptor system/signaling pathways. The experts who have
worked on specific pathways for more than 6 years will be selected as potential authorities of
the pathway. They will be contacted for their approval to become the pathway authorities.
Once approved, we will seek their suggestions on the pathway maps to expedite the
development of respective pathways. The interaction between the pathway authorities and the
coordinators of this project will enhance the development of the pathways accommodating
the current concepts and broad opinion in the field. These experts will constantly work with
the annotators, reviewers and the university faculties to ensure generation of high quality
pathway data. They will also be actively involved in periodically updating the information in
the resource. The involvement of world experts in both the generation and updation
processes of pathways will help keep the faculty as well as others involved in the project
to be up-to-date with the latest concepts and developments in signal transduction
research. The current list of signaling pathway experts on board as pathway authorities are
provided below (Table 4).
Pathway authority Designation/Department/Institute Signaling
pathway
Foreign members
Dr. William P.
Schiemann
Associate Professor, General Medical Sciences
(Oncology), Case Comprehensive Cancer Center, Case
Western Reserve University, USA
TGF beta
Dr. Mark Knepper Principal Investigator, Epithelial Systems Biology
Laboratory, National Heart Lung and Blood Institute, USA
Arginine
vasopressin
Dr. Carrie Shemanko Associate Professor, Department of Biological Sciences,
University of Calgary, Canada Prolactin
Dr. Anirban Maitra Professor, Pathology and Oncology, The Johns Hopkins
University School of Medicine, USA AXL
Dr. Gerald J. Atkins
Professor and Head, Bone Cell Biology Group, NHMRC
RD Wright Fellow Discipline of Orthopaedics and Trauma,
University of Adelaide, Australia
TNF-related
weak inducer of
apoptosis
Dr. Jun Zhong
McKusick-Nathans Institute for Genetic Medicine and
Departments of Biological Chemistry, Pathology, and
Oncology, The Johns Hopkins University School of
Medicine, USA
Thymic stromal
lymphopoietin
Dr. Ge Ruowen Associate Professor, Department of Biological Science,
National University of Singapore, Singapore Angiopoietin
Dr. Stephen Desiderio Professor, Department of Molecular Biology & Genetics,
Johns Hopkins School of Medicine, USA B cell receptor
Dr. Jon C.D. Houtman Assistant Professor, Department of Microbiology, Carver
College of Medicine, University of Iowa, USA T cell receptor
Dr. Warren J. Leonard Laboratory of Molecular Immunology
National Heart, Lung, and Blood Institute, NIH, USA Interleukin-2
Dr. Stefan
Constantinescu
Principal Investigator, The Ludwig Institute for Cancer
Research, Brussels Branch and the Experimental Medicine
Unit, Christian de Duve Institute of Cellular Pathology,
Universite Catholique de Louvain, Belgium
Interleukin-3
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Dr. Masato Kubo
Principal Investigator, Research Institute for Biological
Sciences, Tokyo University of Science. Signal/Network
Team, RCAI, RIKEN Yokohama Institute, Japan
Interleukin-4
Dr. Osamu Ohara Head of Department, Laboratory for Immunogenomics,
RCAI, RIKEN Yokohama Institute, Japan Interleukin-5
Dr. Toshio Hirano
Professor, Laboratory of Developmental Immunology,
Graduate School of Frontier Biosciences and Department
of Molecular Oncology, Graduate School of Medicine,
Osaka University and Laboratory for Cytokine Signaling,
Japan
Interleukin-6
Dr. Jean-Christophe
Renauld
Principal Investigator, The Ludwig Institute for Cancer
Research, Brussels Branch and the Experimental Medicine
Unit, Christian de Duve Institute of Cellular Pathology,
Universite Catholique de Louvain, Belgium
Interleukin-9
Dr. Eva Dimitriadis Associate Professor and Head, Embryo implantation
Laboratory, Prince Henry's Institute, UK Interleukin-11
Dr. Toshio Hirano
Professor, Laboratory of Developmental Immunology,
Graduate School of Frontier Biosciences and Department
of Molecular Oncology, Graduate School of Medicine,
Osaka University and Laboratory for Cytokine Signaling,
Japan
Interleukin-17
National members
Dr. Akhilesh Pandey
Director, Institute of Bioinformatics, Bangalore, India.
Professor, McKusick-Nathans Institute for Genetic
Medicine and Departments of Biological Chemistry,
Pathology, and Oncology, The Johns Hopkins University
School of Medicine, USA
EGFR, EPO,
TGF beta,
Interleukin-7,
TSLP
Dr. Mohan R. Wani Scientist-E, Lab1, Cell Biology, National Centre for Cell
Science, India RANKL/RANK
Dr. Srabani Mukherjee
Scientist C, Department of Molecular Endocrinology,
National Institute for Research in Reproductive Health,
India
Follicle
stimulating
hormone
Dr. P. P. Mathur
Professor and Head, Department of Biochemistry &
Molecular Biology and Bioinformatics Centre, School of
Life Sciences, Pondicherry University, India
Thyroid
stimulating
hormone
Dr. S. N. Umathe
Professor and Head, Department of Pharmaceutical
Sciences, Rashtrasant Tukadoji Maharaj Nagpur
University, India
Corticotropin
releasing
hormone
Dr. P. R. Sudhakaran Professor and Head, Department of Biochemistry,
University of Kerala, India
Advanced
glycation end-
products
Dr. G. Anilkumar Associate Professor, School of Biotechnology, Amrita
Vishwa Vidyapeetham, India Leptin
Dr. Sujay K. Singh President/CEO, IMGENEX INDIA Pvt. Ltd.,
Bhubaneswar, India Interleukin-1
Dr. Sudhir Krishna Cellular Organization and Signaling, NCBS, India Notch
Table 4: The current list of national and foreign signaling pathway experts on board
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Specific Objective 2. Human resource development in signal transduction
IOB had already partnered with Pondicherry University, University of Pune, University of
Mysore, Kuvempu University, and Armed Forces Medical College (Pune) for this
programme. Our initial effort led to the training of over 200 post-graduate students from
these institutes and has also to the development of 20 signaling pathways (table 1). With the
success of our social experiment with these institutes, several departments from various
universities such as Jawaharlal Nehru University, Madurai Kamaraj University, Anna
University, Mangalore University, Bangalore University, University of Kerala, Central
University of Kerala have consented to become a part of this effort.
The students from Central University of Kerala will be involved to engage them in
community efforts and help the University emerge from their initial stage of establishment.
The signal transduction related topics in their curriculum will also be completely covered in
this process.
The participation of research institutes such as NIMHANS and NIRRH would enable
bridging between clinicians and researchers. Moreover, this will also provide a platform for
technology transfer and future collaborations. Students from these Institutes will be
entertained to participate in this programme in the subsequent phases as well.
The MBBS students from AFMC will participate in this effort as a part of the ongoing
collaboration efforts. MBBS students from other medical colleges who approach us (For
example: students from Indian Medical Students Association) will also be enrolled in this
human resource development programme in signaling pathways. This will provide a
platform to develop a prospectus layer of next generation students well-versed to take
research to translational medicine.
2.1. Orientation programmes at Participating Institutes
Workshops will be conducted every year at Participating Institutes to recruit and gather
participation of other universities and institutes in India.
Investigators from IOB along with Project Leaders from current and prospective Participating
Institutes will organize pathway orientation programmes. The students and faculties from all
the biosciences departments will be invited. During these sessions, students will be exposed
to the concepts of signaling pathways, and experimental methods involved in the
investigations of signaling pathways including protein-protein interactions, enzyme-substrate
reactions, various post-translational modifications, gene expression analysis platforms, and
transcriptional regulatory networks. Students will also be introduced to diverse types of data
resources developed by IOB and importance data resources in Systems Biology approaches.
In this process, they will also be introduced to various pathway editing, visualization and
analysis software and the criteria used to develop high-confidence signaling pathway maps
using PathVisio, Cytoscape, GenMAPP and Cell Designer.
2.2. Recruitment of students for Human Resource Development network in building
human signaling pathways
Based on the interactive sessions with the students, along with the involvement of Project
Leaders, 15 to 20 students motivated preferably in their Second year of M.Sc. will be
recruited into this programme. This will take into account the interest of the students,
willingness of their head of the department(s), and duration of the semester break period
available. The recruited post-graduate students will participate in this program during their
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semester breaks. Some students can also use this opportunity for dissertation work if allowed
from their respective departments/universities. Students who have completed or are
pursuing their MBBS/M.Sc. course from different Universities and Institutes in India
will also be considered, if they apply. In all, 200 to 250 students will be recruited in the
programme per year.
2.3. Training in the development of human signaling pathways at IOB
Students will stay for about 60 days at IOB and will be trained in the development of specific
signaling pathways. Training modules for this programme includes,
1. Ligands and their receptors, methods to stimulate the activity of receptors, concept of
agonists and antagonists, and transfection and overexpression of receptors.
2. In vivo/in vitro methods to study protein-protein interactions (yeast-2-hybrid,
mammalian-2-hybrid, co-precipitation, fluorescence resonance energy transfer,
bioluminescence resonance energy transfer assays coupled to identification of
interacting proteins (immuno- and recombinant DNA- based technology, and by mass
spectrometry)
3. In vivo and in vitro assays to detect enzyme-substrate reactions, post-translational
modifications, protein activity assays, use of mutants to identify the site of
modifications, and mapping of specific site and residues to RefSeq protein accession.
4. Identification of protein localization in different cellular compartments
5. Introduction to experimental platforms such as microarrays, northern blotting, in-situ
hybridization, serial analysis of gene expression, and PCR-based methods to study
gene expression at transcriptomics level.
6. Documentation of pathway specific reactions in PathBuilder following NetPath and
NetSlim criteria (as described by Raju et al., 2011).
7. Usage of Controlled Vocabularies including GO, EVOC, PSI-MS and International
pathway data exchange formats such as PSI-MI, BioPAX, SBML and GPML.
8. Formulation of query terms to search for pathway reactions using PubMed
9. Effective screening for relevant research articles pertaining to specific pathways
Initially, students will be demonstrated the documentation of pathway reactions by faculty
level scientists at IOB. Each student will be provided with research articles for hands-on
training. They will also be trained to review pathway reactions captured by another set of
students. Each reaction will be reviewed by IOB researchers. Review comments will be
explained to students. By subsequent cycle of this process, we will ensure their confidence
and error-free as possible documentation of pathway reactions.
Every year, students will be trained to participate in the development of a set of 150
pathways. The certificates will be issued to all the students who participate in this
programme.
2.4. Remote monitoring of human signaling pathway development by students
The research articles for each pathway will be screened by trained scientists at Institute of
Bioinformatics. Specific pathways will be allotted to individual students or a group of two/
three, depending on the number of students and their provisional time available for literature
analysis. Accordingly, during their summer vacation, or if interested to take up NetPath
project as their summer training project, students will visit IOB and their progress will be
directly monitored by faculty scientists. Otherwise, their documentation will be remotely
monitored through PathBuilder, Skype conferences, and/or coupled with frequent visit to
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universities or research institutes. The full text articles which are not open-access will be
provided.
2.5. Development of signaling pathway maps by students
The students will be trained to develop pathway models using various pathways editing
software such as GenMAPP, Cytoscape, PathVisio and Cell Designer. The pathway data
assembled by students, reviewed by experts at IOB, will be integrated into NetPath. The
students who have contributed to development of each pathway in NetPath will be listed
under curators.
2.6. Training students on preparation of manuscripts of specific signaling pathways
The students will be trained to prepare specific pathway manuscripts. The students and
Project Leaders from their respective Participating Institutes will be authors in these
manuscripts. These manuscripts will be edited and reviewed by faculty scientists along with
specific pathway reviewers at IOB. Scientists across the world at the level of professor or
associate professor who have expertise on specific pathway exemplified by the publication
will be invited as pathway authorities. The pathway authority for a signaling pathway will
review the pathway data to ensure data as error-less as possible and ensure the inclusion of
majority of molecules identified in a pathway and also whether studies from major labs
involved in the pathway are incorporated. The manuscripts will be submitted to international
journals for peer-review and publication.
Specific Objective 3. Development of 1000 human signaling pathways
We have already established a resource of signaling pathways named NetPath. NetPath
currently hosts 27 signaling pathways and more than 100 pathways are currently under
development with internal funding. The reactions in NetPath pathways encompass
spatiotemporal biochemical reactions induced by the interaction of specific ligands to their
receptors reported in published research articles. These reactions include protein-protein
interactions, enzyme-catalysis reactions, post-translational modifications, activation-
inhibition reactions and protein translocation events. We have identified over 1000 ligand-
receptor mediated signaling pathways for which pathway specific information are available in
literature.
3.1. Curation of protein-protein interactions
Proteins mediate cellular signaling by protein-protein interactions (PPIs) and protein-non-
protein interactions. PPIs experimentally proved to be stimulated in a pathway will be
documented as binary or complex interactions. Binary interactions correspond to PPIs when
only two proteins involved in complexes are identified. More than two proteins associated in
complexes, when identified by western blotting or by mass spectrometry, the proteins
together are documented as a complex. It should be noted that, the proteins may directly
interact with each other or may be indirectly associated with their stoichiometry of reaction
not devised. This information would provide an ideal platform to integrate more proteins
that may be identified in the future to be part of dynamic complexes. For every interaction,
we will also document domains/motifs, post-translational modifications (PTMs), and
subcellular localisation, whenever reported. PPIs identified in mammalian cells other than
human will also documented if the interactions were never studied in human. This would
facilitate experimental validation in human system. Further to support this information, we
will also catalogue the species of each interaction molecules (whether human, mouse, rat,
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bovine or other mammals) along with the cell/cell line information in which the reactions
were studied. Most of the PPIs studies often involve transfection and expression of receptors
or intracellular proteins from other species. Thus, this information would provide a valuable
tool for the researchers to experimentally replicate and analyse the difference in species
specific interactions. A textual description with the above information will also be
documented for each reaction.
3.2. Curation of enzyme-substrate reactions and post-translational modifications
Array of dynamic PTMs determines the spatiotemporal organization of proteins and their
activity. We will document experimentally derived information on the enzymatic reactions
modulated in signaling pathways. High-throughput experimental platforms capable of
profiling global changes in PTM status of proteins have revolutionised protein biology. This
has led to the emergence of phosphoproteome, acetylome and methylome analogous to the
traditional proteome or genome. The temporal and context-specific studies thus accounting
for the heterogeneous datasets published literature form the basis for analysis of the fluxes in
cellular signaling. Hence, we will catalogue catalytic reactions involving an enzyme and its
substrate as direct and enzyme-unidentified PTM reactions as 'induced'. This classification is
devised based on the concept that an enzyme may have multiple substrates and vice versa.
The PTMs for which high-throughput experimental platforms are currently available such as
phosphorylation, dephosphorylation, sumoylation, desumoylation, ubiquitination,
deubiquitination, acetylation, deacetylation, proteolytic cleavage, methylation,
demethylation, palmitoylation and glycosylation will be focussed more in this effort. The
influence of PTMs on the activity of proteins whether activated or inhibited in the context of
the study will also be documented. Identification of site of PTMs mostly depends on the
availability of site-specific antibodies, site-directed mutagenesis approaches, and analysis by
mass spectrometry. Such information is often reported with the sites mapped to one or other
protein isoforms or based on the antibody information. Hence, whenever site and residue
information are available for PTMs, we will map them to either the specific or longest
isoforms in the current version of the RefSeq protein database.
3.3. Protein translocation
The variations in spatiotemporal distribution of proteins across cellular compartments to
mediate signaling events will be cataloged in this category. The PTM dependence or
molecular interactions underlying these events will also be documented along with the sub-
cellular compartments in accordance with Gene Ontology controlled vocabulary (Ashburner
et al., 2000).
3.4. Genes transcriptionally regulated by signaling pathways
Differential responses to stimuli are brought about by temporal changes in gene expression.
Qualitative and quantitative changes observed at mRNA level are determined by
transcriptional regulatory networks. We will document genes which are experimentally
identified to be regulated at mRNA level in humans by specific pathways. This will be
documented from mRNA profiling studies employing cDNA microarrays and non-microarray
approaches such as northern blotting, PCR-based methods, in-situ hybridization and
ribonuclease protection assay. A minimum fold change value of 2 and p-value of < 0.05 will
be taken as arbitrary cutoffs for inclusion of gene expression data from microarray studies.
Further, name of cells or cell types in which the genes are identified to be up- or down-
regulated by specific pathways will be also documented.
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3.5. Identification of transcriptional regulators
We will capture transcription regulators (transcription factors, or their co-activators/co-
repressors) of the genes whose expressions are regulated by specific pathways. Such
transcriptional regulators will be included only if they are proved using chromatin
immunoprecipitation assay, electrophoretic mobility shift assay, gene silencing, and promoter
activity assays in specific pathways.
3.6. Protein expression regulated by signaling pathways
Identification of protein expression regulated by specific pathways would contribute to a
better understanding of proteome reorganization and functional response of cells to specific
stimuli. The proteins up- or down- regulated by specific signaling pathways will be cataloged
along with the information on the cell system.
3.7. Development of a high-confidence graphical regulatory map of signaling pathways
Composite maps of signaling events are often used to visualize, hypothesize and to develop
mathematical models to predict the behaviors of normal and diseased cells. Moreover,
signaling maps are also overlaid with biological data from various high-throughput
experimental platforms to obtain an integrated view of biological processes. There were
numerous molecules and reactions in NetPath which were not included in existing pathway
models or signaling maps available elsewhere (e.g., induced PTMs discussed under enzyme-
substrate reactions and post-translational modifications). Most of these molecules remain
unconnected to the core network due to lack of information on the interaction partners,
upstream enzymes or downstream effector molecules and hence can be called a novel
molecules in the pathway. All the information for a specific pathway in NetPath will be made
available in standard formats that can be used to visualize the networks using various
visualization and analysis software such as PathVisio, GenMAPP, GO-Elite, and Cytoscape.
However, to reduce the complexity and to provide effective visualization, we will develop
network maps for each signaling pathway by applying a set of confidence criteria.
3.7.1. Analysis of high-confidence reactions in NetPath pathway
We will apply the following inclusion criteria to extract a high confidence set of reactions
from each of the pathways in NetPath as described in (Raju et al., 2011): (a) reactions
supported by at least 2 research articles; (b) reactions such as PPIs reported through high-
throughput analyses, as well as PTMs identified using mass spectrometry provided that they
are validated by a focused experiment; (c) components of known protein complexes; (d)
molecules or reactions established through expert review articles; and (e) direct PPIs
provided they are derived from both in vitro and in vivo experiments.
3.7.2. Graphical Representation of NetSlim
All molecular reactions that occur downstream of activated receptors will be represented by
solid edges, which depict direct interactions/reactions, or by broken edges, which depict
indirect/induced events. Signaling nodes will be depicted based on the ability of molecules to
interact with their partners, and on the availability of protein regulators to cross-talk with
other signaling modules. The topology of the pathway, which determines whether a given
molecule lies upstream or downstream from another reference molecule, will be determined
based on the biological information obtained from studies using mutants,
activators/inhibitors, knock-out and silencing approaches. The edges which represent various
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PPIs, enzymatic reactions, or protein translocation events will be distinguished by distinct
colors. Detailed legends will be provided in all the pathway maps.
Specific Objective 4. Development of a software suite to convert pathway data into
standard community data formats.
We have developed PathBuilder, an open-source web application to annotate biological
information pertaining to signaling pathways. PathBuilder enables annotation of molecular
events including protein–protein interactions, enzyme–substrate relationships, protein
translocation events and gene regulation. The PathBuilder should be enabled to accomplish
extensive curation, review and constant revision of pathway by community participation.
This demands that there should be provision to store various query terms, accessibility to
students of participating centers, list of articles curated, period when pathways were last
updated, and to facilitate internal review and review by pathway authorities Availability of
Pathway data in NetPath and NetSlim in computer-readable formats such as BioPAX, PSI-MI
and SBML are essential for data exchange and interoperability with available pathway
analysis software. Current version of PathBuilder does not facilitate automated conversion of
pathway data into these formats pathways. PathBuilder tool should also undertake various
quality control measures and consistency checks of curation by at student level. Taking into
account the large number of pathways, we propose to enable provisions for constant revision,
quality control measures and automated export of pathway data into BioPAX level 3.0, PSI-
MI version 2.5 and SBML version 2.1 formats.
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18.2 Proprietary/patented items, if any, expected to be used for this project.
No other proprietary or patented item will be used for this project.
18.3 Organization of work elements
Dr. Keshava Prasad, Dr. Akhilesh Pandey and Dr. Rajesh Raju will coordinate the
implementation of overall program between IOB and all Participating Institutes. Coordinators
along with Dr. Sowmya Soman and Dr. Aditi Chatterjee and the Research Associates
appointed in this project will provide the orientation programme, selection of students and
training for the development of signaling pathways. Project Leaders from Participating
Institutes will coordinate orientation program, workshops and monitor curation of signaling
pathways of their students in the respective Participating Institutes. Dr. Prasad, Dr. Raju, Dr.
Pandey, Dr. Chatterjee, Dr. Soman and all Project Leaders from Participating Institutes will
be involved in the development of publication quality work emanating from the program. The
Project Leaders from each of the institutes will coordinate this human resource development
programme in their respective institutes. The network of organization of work elements by
the nodal centre (IOB) with the Participating Institutes are provided in Figure 10.
Figure 10: The current, new and prospective Participating Institutes in the human
resource development programme on signaling pathways- The current Participating
institutes are in light blue color. The new and prospectively future Participating Institutes are
colored in dark blue.
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Two Research Associates and 10 Senior Research Fellows recruited for this programme will
be trained by Faculty Scientists and Research Scientists from IOB. The research scientists,
Research Associates and the Senior Research Fellows will be involved in the initial screening
of the articles for pathways specific to ligands or specific ligand-receptor combinations. A
basic query term will be used to screen for articles containing pathway information on
specific pathways (e.g. 'epidermal growth factor' along with its other MeSH terms will be
used to screen articles for EGF pathway) to increase the coverage of literature survey. Based
on the number of articles to be screened for curation of specific pathways, pathways are
categorized into 5 different groups containing- (i) 100 to 500 articles to be screened, (ii) 500
to 1000 articles to be screened, (iii) 1000 to 3000 articles to be screened, (iv) 3000 to 6000
articles to be screened, and (v) more than 6000 articles to be screened. In the first year, 10
research scientists from IOB will be involved with 2 Research Associates and 10 Senior
Research Fellows in screening the articles.
The overall workflow of the components involved in this project is outlined in Figure 11.
The screened articles will be distributed to the students on an average of 100 research articles
per student. Wherever there are more than 100 articles to be curated, more students will be
allocated a pathway with every student per further 100 further articles. Over 100 pathways
will be chosen according to the number of articles to be curated so as to accommodate all the
students as co-authors in publication. After their initial curation required for the respective
manuscripts, the students can also work on other pathways in which the students can be co-
authors, thus, would ensure effective time-management and dedication to pathway
development process by the students. Reaction curated by students will be reviewed by
specific reviewers (research scientists from IOB, Senior Research Fellows and Research
Associates) every day to make sure that the curation criteria is clear and also will be
discussed with all the students so that students may not repeat the mistakes again and again.
Over a period of one month, the students (in cases where more than one student is involved in
a pathway) will also be assessed by inter-review of curation amongst themselves. The
authorship position of students will be based on the dedicated time and quality of the
literature analysis by each and every student(s) analyzing specific pathways.
The students will also be introduced to the manuscript preparation process during their
literature analysis. Manuscript preparation will be initiated from the initial process of seeking
pathway information pertaining to specific signaling pathways from review articles. More
information will be furnished into the manuscript as and when they analyze more research
articles which study signaling pathways in the context of their function in different cell types
and molecules of therapeutic interest. This process would also help them define and interpret
pathway reactions in the manuscript based on the results obtained from various experimental
platforms.
The pathway reactions obtained by literature analysis will be further filtered using the
NetSlim criteria. Further PubMed search using the specific molecules involved, in
combination with the name of specific ligands and/or receptors will also be carried out at this
stage to ensure comprehensiveness and effective application of NetSlim criteria. The filtered
reactions will be graphically represented in a topological manner using PathVisio by the
students with the help of their respective mentors. The information obtained from silencing,
mutant, activator/inhibitor approaches will be used to device the relationships amongst the
molecules as to whether a molecule is upstream or downstream to another molecule in a
pathway and also to identify positive and negative feedback regulations. The international
experts on specific pathways will also be selected from the articles which had been curated
based on the number of articles and their current focus. They will be requested and invited to
become the pathway authority for specific pathways. The comments from the pathway
authority will be incorporated in the pathway resource as well as the manuscript. The
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pathway data will be released into the public along with the data in standard community
formats for the review by the peer-reviewers assigned by international journals.
Figure 9: An overview of the sequential process involved in the development of 1000
signaling pathways.
Figure 11: The overall workflow of the components involved in this project
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18.4 Suggested plan of action for utilization of research outcome expected from the
project.
1. The development of signaling pathways by the student bioscience community would
generate a cream of interdisciplinary scientists who would pace up with evolving technology
and reinforce technological development in biomedical research and education in India.
2. Human resource development programme for signaling pathways with the involvement
of scientists from various research institutes in India would facilitate technology transfer and
mutual collaborative efforts for the next phase of the research on signaling pathways as well
as on different technology platforms.
In continuation, the high-quality data emanating from this described project will be used for
the computational analysis and to develop open-access pathway analysis suites. This phase
will involve eminent bioinformaticians and their students from different institutes in India.
The outcome of predictions will be validated experimentally and further hypothesis-driven
approaches will be undertaken to study cross-talks and temporal behavior of signaling
networks (Figure 12).
Figure 12: A diagrammatic representation of the three-tier components originating with
this proposal
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3. NetPath will serve as an initial platform to integrate signaling pathways involved in
specific biological processes.
4. The pathways in NetPath would enable integration and analysis of cell/cell type specific
information which is currently not available in any other resources in the public domain.
5. Thousand signaling pathways that will be publicly available in NetPath
(www.netpath.org) with additional information linked to Human Protein Reference Database,
Human Proteinpedia and NCBI will serve as a unique platform for systems biology
approaches.
6. Information in NetPath would accelerate research on specific signaling pathways and
identification of missing links and relationships of several orphan molecules.
7. The molecules and their reactions in 1000 signaling pathways will form the basis for
prediction and validation of several known and novel molecules as potential therapeutic
targets for diseases.
8. NetPath pathways enriched based on specific functions and disease processes would
enable network approaches to identify key components that cross-talks in signaling networks.
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Bibliography
Ackermann M, Strimmer K (2009) A general modular framework for gene set enrichment
analysis. BMC Bioinformatics 10: 47.
Amanchy, R., Zhong, J., Molina, H., Chaerkady, R., Iwahori, A., Kalume, D. E., Grønborg,
M., Joore, J., Cope, L. and Pandey, A. (2008). Identification of c-Src tyrosine kinase
substrates using mass spectrometry and peptide microarrays. Journal of Proteome Research.
7, 3900-3910.
Amanchy, R., Kandasamy, K., Mathivanan, S., Periaswamy, B., Reddy, R., Yoon, W. H.,
Joore, J., Beer, M. A., Cope, L. and Pandey, A. (2011). Identification of novel
phosphorylation motifs through an integrative computational and experimental analysis of the
human phosphoproteome. Journal of Proteomics and Bioinformatics. 4, 22-35.
Astsaturov I, Ratushny V, Sukhanova A, Einarson MB, Bagnyukova T, Zhou Y, Devarajan
K, Silverman JS, Tikhmyanova N, Skobeleva N, Pecherskaya A, Nasto RE, Sharma C,
Jablonski SA, Serebriiskii IG, Weiner LM, Golemis EA. Synthetic lethal screen of an EGFR-
centered network to improve targeted therapies. Sci Signal. 2010; 3(140): ra67.
Bhattacharjee M, Raju R, Radhakrishnan A, Nanjappa V, Muthusamy B, Singh K,
Kuppusaami D, Lingala BT, Pan A, Mathur PP, Harsha HC, Prasad TSK, Atkins GJ, Pandey
A and Chatterjee A. A Bioinformatics Resource for TWEAK-Fn14 Signaling Pathway.
Journal of Signal Transduction. 2012.
BioGPS (Wu et al., 2009) Wu C, Orozco C, Boyer J, Leglise M, Goodale J, Batalov S,
Hodge CL, Haase J, Janes J, Huss JW 3rd, Su AI. BioGPS: an extensible and customizable
portal for querying and organizing gene annotation resources. Genome Biol. 2009; 10(11):
R130.
Kandasamy, K., Keerthikumar, S., Raju, R., Prasad, T. S. K., Ramachandra, Y. L., Mohan, S.
and Pandey, A. PathBuilder - open source software for annotating and developing pathway
resources. Bioinformatics. 2009; 25(21): 2860-2.
Bouwens M, van de Rest O, Dellschaft N, Bromhaar MG, de Groot LC, Geleijnse JM, Müller
M, Afman LA. Fish-oil supplementation induces antiinflammatory gene expression profiles
in human blood mononuclear cells. Am J Clin Nutr. 2009; 90(2):415-24.
Bose, R., Molina, H., Patterson, A. S., Bitok, J. K., Periaswamy, B., Bader, J. S., Pandey, A.
and Cole, P. A. Phosphoproteomic analysis of Her2/neu signaling and inhibition. Proceedings
of the National Academy of Sciences, USA. 2006; Jun:103(26):9773-8.
Bush WS, Dudek SM, Ritchie MD. Biofilter: a knowledge-integration system for the multi-
locus analysis of genome-wide association studies. Pac Symp Biocomput. 2009:368-79.
Ciardiello F, Tortora G. EGFR antagonists in cancer treatment. N Engl J Med. 2008 Mar
13;358(11):1160-74.
Civelli O, Saito Y, Wang Z, Nothacker HP, Reinscheid RK. Orphan GPCRs and their
ligands. Pharmacol Ther. 2006 Jun;110(3):525-32.
![Page 47: PROFORMA FOR SUBMISSION OF RESEARCH ...dbtepromis.gov.in/Documents/TechnicalDetails/ProposalID...State: Karnataka 3. Status of the Institute: Private Non-Profit Institute Recognized](https://reader034.vdocuments.mx/reader034/viewer/2022051800/5acf1ed67f8b9ad24f8c0d5c/html5/thumbnails/47.jpg)
47
Collingridge GL, Olsen RW, Peters J, Spedding M. A nomenclature for ligand-gated ion
channels. Neuropharmacology. 2009 Jan;56(1):2-5.
Cook SJ, McCormick F.Inhibition by cAMP of Ras-dependent activation of Raf. Science.
1993; 262(5136):1069-72.
Croft D, O'Kelly G, Wu G, Haw R, Gillespie M, Matthews L, Caudy M, Garapati P,
Gopinath G, Jassal B, et al. Reactome: a database of reactions, pathways and biological
processes. Nucleic Acids Res. 2011; 39: 691–7.
Demir E, Cary MP, Paley. S, et al. The BioPAX community standard for pathway data
sharing. Nat. Biotechnol. 2010; 28: 935–42.
Draghici S, Khatri P, Martins RP, Ostermeier GC, Krawetz SA (2003) Global functional
profiling of gene expression. Genomics 81: 98–104.
Draghici S, Khatri P, Tarca AL, Amin K, Done A, et al. (2007) A systems biology approach
for pathway level analysis. Genome Res 17: 1537–1545.
Ehrnhoefer DE, Wong BK, Hayden MR. Convergent pathogenic pathways in Alzheimer's
and Huntington's diseases: shared targets for drug development. Nat Rev Drug Discov. 2011
Oct 21;10(11):853-67.
Freudlsperger C, Burnett JR, Friedman JA, Kannabiran VR, Chen Z, Van Waes C. EGFR-
PI3K-AKT-mTOR signaling in head and neck squamous cell carcinomas: attractive targets
for molecular-oriented therapy. Expert Opin Ther Targets. 2011;15(1):63-74.
Gandhi, T. K. B., Zhong, J., Mathivanan, S., Karthick, L., Chandrika, K. N., Mohan, S. S.,
Sharma, S., Pinkert, S., Nagaraju, S., Periyaswamy, B., Mishra, G., Nandakumar, K., Shen,
B., Deshpande, N., Nayak, R., Sarker, M., Boeke, J. D., Parmigiani, G., Schultz, J., Bader, J.
S. and Pandey, A. Analysis of the human protein interactome and comparison with yeast,
worm and fly interaction datasets. Nature Genetics. 2006;Mar;38(3):285-93
Geer LY, Marchler-Bauer A, Geer RC, Han L, He J, He S, Liu C, Shi W, Bryant SH. The
NCBI BioSystems database. Nucleic Acids Res. 2010; 38(Database issue): D492-6.
Giguère V. Orphan nuclear receptors: from gene to function. Endocr Rev. 1999
Oct;20(5):689-725.
Goel R, Harsha HC, Pandey A, Prasad TS.Human Protein Reference Database and Human
Proteinpedia as resources for phosphoproteome analysis. Mol Biosyst. 2012;8(2):453-63.
Goel R, Raju R, Maharudraiah J, Kumar GSS, Ghosh K, Kumar A, Lashmi PT, Sharma J,
Sharma R, Balakrishnan L, Pan A, Kandasamy K, Christopher R, Krishna V, Mohan SS,
Harsha HC, Mathu, PP, Pandey A and Prasad T S K). A signaling network of thyroid-
stimulating hormone. Journal of Proteomics and Bioinformatics. . 2011.
Goel, R., Muthusamy, B., Pandey, A. and Prasad, T. S. K. (2010). Human Protein Reference
Database and Human Proteinpedia as discovery resources for molecular biotechnology.
Molecular Biotechnology. 48, 87-95.
Gough NR. Science's signal transduction knowledge environment: the connections maps
database. Ann N Y Acad Sci. 2002; 971: 585-7.
![Page 48: PROFORMA FOR SUBMISSION OF RESEARCH ...dbtepromis.gov.in/Documents/TechnicalDetails/ProposalID...State: Karnataka 3. Status of the Institute: Private Non-Profit Institute Recognized](https://reader034.vdocuments.mx/reader034/viewer/2022051800/5acf1ed67f8b9ad24f8c0d5c/html5/thumbnails/48.jpg)
48
Grady BJ, Torstenson ES, McLaren PJ, DE Bakker PI, Haas DW, Robbins GK, Gulick RM,
Haubrich R, Ribaudo H, Ritchie MD. Use of biological knowledge to inform the analysis of
gene-gene interactions involved in modulating virologic failure with efavirenz-containing
treatment regimens in art-naïve actg clinical trials participants. Pac Symp Biocomput.
2011:253-64.
Gu J, Chen Y, Li S, Li Y. Identification of responsive gene modules by network-based gene
clustering and extending: application to inflammation and angiogenesis. BMC Syst Biol.
2010; 4:47.
Hammond DE, Hyde R, Kratchmarova I, Beynon RJ, Blagoev B, Clague MJ. Quantitative
analysis of HGF and EGF-dependent phosphotyrosine signaling networks. J Proteome Res.
2010; 9(5):2734-42.
Harmar AJ, Hills RA, Rosser EM, Jones M, Buneman OP, Dunbar DR, Greenhill SD, Hale
VA, Sharman JL, Bonner TI, Catterall WA, Davenport AP, Delagrange P, Dollery CT, Foord
SM, Gutman GA, Laudet V, Neubig RR, Ohlstein EH, Olsen RW, Peters J, Pin JP, Ruffolo
RR, Searls DB, Wright MW, Spedding M. IUPHAR-DB: the IUPHAR database of G protein-
coupled receptors and ion channels. Nucleic Acids Res. 2009 Jan;37(Database issue):D680-5.
Harari PM. Epidermal growth factor receptor inhibition strategies in oncology. Endocr Relat
Cancer. 2004 Dec;11(4):689-708.
Harsha, H. C., Jimeno, A., Molina, H., Mihalas, A., Goggins, M., Hruban, R., Schulick, R.,
Kamath, U., Maitra, A., Hidalgo, M. and Pandey, A. (2008). Activated epidermal growth
factor receptor as a novel target in pancreatic cancer therapy. Journal of Proteome Research.
7, 4651-4658.
Hennessy BT, Smith DL, Ram PT, Lu Y, Mills GB. Exploiting the PI3K/AKT pathway for
cancer drug discovery. Nat Rev Drug Discov. 2005 Dec;4(12):988-1004.
Hermjakob H, Montecchi-Palazzi L, Bader G, et al. The HUPO PSI's molecular interaction
format–a community standard for the representation of protein interaction data. Nat
Biotechnol. 2004; 22:177–83.
Hoang LT, Lynn DJ, Henn M, Birren BW, Lennon NJ, Le PT, Duong KT, Nguyen TT, Mai
LN, Farrar JJ, Hibberd ML, Simmons CP. The early whole-blood transcriptional signature of
dengue virus and features associated with progression to dengue shock syndrome in
Vietnamese children and young adults. J Virol. 2010; 84(24):12982-94.
Hucka M, Finney A, Sauro HM, et al. The systems biology markup language (SBML): a
medium for representation and exchange of biochemical network models. Bioinformatics.
2003; 19: 524–31.
Igarashi T, Kaminuma T. Development of a cell signaling networks database. Pac Symp
Biocomput. 1997:187-97.
Imamura H, Yachie N, Saito R, Ishihama Y, Tomita M. Towards the systematic discovery of
signal transduction networks using phosphorylation dynamics data. BMC Bioinformatics.
2010; 11: 232.
![Page 49: PROFORMA FOR SUBMISSION OF RESEARCH ...dbtepromis.gov.in/Documents/TechnicalDetails/ProposalID...State: Karnataka 3. Status of the Institute: Private Non-Profit Institute Recognized](https://reader034.vdocuments.mx/reader034/viewer/2022051800/5acf1ed67f8b9ad24f8c0d5c/html5/thumbnails/49.jpg)
49
Isserlin R, Merico D, Alikhani-Koupaei R, Gramolini A, Bader GD, Emili A. Pathway
analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps.
Proteomics. 2010 ;10(6):1316-27.
Jiao Y, Lawler K, Patel GS, Purushotham A, Jones AF, Grigoriadis A, Tutt A, Ng T,
Teschendorff AE. DART: Denoising Algorithm based on Relevance network Topology
improves molecular pathway activity inference. BMC Bioinformatics. 2011; 12: 403.
Kandasamy K, Keerthikumar S, Goel R, Mathivanan S, Patankar N, Shafreen B, Renuse S,
Pawar H, Ramachandra YL, Acharya PK, Ranganathan P, Chaerkady R, Keshava Prasad TS,
Pandey A.Human Proteinpedia: a unified discovery resource for proteomics research. Nucleic
Acids Res. 2009 Jan;37(Database issue):D773-81.
Kandasamy K, Keerthikumar S, Raju R, Keshava Prasad TS, Ramachandra YL, Mohan S,
Pandey A. PathBuilder--open source software for annotating and developing pathway
resources.
Kandasamy K, Mohan SS, Raju R, Keerthikumar S, Kumar GS, Venugopal AK, Telikicherla
D, Navarro JD, Mathivanan S, Pecquet C, Gollapudi SK, Tattikota SG, Mohan S,
Padhukasahasram H, Subbannayya Y, Goel R, Jacob HK, Zhong J, Sekhar R, Nanjappa V,
Balakrishnan L, Subbaiah R, Ramachandra YL, Rahiman BA, Prasad TS, Lin JX, Houtman
JC, Desiderio S, Renauld JC, Constantinescu SN, Ohara O, Hirano T, Kubo M, Singh S,
Khatri P, Draghici S, Bader GD, Sander C, Leonard WJ, Pandey A.NetPath: a public resource
of curated signal transduction pathways. Genome Biol. 2010;11(1): R3.
Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M: The KEGG resource for
deciphering the genome. Nucleic Acids Res 2004; 32: 277-80.
Kanehisa M, Goto S.KEGG: kyoto encyclopedia of genes and genomes.Nucleic Acids Res.
2000; 28(1):27-30.
Kanehisa M. Toward pathway engineering: a new database of genetic and molecular
pathways. Science & Technology Japan, 1996; 59: 34-8.
Keerthikumar S, Raju R, Kandasamy K, Hijikata A, Ramabadran S, Balakrishnan L, Ahmed
M, Rani S, Selvan LD, Somanathan DS, Ray S, Bhattacharjee M, Gollapudi S, Ramachandra
YL, Bhadra S, Bhattacharyya C, Imai K, Nonoyama S, Kanegane H, Miyawaki T, Pandey A,
Ohara O, Mohan S.RAPID: Resource of Asian Primary Immunodeficiency Diseases. Nucleic
Acids Res. 2009;37(Database issue):D863-7.
Kelder T, van Iersel MP, Hanspers K, Kutmon M, Conklin BR, Evelo CT, Pico AR.
WikiPathways: building research communities on biological pathways. Nucleic Acids Res.
2012; 40(Database issue): D1301-7.
Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S,
Telikicherla D, Raju R, Shafreen B, Venugopal A, Balakrishnan L, Marimuthu A, Banerjee
S, Somanathan DS, Sebastian A, Rani S, Ray S, Harrys Kishore CJ, Kanth S, Ahmed M,
Kashyap MK, Mohmood R, Ramachandra YL, Krishna V, Rahiman BA, Mohan S,
Ranganathan P, Ramabadran S, Chaerkady R, Pandey A.Human Protein Reference Database-
-2009 update. Nucleic Acids Res. 2009 Jan;37(Database issue):D767-72.
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K,
Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L,
![Page 50: PROFORMA FOR SUBMISSION OF RESEARCH ...dbtepromis.gov.in/Documents/TechnicalDetails/ProposalID...State: Karnataka 3. Status of the Institute: Private Non-Profit Institute Recognized](https://reader034.vdocuments.mx/reader034/viewer/2022051800/5acf1ed67f8b9ad24f8c0d5c/html5/thumbnails/50.jpg)
50
Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris
W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, et al. Initial
sequencing and analysis of the human genome. Nature. 2001;409:860–921. doi:
10.1038/35057062.
Mathivanan S, Ahmed M, Ahn NG, Alexandre H, Amanchy R, Andrews PC, Bader JS,
Balgley BM, Bantscheff M, Bennett KL, Björling E, Blagoev B, Bose R, Brahmachari SK,
Burlingame AS, Bustelo XR, Cagney G, Cantin GT, Cardasis HL, Celis JE, Chaerkady R,
Chu F, Cole PA, Costello CE, Cotter RJ, Crockett D, DeLany JP, De Marzo AM, DeSouza
LV, Deutsch EW, Dransfield E, Drewes G, Droit A, Dunn MJ, Elenitoba-Johnson K, Ewing
RM, Van Eyk J, Faca V, Falkner J, Fang X, Fenselau C, Figeys D, Gagné P, Gelfi C, Gevaert
K, Gimble JM, Gnad F, Goel R, Gromov P, Hanash SM, Hancock WS, Harsha HC, Hart G,
Hays F, He F, Hebbar P, Helsens K, Hermeking H, Hide W, Hjernø K, Hochstrasser DF,
Hofmann O, Horn DM, Hruban RH, Ibarrola N, James P, Jensen ON, Jensen PH, Jung P,
Kandasamy K, Kheterpal I, Kikuno RF, Korf U, Körner R, Kuster B, Kwon MS, Lee HJ, Lee
YJ, Lefevre M, Lehvaslaiho M, Lescuyer P, Levander F, Lim MS, Löbke C, Loo JA, Mann
M, Martens L, Martinez-Heredia J, McComb M, McRedmond J, Mehrle A, Menon R, Miller
CA, Mischak H, Mohan SS, Mohmood R, Molina H, Moran MF, Morgan JD, Moritz R,
Morzel M, Muddiman DC, Nalli A, Navarro JD, Neubert TA, Ohara O, Oliva R, Omenn GS,
Oyama M, Paik YK, Pennington K, Pepperkok R, Periaswamy B, Petricoin EF, Poirier GG,
Prasad TS, Purvine SO, Rahiman BA, Ramachandran P, Ramachandra YL, Rice RH, Rick J,
Ronnholm RH, Salonen J, Sanchez JC, Sayd T, Seshi B, Shankari K, Sheng SJ, Shetty V,
Shivakumar K, Simpson RJ, Sirdeshmukh R, Siu KW, Smith JC, Smith RD, States DJ,
Sugano S, Sullivan M, Superti-Furga G, Takatalo M, Thongboonkerd V, Trinidad JC, Uhlen
M, Vandekerckhove J, Vasilescu J, Veenstra TD, Vidal-Taboada JM, Vihinen M, Wait R,
Wang X, Wiemann S, Wu B, Xu T, Yates JR, Zhong J, Zhou M, Zhu Y, Zurbig P, Pandey A.
Human Proteinpedia enables sharing of human protein data. Nat Biotechnol. 2008;
26(2):164-7.
Mathivanan, S., Periaswamy, B., Gandhi, T. K. B., Kandasamy, K., Suresh, S., Mohmood,
R., Ramachandra, Y. L. and Pandey, A. An evaluation of human protein-protein interaction
data in the public domain. BMC Bioinformatics. 2006; Dec;7 Suppl 5:S19.
Mathivanan S, Pandey A.Human Proteinpedia as a resource for clinical proteomics. Mol Cell
Proteomics. 2008; Oct;7(10):2038-47.
Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, de Bono B, Garapati P, Hemish J,
Hermjakob H, Jassal B, Kanapin A, Lewis S, Mahajan S, May B, Schmidt E, Vastrik I, Wu
G, Birney E, Stein L, D'Eustachio P. Reactome knowledgebase of human biological
pathways and processes. Nucleic Acids Res. 2009; 37(Database issue):D619-22.
Milenković T, Memišević V, Bonato A, Pržulj N. Dominating biological networks. PLoS
One. 2011; 6(8): e23016.
Mishra GR, Suresh M, Kumaran K, Kannabiran N, Suresh S, Bala P, Shivakumar K,
Anuradha N, Reddy R, Raghavan TM, Menon S, Hanumanthu G, Gupta M, Upendran S,
Gupta S, Mahesh M, Jacob B, Mathew P, Chatterjee P, Arun KS, Sharma S, Chandrika KN,
Deshpande N, Palvankar K, Raghavnath R, Krishnakanth R, Karathia H, Rekha B, Nayak R,
Vishnupriya G, Kumar HG, Nagini M, Kumar GS, Jose R, Deepthi P, Mohan SS, Gandhi
TK, Harsha HC, Deshpande KS, Sarker M, Prasad TS, Pandey A.Human protein reference
database--2006 update. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D411-4.
Morgensztern D, McLeod HL. PI3K/Akt/mTOR pathway as a target for cancer therapy.
Anticancer Drugs. 2005 ;Sep;16(8):797-803.
![Page 51: PROFORMA FOR SUBMISSION OF RESEARCH ...dbtepromis.gov.in/Documents/TechnicalDetails/ProposalID...State: Karnataka 3. Status of the Institute: Private Non-Profit Institute Recognized](https://reader034.vdocuments.mx/reader034/viewer/2022051800/5acf1ed67f8b9ad24f8c0d5c/html5/thumbnails/51.jpg)
51
Morris MK, Saez-Rodriguez J, Clarke DC, Sorger PK, Lauffenburger DA. Training signaling
pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver
cell responses to inflammatory stimuli. PLoS Comput Biol. 2011; 7(3): e1001099.
Mostaghel EA, Geng L, Holcomb I, Coleman IM, Lucas J, True LD, Nelson PS. Variability
in the androgen response of prostate epithelium to 5alpha-reductase inhibition: implications
for prostate cancer chemoprevention. Cancer Res. 2010 Feb 15;70(4):1286-95.
Muthusamy B, Hanumanthu G, Suresh S, Rekha B, Srinivas D, Karthick L, Vrushabendra
BM, Sharma S, Mishra G, Chatterjee P, Mangala KS, Shivashankar HN, Chandrika KN,
Deshpande N, Suresh M, Kannabiran N, Niranjan V, Nalli A, Prasad TS, Arun KS, Reddy R,
Chandran S, Jadhav T, Julie D, Mahesh M, John SL, Palvankar K, Sudhir D, Bala P, Rashmi
NS, Vishnupriya G, Dhar K, Reshma S, Chaerkady R, Gandhi T K, Harsha HC, Mohan SS,
Deshpande KS, Sarker M, Pandey A. Plasma Proteome Database as a resource for proteomics
research. Proteomics. 2005;5(13):3531-6.
Nanjappa V, Raju R, Muthusamy B, Sharma J, Thomas JK, Nidhina PAH, Harsha HC,
Pandey A, Anilkumar G and Prasad TSK. A comprehensive curated reaction map of leptin
signaling pathway. Journal of Proteomics and Bioinformatics. 2011.
Navab R, Strumpf D, Bandarchi B, Zhu CQ, Pintilie M, Ramnarine VR, Ibrahimov E,
Radulovich N, Leung L, Barczyk M, Panchal D, To C, Yun JJ, Der S, Shepherd FA, Jurisica
I, Tsao MS. Prognostic gene-expression signature of carcinoma-associated fibroblasts in non-
small cell lung cancer. Proc Natl Acad Sci U S A. 2011; 108(17): 7160-5.
Oler G, Camacho CP, Hojaij FC, Michaluart P Jr, Riggins GJ, Cerutti JM. Gene expression
profiling of papillary thyroid carcinoma identifies transcripts correlated with BRAF
mutational status and lymph node metastasis. Clin Cancer Res. 2008 Aug 1;14(15):4735-42.
Peri S, Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK, Surendranath V,
Niranjan V, Muthusamy B, Gandhi TK, Gronborg M, Ibarrola N, Deshpande N, Shanker K,
Shivashankar HN, Rashmi BP, Ramya MA, Zhao Z, Chandrika KN, Padma N, Harsha HC,
Yatish AJ, Kavitha MP, Menezes M, Choudhury DR, Suresh S, Ghosh N, Saravana R,
Chandran S, Krishna S, Joy M, Anand SK, Madavan V, Joseph A, Wong GW, Schiemann
WP, Constantinescu SN, Huang L, Khosravi-Far R, Steen H, Tewari M, Ghaffari S, Blobe
GC, Dang CV, Garcia JG, Pevsner J, Jensen ON, Roepstorff P, Deshpande KS, Chinnaiyan
AM, Hamosh A, Chakravarti A, Pandey A.Development of human protein reference database
as an initial platform for approaching systems biology in humans. Genome Res. 2003
Oct;13(10):2363-71.
Peri S, Navarro JD, Kristiansen TZ, Amanchy R, Surendranath V, Muthusamy B, Gandhi
TK, Chandrika KN, Deshpande N, Suresh S, Rashmi BP, Shanker K, Padma N, Niranjan V,
Harsha HC, Talreja N, Vrushabendra BM, Ramya MA, Yatish AJ, Joy M, Shivashankar HN,
Kavitha MP, Menezes M, Choudhury DR, Ghosh N, Saravana R, Chandran S, Mohan S,
Jonnalagadda CK, Prasad CK, Kumar-Sinha C, Deshpande KS, Pandey A.Human protein
reference database as a discovery resource for proteomics. Nucleic Acids Res. 2004 Jan
1;32(Database issue):D497-501.
Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C. WikiPathways:
pathway editing for the people. PLoS Biol. 2008; 6(7): e184.
Prasad TS, Kandasamy K, Pandey A. Human Protein Reference Database and Human
Proteinpedia as discovery tools for systems biology. Methods Mol Biol. 2009; 577: 67-79.
![Page 52: PROFORMA FOR SUBMISSION OF RESEARCH ...dbtepromis.gov.in/Documents/TechnicalDetails/ProposalID...State: Karnataka 3. Status of the Institute: Private Non-Profit Institute Recognized](https://reader034.vdocuments.mx/reader034/viewer/2022051800/5acf1ed67f8b9ad24f8c0d5c/html5/thumbnails/52.jpg)
52
Raju R, Balakrishnan L, Nanjappa V, Bhattacharjee M, Getnet D, Muthusamy B, Kurian
Thomas J, Sharma J, Rahiman BA, Harsha HC, Shankar S, Prasad TS, Mohan SS, Bader GD,
Wani MR, Pandey A.A comprehensive manually curated reaction map of RANKL/RANK-
signaling pathway. Database (Oxford). 2011; bar021.
Raju, R., Balakrishnan, L., Nanjappa, V., Bhattacharjee, M., Getnet, D., Muthusamy, B.,
Thomas, J. K., Sharma, J., Rahiman, B. A., Harsha, H. C., Shankar, S., Prasad, T. S. K.,
Mohan, S. S., Bader, G. D., Wani, M. R. and Pandey, A. (2011). A comprehensive manually
curated reaction map of RANKL/RANK signaling pathway. Database.
Raju R, Nanjappa V, Balakrishnan L, Radhakrishnan A, Thomas JK, Sharma J, Tian M,
Palapetta SM, Subbannayya T, Sekhar NR, Muthusamy B, Goel R, Subbannayya Y,
Telikicherla D, Bhattacharjee M, Pinto SM, Syed N, Srikanth MS, Sathe GJ, Ahmad S,
Chavan SN, Kumar GS, Marimuthu A, Prasad TS, Harsha HC, Rahiman BA, Ohara O, Bader
GD, Sujatha Mohan S, Schiemann WP, Pandey A. NetSlim: high-confidence curated
signaling maps. Database (Oxford). 2011; bar 032.
Goel, R., Raju, R., Maharudraiah, J., Kumar, G. S. S., Ghosh, K., Kumar, A., Lashmi, P. T.,
Sharma, J., Sharma, R., Balakrishnan, L., Pan, A., Kandasamy, K., Christopher, R., Krishna,
V., Mohan, S. S., Harsha, H. C., Mathur, P. P., Pandey, A. and Prasad, T. S. K. (2011). A
signaling network of thyroid-stimulating hormone. Journal of Proteomics and Bioinformatics.
4, 238-241.
Ritchie MD. Using prior knowledge and genome-wide association to identify pathways
involved in multiple sclerosis. Genome Med. 2009; 1(6):65.
Robinson DR, Wu YM, Lin SF. The protein tyrosine kinase family of the human genome.
Oncogene. 2000 Nov 20;19(49):5548-57.
Rosen LS, Ashurst HL, Chap L. Targeting signal transduction pathways in metastatic breast
cancer: a comprehensive review. Oncologist. 2010;15(3):216-35
Rutella S, Bonanno G, Procoli A, Mariotti A, Corallo M, Prisco MG, Eramo A, Napoletano
C, Gallo D, Perillo A, Nuti M, Pierelli L, Testa U, Scambia G, Ferrandina G. Cells with
characteristics of cancer stem/progenitor cells express the CD133 antigen in human
endometrial tumors. Clin Cancer Res. 2009;15(13):4299-4311.
Salomonis N, Hanspers K, Zambon AC, et al. GenMAPP 2: new features and resources for
pathway analysis. BMC Bioinformatics. 2007; 8: 217.
Santarpia L, Lippman SM, El-Naggar AK. Targeting the MAPK-Research Associates-RAF
signaling pathway in cancer therapy. Expert Opin Ther Targets. 2012.
Schaefer CF, Anthony K, Krupa S, Buchoff J, Day M, Hannay T, Buetow KH.PID: the
Pathway Interaction Database. Nucleic Acids Res. 2009; 37(Database issue): D674-679.
Schmid K, Bago-Horvath Z, Berger W, Haitel A, Cejka D, Werzowa J, Filipits M, Herberger
B, Hayden H, Sieghart W. Dual inhibition of EGFR and mTOR pathways in small cell lung
cancer. Br J Cancer. 2010;103(5):622-628
![Page 53: PROFORMA FOR SUBMISSION OF RESEARCH ...dbtepromis.gov.in/Documents/TechnicalDetails/ProposalID...State: Karnataka 3. Status of the Institute: Private Non-Profit Institute Recognized](https://reader034.vdocuments.mx/reader034/viewer/2022051800/5acf1ed67f8b9ad24f8c0d5c/html5/thumbnails/53.jpg)
53
Shao M, Hollar S, Chambliss D, Schmitt J, Emerson R, Chelladurai B, Perkins S, Ivan M,
Matei D. Targeting the insulin growth factor and the vascular endothelial growth factor
pathways in ovarian cancer. Mol Cancer Ther. 2012;11(7):1576-86.
Shannon P, Markiel A, Ozier O, et al. Cytoscape: a software environment for integrated
models of biomolecular interaction networks. Genome Res. 2003; 13: 2498–504.
Sioud M, Leirdal M. Druggable signaling proteins. Methods Mol Biol. 2007; 361: 1-24.
Sivakumaran S, Hariharaputran S, Mishra J, Bhalla US. The Database of Quantitative
Cellular Signaling: management and analysis of chemical kinetic models of signaling
networks. Bioinformatics. 2003; 19(3): 408-15.
Sreenivasaiah PK, Rani S, Cayetano J, Arul N, Kim do H. IPAVS: Integrated Pathway
Resources, Analysis and Visualization System. Nucleic Acids Res. 2012; 40(Database issue):
D803-8.
Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, et al. Gene set enrichment
analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc
Natl Acad Sci U S A. 2005; 102: 15545–15550.
Telikicherla D, Ambekar A, Palapetta SM, Dwivedi SB, Raju R, Sharma J, Prasad TsK,
Ramachandra Y, Mohan SS, Maharudraiah J, Mukherjee S, Pandey A.A comprehensive
curated resource for follicle stimulating hormone signaling. BMC Res Notes. 2011; 4: 408.
ten Dijke P, Franzén P, Yamashita H, Ichijo H, Heldin CH, Miyazono K. Serine/threonine
kinase receptors. Prog Growth Factor Res. 1994;5(1):55-72.
Thomas PD, Campbell MJ, Kejariwal A, Mi H, Karlak B, Daverman R, Diemer K,
Muruganujan A, Narechania A. PANTHER: a library of protein families and subfamilies
indexed by function. Genome Res. 2003; 13: 2129–41.
Turner SD, Berg RL, Linneman JG, Peissig PL, Crawford DC, Denny JC, Roden DM,
McCarty CA, Ritchie MD, Wilke RA. Knowledge-driven multi-locus analysis reveals gene-
gene interactions influencing HDL cholesterol level in two independent EMR-linked
biobanks. PLoS One. 2011 ; 6(5): e19586.
van Iersel MP, Kelder T, Pico AR, Hanspers K, Coort S, Conklin BR, Evelo C. Presenting
and exploring biological pathways with PathVisio. BMC Bioinformatics. 2008 ; 9: 399.
Wasiliew P, Weber A, Dittrich-Breiholz, Schneider H and Kracht M. A comprehensive map
of the INTERLEUKIN-1R signalling network. Cell Communication and Signaling 2009,
7(Suppl 1):A25.
Wu J, Dent P, Jelinek T, Wolfman A, Weber MJ, Sturgill TW.Inhibition of the EGF-activated
MAP kinase signaling pathway by adenosine 3',5'-monophosphate. Science. 1993;
262(5136):1065-9.
Xia Y, Rocchi P, Iovanna JL, Peng L. Targeting heat shock response pathways to treat
pancreatic cancer. Drug Discov Today. 2012;17(1-2):35-43.
Yamamoto S, Sakai N, Nakamura H, Fukagawa H, Fukuda K, Takagi T. INOH: ontology-
based highly structured database of signal transduction pathways. Database (Oxford).
2011;bar052.
![Page 54: PROFORMA FOR SUBMISSION OF RESEARCH ...dbtepromis.gov.in/Documents/TechnicalDetails/ProposalID...State: Karnataka 3. Status of the Institute: Private Non-Profit Institute Recognized](https://reader034.vdocuments.mx/reader034/viewer/2022051800/5acf1ed67f8b9ad24f8c0d5c/html5/thumbnails/54.jpg)
54
Yaspan BL and Veatch OJ. Strategies for pathway analysis from GWAS data. Curr Protoc
Hum Genet. 2011; Chapter 1:Unit1.20.
Zhong, J., Chaerkady, R., Kandasamy, K., Gucek, M., Cole, R.N. and Pandey, A. (2011). The
interactome of a PTB domain-containing adapter protein, Odin, revealed by SILAC. Journal
of Proteomics. 74, 294-303.
Zhong, J., Kim, M. S., Chaerkady, R., Wu, X., Huang, T. C., Getnet, D., Mitchell, C. J.,
Palapetta, S. M., Sharma, J., O'Meally, R. N., Cole, R. N., Yoda, A., Moritz, A., Loriaux, M.
M., Rush, J., Weinstock, D. M., Tyner, J. W. and Pandey, A. (2012). TSLP signaling network
revealed by SILAC-based phosphoproteomics. Molecular and Cellular Proteomics.
![Page 55: PROFORMA FOR SUBMISSION OF RESEARCH ...dbtepromis.gov.in/Documents/TechnicalDetails/ProposalID...State: Karnataka 3. Status of the Institute: Private Non-Profit Institute Recognized](https://reader034.vdocuments.mx/reader034/viewer/2022051800/5acf1ed67f8b9ad24f8c0d5c/html5/thumbnails/55.jpg)
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18.5 Time schedule of activities giving milestones. (Physical/Scientific separately)
S.
No. Milestone (physical)
Expected
Start
(Month/Year)
Expected
Completion
(Month/Year)
1.
2.
Establishing computational facility exclusively
for the community participation programme at
participating institutes
Recruitment of Research associates and Senior
Research Fellows
0-3 months
0-3 months
S.
No. Milestone (Scientific)
Expected
Start
(Month/Year)
Expected
Completion
(Month/Year)
1.
2.
3.
4.
5.
Orientation, workshops, monitoring and
internal assessment of biocuration
Internal review of reactions curated in specific
pathways
Development of NetSlim maps for each
pathways
Data integration into NetPath, NetSlim and
WikiPathways
Manuscript preparation and review by pathway
authorities
Every Year
Every Year
Every Year
Every Year
Every Year
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19. Name and address of 5 experts in the field
Name & Designation Address Email
Dr. G. P. S. Raghava
Scientist & Head
Bioinformatics Centre, Institute
of Microbial Technology,
Sector-39A, Chandigarh-
160036
Dr. Indira Ghosh,
Professor and Dean
School of Information
Technology, Jawaharlal Nehru
University, New Delhi -110067
Dr. Sudhir Krishna,
Professor
National Centre for Biological
Sciences, Tata Institute of
Fundamental Research, GKVK,
Bellary Road, Bangalore-560065
Dr. Debasisa Mohanty
Scientist
Bioinformatics Center, National
Institute of Immunology,
Aruna Asaf Ali Road,
New Delhi- 110067
Dr. N. Srinivasan
Faculty
Molecular Biophysics Unit,
Indian Institute of Science,
Bangalore – 560012
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PART IV: BUDGET PARTICULARS
20. Budget (In Rupees)
Name of the Institute Amount of Budget
1 Institute of Bioinformatics, Bangalore Rs. 7,54,95,802/-
2 University of Pune Rs. 9,43,000/-
3 Pondicherry University Rs. 9,43,000/-
4 Madurai Kamaraj University Rs. 9,43,000/-
5 University of Mysore Rs. 9,43,000/-
6 Kuvempu University Rs. 9,43,000/-
7 Mangalore University Rs. 9,43,000/-
8 University of Kerala Rs. 9,43,000/-
9 Central University of Kerala Rs. 9,43,000/-
10 Armed Forces Medical College Rs. 9,43,000/-
11 Anna University Rs. 9,43,000/-
Total Rs. 8,49,25,802/-
The imbalance in the assigned budget across Institute of bioinformatics (IOB) and the
Participating Centres are due to the following aspects:
1) The fellowships of 2 Research Associates and 10 Senior Research Fellows to execute the
human resource development programme with the Participating Centres will be conferred by
IOB.
2) The training of over 130 students from the Universities is hosted at IOB. The allowances
pertaining to their travel, accomodation, food and training will be provided by IOB. The
Participating centres will confer training only to 5 students (handicapped students or students
who are not in a position to travel to Bangalore under certain circumstances) and further
coordinate and facilitate this human resource development programme in signal transduction.
3) The hardware and the software required for the development of pathways at IOB will be
provided by IOB.
4) Two conferences with the participation of 10 leaders in signal transduction around the world
will be coordinated and organized by IOB. The expenses include travel and accommodation
of the experts and the overall organization charges to conduct these conferences.
5) The charges for the publication of over 400 pathways in various international peer- reviewed
journals will be met by IOB.
6) The travel expenses of the coordinators, investigators, 2 Research Associates and 10 Senior
Research Fellows from IOB to the current 10 Participating Centres and the prospectively
new centres for the orientation programmes and hands-on training workshops will be met by
IOB.
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20. Budget (In Rupees) (Institution wise):
Institute of Bioinformatics, Bangalore A. Non-Recurring
S. No. Item Year 1 Year 2 Year 3 Year 4 Total (INR)
1 High efficiency Netapp FAS 2020 storage server x 1 nos. 15,50,550 15,50,550
2 Windows Work station with advanced configuration x 20 nos. 19,71,930 19,71,930
3 Windows PCs x 30 nos. 11,49,375 11,49,375
4 Interactive white board x 1 nos. 1,82,500 1,82,500
5 Canon Digital Copier Model iR 2525 1,50,865 1,50,865
Total 50,05,220 50,05,220
Sub-Total (A) = Rs. 48,11,670/-
Justification:
i) High efficiency Netapp FAS storage server- is required to store large amount of data pertaining to signaling pathways. At a given point of
time, more than 50 students from various Participating Institutes, Senior Research Fellows and Research Associates will be working to develop
signaling pathways.
ii) Windows Work station with advanced configuration x 20 nos and Windows PCs with basic configuration- are required for the
biocurators and bioinformaticians to annotate and review pathway data and also to convert the data into community standard formats. Further, it
is neccessary to represent pathway graphically in the form of high-end pathway images in different formats using several visualization software.
iii) Interactive white board - allows keeping notes and annotations as an electronic file for later distribution either on paper or through a
number of electronic formats. It facilitates integration of pathway diagrams, spreadsheet or text from a Microsoft Word file for effective and
illustrative orientation and training modules for the development of signaling pathways.
iv) Canon Digital Copier Model iR 2525- is required to prepare the training modules and assignments for the students from Participating
Institutes.
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B. Recurring
B1. Manpower
Position No Consolidated Emolument +
allowances Year 1 Year 2 Year 3 Year 4 Total (INR)
Research Associates (2) Rs. 22000 + 30% HRA 6,86,400 6,86,400 6,86,400 6,86,400 27,45,600
Senior Research Fellows
(10) Rs. 18000 + 30% HRA 28,08,000 28,08,000 28,08,000 28,08,000 1,12,32,000
Trainees from current
participating centers
(130 per year)
Fellowship (Rs. 5000/- per month),
travel allowance (onetime Rs. 2000/-),
food allowance (Rs. 5000/- per month)
and accommodation (Rs. 8000/- per
month) for trainees -
(Total: Rs. 38,000/- for 60 days)
49,40,000 49,40,000 49,40,000 49,40,000 1,97,60,000
Trainees from other
institutes (50 per year)
Fellowship support
(Total: Rs. 15,000/- for 60 days) 7,50,000 7,50,000 7,50,000 7,50,000 30,00,000
Total 63,34,400 63,34,400 63,34,400 63,34,400 3,67,37,600
Sub-Total (B.1) = Rs. 3,67,37,600/-
Justification:
i) Research Associates (2) - Research associates (M.Sc./Ph.D.) who have a minimum of 2 years experience in biocuration (with one or two
publications relevant to biocuration) will be recruited. RAs will be involved in the training of the Senior Research Fellows along with the
investigators. Each Research associate will be involved in training students from 5 different Participating Institutes every year.
ii) Senior Research Fellows (10) - Trained Senior Research Fellows will be responsible for training students from each Participating Institutes
every year. They will be involved in screening research articles pertaining to each signaling pathway, providing full text research articles, direct
and remote monitoring of the biocuration by students, review of pathway data, development of signaling pathway maps for each pathway and
preparation pathway manuscripts. Each Senior Research Fellows will be involved in this process to develop more than 10 signaling pathways
with a Participating Institute every year.
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iii) Trainees from participating centres will visit IOB during their holidays or summer vacations and will be under direct training at IOB for a
period of 2 months every year. This will facilitate effective focused training sessions at IOB by the faculty scientists and Senior Research
Fellows at IOB. A fellowship of Rs. 5000/- per month, food allowance of Rs. 5000/- per month and accommodation charge of Rs. 8000/- per
month will be provided for the respective categories based on the living cost in Bangalore. Further, an onetime payment of Rs. 2000/- on an
average will be provided towards their travel allowance to and fro to Bangalore and their respective Universities. This will promote the active
participation of the students from the Universities beyond the apprehension of expense of travel, food and accommodation in Bangalore.
iv) Trainees from other Institutes will be selected based on the applications from different colleges and Universities for summer training and
also from various medical students for short term exposure to development of signaling pathways. A fellowship of Rs.15000/- for a total of 60
days will be provided as support.
B.2 Consumables
Item Year 1 Year 2 Year 3 Year 4 Total (INR)
1 Conferences and workshops - 30,00,000 - 30,00,000 60,00,000
2 Open access charges for publications 55,00,000 55,00,000 55,00,000 55,00,000 2,20,00,000
3 Partial internet charges 50,000 50,000 50,000 50,000 2,00,000
4 Microsoft Windows 7 Pro 32 bit OEM (3x10 users) 2,51,000 - - - 2,51,000
5 Microsoft Office Home & business 2010 Full pack
(30 users) 2,81,910 - - - 2,81,910
6 Adobe suite master collection version 6 (30 users) 20,35,020 - - - 20,35,020
7 Kaspersky antivirus business pack 30 user 27, 783 27, 783 27, 783 27, 783 1,11,132
8 Navicat Premium (4 users) 73, 920 - - - 73, 920
TOTAL 82,19,633 85,77,783 55,77,783 85,77,783 3,09,52,982
Sub-Total (B.2) =Rs. 3,09,52,982/-
Justification:
1. Conferences- will be organized on the second and fourth years of this project. A set of 10 world leaders in signal transduction who have
significantly contributed to the field of signal transduction will be invited for lectures. The students and the faculty members from the
Participating Centres; and the scientists from Institute of Bioinformatics will attend these conferences. The pathways developed and those which
are under development during the span of 1-2 years will be presented in these conferences for effective interaction on specific signaling
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pathways and also to seek future directions on pathway development and analysis. In the second conference, the prime focus will be on the
global perspectives to pathway data analysis with the active participation of the bioinformatics community in India.
2. Open access charges for publications- Currently, 5 individual pathways developed at IOB with the participation of Participating Institutes
(viz: RANKL pathway with Armed Forces Medical College, Leptin pathway with Amrita Viswa Vidypeedm, FSH pathway with National
Institute for Research in Reproductive Health, and TSH & TWEAK pathways with Pondicherry University) had been published in international
journals (Raju et al., 2011, Nanjappa et l., 2011, Telikicherla et al., 2011, Goel et al., 2011 and Bhattacharjee et al, 2012). With the involvement
of large number of students (around 130 students per year) and focused effort of individual students supported by the faculty scientists, 2
Research associates and 10 Senior Research Fellows from IOB and Project Leaders from the Participating Institutes, there will be over 100
pathway manuscripts ready for publication in international journals per year. With ~US$1000 (Rs. 55,000/-) on the average as the amount for
publication, this amounts to Rs. 55,00,000/-. For example, publication charges of the research articles already published are provided in table
below:
Journal Publishers Pathway published Reference Article processing charge
1 Database Oxford University
Press RANKL signaling pathway Raju et al., 2011 US$1600
2 BMC Research Notes BioMed Central Follicle Stimulating Hormone
signaling pathway Telikicherla et al., 2011 US$1090
3 Journal of Proteomics
and Bioinformatics
OMICS Publishing
Group Leptin signaling pathway Nanjappa et al., 2011 US$1300
4 Journal of Proteomics
and Bioinformatics
OMICS Publishing
Group
Thyroid Stimulating Hormone
signaling pathway Goel et al., 2011 US$700
5 Journal of Signal
Transduction
Hindawi Publishing
Corporation
TWEAK-Fn14
signaling pathway Bhattacharjee et al, 2012 US$500
3. Partial internet charges- The development of signaling pathways requires high-speed internet to access research articles, PathBuilder tool for
documentation of pathway data, training, and remote monitoring of pathway development.
4. Microsoft Windows 7 Pro 32 bit OEM- is required for the basic graphical user interface.
Microsoft Office Home & business 2010 Full pack- is required for documentation, pathway curation, editing, and manuscript preparation
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5. Kaspersky antivirus business pack - is essential for the anti-virus support to safeguard the pathway information obtained by the rigorous
manual work
6. Adobe suite master collection version 6- is required to generate signaling pathway data, development of high-quality pathway images, and
also for the manuscript preparation.
7. Navicat premium- Navicat Premium is a multi-connections Database Administration tool which allows to connect to MySQL, SQL Server,
SQLite, Oracle and PostgreSQL databases simultaneously within a single application. This facilitates better database administration to multiple
kinds of databases associated with NetPath and NetSlim.
5. Travel
Item Year 1 Year 2 Year 3 Year 4 Total (INR)
B.3 Travel 5,00,000 5,00,000 5,00,000 5,00,000 20,00,000
B.4 Contingency 2,00,000 2,00,000 2,00,000 2,00,000 8,00,000
Total 7,00,000 7,00,000 7,00,000 7,00,000 28,00,000
Justification:
1. Travel- This includes the travel expenses of the Principal Investigator, Co- Principal Investigators, Research Associates, and Senior Research
Fellows to the Participating Institutes for the orientation, workshops and hands-on training programmes. The faculty scientists, RAs and JRFs
will also visit the Participating Institutes to improve the curation quality after their review of pathway curation made by the students.
Sub-Total (B = B.1 + B.2 + B.3 + B.4) = Rs. 7,04,90,582/-
Grand Total (A + B) = Rs. 7,54,95,802/-
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University of Pune A. Non-Recurring: None B. Recurring B1. Manpower
Position No Consolidated Emolument +
allowances Year 1 Year 2 Year 3 Year 4 Total
1 Trainees
(5 per year) Rs. 10,000/-
(Onetime payment for 60 days) 50,000 50,000 50,000 50,000 2,00,000
Total 50,000 50,000 50,000 50,000 2,00,000
Sub-Total (B.1) = Rs. 2,00,000/- Justification: In addition to the trainees selected and funded by IOB (nodal center), University of Pune can also fund 5 trainees, who may not opt for travelling to IOB. These trainees will be trained locally by the project leaders in University of Pune. IOB Senior Research Fellows and Investigators will remotely monitor the training. This opportunity will help several female students, who may have special circumstances, which may not allow their 60 days visit to IOB, the nodal center of this program. Selected trainees will participate in this project during their semester breaks and summer vacations. B.2 Consumables
Item Year 1 Year 2 Year 3 Year 4 Total Partial internet charges 25,000 25,000 25,000 25,000 1,00,000 Software (Adobe and Windows related) 2,00,000 - - - 2,00,000 TOTAL 2,25,000 25,000 25,000 25,000 3,00,000
Sub-Total (B.2) =Rs. 3,00,000/-
Item Year 1 Year 2 Year 3 Year 4 Total
B.3 Travel 30,000 30,000 30,000 30,000 1,20,000
B.4 Contingency 50,000 50,000 50,000 50,000 2,00,000
B.5 Overhead Charges (15% of recurring) 53,250 23,250 23,250 23,250 123,000 Sub-Total (B = B.1 + B.2 + B.3 + B.4 + B.5) = Rs. 9,43,000/- Grand Total (A + B) = Rs. 9,43,000/-
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Pondicherry University A. Non-Recurring: None B. Recurring B1. Manpower
Position No Consolidated Emolument +
allowances Year 1 Year 2 Year 3 Year 4 Total
1 Trainees
(5 per year) Rs. 10,000/-
(Onetime payment for 60 days) 50,000 50,000 50,000 50,000 2,00,000
Total 50,000 50,000 50,000 50,000 2,00,000
Sub-Total (B.1) = Rs. 2,00,000/- Justification: In addition to the trainees selected and funded by IOB (nodal center), Pondicherry University can also fund 5 trainees, who may not opt for travelling to IOB. These trainees will be trained locally by the project leaders in Pondicherry University. IOB Senior Research Fellows and Investigators will remotely monitor the training. This opportunity will help several female students, who may have specia l circumstances, which may not allow their 60 days visit to IOB, the nodal center of this program. Selected trainees will participate in this project during their semester breaks and summer vacations. B.2 Consumables
Item Year 1 Year 2 Year 3 Year 4 Total Partial internet charges 25,000 25,000 25,000 25,000 1,00,000 Software (Adobe and Windows related) 2,00,000 - - - 2,00,000 TOTAL 2,25,000 25,000 25,000 25,000 3,00,000
Sub-Total (B.2) =Rs. 3,00,000/-
Item Year 1 Year 2 Year 3 Year 4 Total
B.3 Travel 30,000 30,000 30,000 30,000 1,20,000
B.4 Contingency 50,000 50,000 50,000 50,000 2,00,000
B.5 Overhead Charges (15% of recurring) 53,250 23,250 23,250 23,250 123,000 Sub-Total (B = B.1 + B.2 + B.3 + B.4 + B.5) = Rs. 9,43,000/- Grand Total (A + B) = Rs. 9,43,000/-
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Madurai Kamaraj University A. Non-Recurring: None B. Recurring B1. Manpower
Position No Consolidated Emolument +
allowances Year 1 Year 2 Year 3 Year 4 Total
1 Trainees
(5 per year) Rs. 10,000/-
(Onetime payment for 60 days) 50,000 50,000 50,000 50,000 2,00,000
Total 50,000 50,000 50,000 50,000 2,00,000
Sub-Total (B.1) = Rs. 2,00,000/- Justification: In addition to the trainees selected and funded by IOB (nodal center), Madurai Kamaraj University can also fund 5 trainees, who may not opt for travelling to IOB. These trainees will be trained locally by the project leaders in Madurai Kamaraj University. IOB Senior Research Fellows and Investigators will remotely monitor the training. This opportunity will help several female students, who may have specia l circumstances, which may not allow their 60 days visit to IOB, the nodal center of this program. Selected trainees will participate in this project during their semester breaks and summer vacations. B.2 Consumables
Item Year 1 Year 2 Year 3 Year 4 Total Partial internet charges 25,000 25,000 25,000 25,000 1,00,000 Software (Adobe and Windows related) 2,00,000 - - - 2,00,000 TOTAL 2,25,000 25,000 25,000 25,000 3,00,000
Sub-Total (B.2) =Rs. 3,00,000/-
Item Year 1 Year 2 Year 3 Year 4 Total
B.3 Travel 30,000 30,000 30,000 30,000 1,20,000
B.4 Contingency 50,000 50,000 50,000 50,000 2,00,000
B.5 Overhead Charges (15% of recurring) 53,250 23,250 23,250 23,250 123,000 Sub-Total (B = B.1 + B.2 + B.3 + B.4 + B.5) = Rs. 9,43,000/- Grand Total (A + B) = Rs. 9,43,000/-
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University of Mysore A. Non-Recurring: None B. Recurring B1. Manpower
Position No Consolidated Emolument +
allowances Year 1 Year 2 Year 3 Year 4 Total
1 Trainees
(5 per year) Rs. 10,000/-
(Onetime payment for 60 days) 50,000 50,000 50,000 50,000 2,00,000
Total 50,000 50,000 50,000 50,000 2,00,000
Sub-Total (B.1) = Rs. 2,00,000/- Justification: In addition to the trainees selected and funded by IOB (nodal center), University of Mysore can also fund 5 trainees, who may not opt for travelling to IOB. These trainees will be trained locally by the project leaders in University of Mysore. IOB Senior Research Fellows and Investigators will remotely monitor the training. This opportunity will help several female students, who may have special circumstances, which may not allow their 60 days visit to IOB, the nodal center of this program. Selected trainees will participate in this project during their semester breaks and summer vacations. B.2 Consumables
Item Year 1 Year 2 Year 3 Year 4 Total Partial internet charges 25,000 25,000 25,000 25,000 1,00,000 Software (Adobe and Windows related) 2,00,000 - - - 2,00,000 TOTAL 2,25,000 25,000 25,000 25,000 3,00,000
Sub-Total (B.2) =Rs. 3,00,000/-
Item Year 1 Year 2 Year 3 Year 4 Total
B.3 Travel 30,000 30,000 30,000 30,000 1,20,000
B.4 Contingency 50,000 50,000 50,000 50,000 2,00,000
B.5 Overhead Charges (15% of recurring) 53,250 23,250 23,250 23,250 123,000 Sub-Total (B = B.1 + B.2 + B.3 + B.4 + B.5) = Rs. 9,43,000/- Grand Total (A + B) = Rs. 9,43,000/-
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Kuvempu University A. Non-Recurring: None B. Recurring B1. Manpower
Position No Consolidated Emolument +
allowances Year 1 Year 2 Year 3 Year 4 Total
1 Trainees
(5 per year) Rs. 10,000/-
(Onetime payment for 60 days) 50,000 50,000 50,000 50,000 2,00,000
Total 50,000 50,000 50,000 50,000 2,00,000
Sub-Total (B.1) = Rs. 2,00,000/- Justification: In addition to the trainees selected and funded by IOB (nodal center), Kuvempu University can also fund 5 trainees, who may not opt for travelling to IOB. These trainees will be trained locally by the project leaders in Kuvempu University. IOB Senior Research Fellows and Investigators will remotely monitor the training. This opportunity will help several female students, who may have special circumstances, which may not allow their 60 days visit to IOB, the nodal center of this program. Selected trainees will participate in this project during their semester breaks and summer vacations. B.2 Consumables
Item Year 1 Year 2 Year 3 Year 4 Total Partial internet charges 25,000 25,000 25,000 25,000 1,00,000 Software (Adobe and Windows related) 2,00,000 - - - 2,00,000 TOTAL 2,25,000 25,000 25,000 25,000 3,00,000
Sub-Total (B.2) =Rs. 3,00,000/-
Item Year 1 Year 2 Year 3 Year 4 Total
B.3 Travel 30,000 30,000 30,000 30,000 1,20,000
B.4 Contingency 50,000 50,000 50,000 50,000 2,00,000
B.5 Overhead Charges (15% of recurring) 53,250 23,250 23,250 23,250 123,000 Sub-Total (B = B.1 + B.2 + B.3 + B.4 + B.5) = Rs. 9,43,000/- Grand Total (A + B) = Rs. 9,43,000/-
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Mangalore University A. Non-Recurring: None B. Recurring B1. Manpower
Position No Consolidated Emolument +
allowances Year 1 Year 2 Year 3 Year 4 Total
1 Trainees
(5 per year) Rs. 10,000/-
(Onetime payment for 60 days) 50,000 50,000 50,000 50,000 2,00,000
Total 50,000 50,000 50,000 50,000 2,00,000
Sub-Total (B.1) = Rs. 2,00,000/- Justification: In addition to the trainees selected and funded by IOB (nodal center), Mangalore University can also fund 5 trainees, who may not opt for travelling to IOB. These trainees will be trained locally by the project leaders in Mangalore University. IOB Senior Research Fellows and Investigators will remotely monitor the training. This opportunity will help several female students, who may have special circumstances, which may not allow their 60 days visit to IOB, the nodal center of this program. Selected trainees will participate in this project during their semester breaks and summer vacations. B.2 Consumables
Item Year 1 Year 2 Year 3 Year 4 Total Partial internet charges 25,000 25,000 25,000 25,000 1,00,000 Software (Adobe and Windows related) 2,00,000 - - - 2,00,000 TOTAL 2,25,000 25,000 25,000 25,000 3,00,000
Sub-Total (B.2) =Rs. 3,00,000/-
Item Year 1 Year 2 Year 3 Year 4 Total
B.3 Travel 30,000 30,000 30,000 30,000 1,20,000
B.4 Contingency 50,000 50,000 50,000 50,000 2,00,000
B.5 Overhead Charges (15% of recurring) 53,250 23,250 23,250 23,250 123,000 Sub-Total (B = B.1 + B.2 + B.3 + B.4 + B.5) = Rs. 9,43,000/- Grand Total (A + B) = Rs. 9,43,000/-
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Central University of Kerala A. Non-Recurring: None B. Recurring B1. Manpower
Position No Consolidated Emolument +
allowances Year 1 Year 2 Year 3 Year 4 Total
1 Trainees
(5 per year) Rs. 10,000/-
(Onetime payment for 60 days) 50,000 50,000 50,000 50,000 2,00,000
Total 50,000 50,000 50,000 50,000 2,00,000
Sub-Total (B.1) = Rs. 2,00,000/- Justification: In addition to the trainees selected and funded by IOB (nodal center), Central University of Kerala can also fund 5 trainees, who may not opt for travelling to IOB. These trainees will be trained locally by the project leaders in Central University of Kerala. IOB Senior Research Fellows and Investigators will remotely monitor the training. This opportunity will help several female students, who may have specia l circumstances, which may not allow their 60 days visit to IOB, the nodal center of this program. Selected trainees will participate in this project during their semester breaks and summer vacations. B.2 Consumables
Item Year 1 Year 2 Year 3 Year 4 Total Partial internet charges 25,000 25,000 25,000 25,000 1,00,000 Software (Adobe and Windows related) 2,00,000 - - - 2,00,000 TOTAL 2,25,000 25,000 25,000 25,000 3,00,000
Sub-Total (B.2) =Rs. 3,00,000/-
Item Year 1 Year 2 Year 3 Year 4 Total
B.3 Travel 30,000 30,000 30,000 30,000 1,20,000
B.4 Contingency 50,000 50,000 50,000 50,000 2,00,000
B.5 Overhead Charges (15% of recurring) 53,250 23,250 23,250 23,250 123,000 Sub-Total (B = B.1 + B.2 + B.3 + B.4 + B.5) = Rs. 9,43,000/- Grand Total (A + B) = Rs. 9,43,000/-
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University of Kerala A. Non-Recurring: None B. Recurring B1. Manpower
Position No Consolidated Emolument +
allowances Year 1 Year 2 Year 3 Year 4 Total
1 Trainees
(5 per year) Rs. 10,000/-
(Onetime payment for 60 days) 50,000 50,000 50,000 50,000 2,00,000
Total 50,000 50,000 50,000 50,000 2,00,000
Sub-Total (B.1) = Rs. 2,00,000/- Justification: In addition to the trainees selected and funded by IOB (nodal center), University of Kerala can also fund 5 trainees, who may not opt for travelling to IOB. These trainees will be trained locally by the project leaders in University of Kerala. IOB Senior Research Fellows and Investigators will remotely monitor the training. This opportunity will help several female students, who may have special circumstances, which may not allow their 60 days visit to IOB, the nodal center of this program. Selected trainees will participate in this project during their semester breaks and summer vacations. B.2 Consumables
Item Year 1 Year 2 Year 3 Year 4 Total Partial internet charges 25,000 25,000 25,000 25,000 1,00,000 Software (Adobe and Windows related) 2,00,000 - - - 2,00,000 TOTAL 2,25,000 25,000 25,000 25,000 3,00,000
Sub-Total (B.2) =Rs. 3,00,000/-
Item Year 1 Year 2 Year 3 Year 4 Total
B.3 Travel 30,000 30,000 30,000 30,000 1,20,000
B.4 Contingency 50,000 50,000 50,000 50,000 2,00,000
B.5 Overhead Charges (15% of recurring) 53,250 23,250 23,250 23,250 123,000 Sub-Total (B = B.1 + B.2 + B.3 + B.4 + B.5) = Rs. 9,43,000/- Grand Total (A + B) = Rs. 9,43,000/-
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Anna University A. Non-Recurring: None B. Recurring B1. Manpower
Position No Consolidated Emolument +
allowances Year 1 Year 2 Year 3 Year 4 Total
1 Trainees
(5 per year) Rs. 10,000/-
(Onetime payment for 60 days) 50,000 50,000 50,000 50,000 2,00,000
Total 50,000 50,000 50,000 50,000 2,00,000
Sub-Total (B.1) = Rs. 2,00,000/- Justification: In addition to the trainees selected and funded by IOB (nodal center), Anna University can also fund 5 trainees, who may not opt for travelling to IOB. These trainees will be trained locally by the project leaders in Anna University. IOB Senior Research Fellows and Investigators will remotely monitor the training. This opportunity will help several female students, who may have special circumstances, which may not allow their 60 days visit to IOB, the nodal center of this program. Selected trainees will participate in this project during their semester breaks and summer vacations. B.2 Consumables
Item Year 1 Year 2 Year 3 Year 4 Total Partial internet charges 25,000 25,000 25,000 25,000 1,00,000 Software (Adobe and Windows related) 2,00,000 - - - 2,00,000 TOTAL 2,25,000 25,000 25,000 25,000 3,00,000
Sub-Total (B.2) =Rs. 3,00,000/-
Item Year 1 Year 2 Year 3 Year 4 Total
B.3 Travel 30,000 30,000 30,000 30,000 1,20,000
B.4 Contingency 50,000 50,000 50,000 50,000 2,00,000
B.5 Overhead Charges (15% of recurring) 53,250 23,250 23,250 23,250 123,000 Sub-Total (B = B.1 + B.2 + B.3 + B.4 + B.5) = Rs. 9,43,000/- Grand Total (A + B) = Rs. 9,43,000/-
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Armed Forces Medical College A. Non-Recurring: None B. Recurring B1. Manpower
Position No Consolidated Emolument +
allowances Year 1 Year 2 Year 3 Year 4 Total
1 Trainees
(5 per year) Rs. 10,000/-
(Onetime payment for 60 days) 50,000 50,000 50,000 50,000 2,00,000
Total 50,000 50,000 50,000 50,000 2,00,000
Sub-Total (B.1) = Rs. 2,00,000/- Justification: In addition to the trainees selected and funded by IOB (nodal center), Armed Forces Medical College can also fund 5 trainees, who may not opt for travelling to IOB. These trainees will be trained locally by the project leaders in Armed Forces Medical College. IOB Senior Research Fellows and Investigators will remotely monitor the training. This opportunity will help several female students, who may have special circumstances, which may not allow their 60 days visit to IOB, the nodal center of this program. Selected trainees will participate in this project during their semester breaks and summer vacations. B.2 Consumables
Item Year 1 Year 2 Year 3 Year 4 Total Partial internet charges 25,000 25,000 25,000 25,000 1,00,000 Software (Adobe and Windows related) 2,00,000 - - - 2,00,000 TOTAL 2,25,000 25,000 25,000 25,000 3,00,000
Sub-Total (B.2) =Rs. 3,00,000/-
Item Year 1 Year 2 Year 3 Year 4 Total
B.3 Travel 30,000 30,000 30,000 30,000 1,20,000
B.4 Contingency 50,000 50,000 50,000 50,000 2,00,000
B.5 Overhead Charges (15% of recurring) 53,250 23,250 23,250 23,250 123,000 Sub-Total (B = B.1 + B.2 + B.3 + B.4 + B.5) = Rs. 9,43,000/- Grand Total (A + B) = Rs. 9,43,000/-
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PART V: EXISTING FACILITIES
21. Available equipment and accessories to be utilized for the project:
S.
No.
Name of
equipment
/Accessories
Make Model
1
Sun Server Sun Sun Fire V60x Sun Fire CGM
2 PCs x 40
(Occupied)
256 MB Ram, AMD Athlon
XP 2GHz Processor, 40 GB
hard disk
-
3 LCD projector Toshiba TLP-B2UltraSU
4. Server Sun Sun Fire X4450, Sun Fire X4150
6 Ink jet printers Hewlett Packard -
7 Scanner Canon -