examples of functional modeling
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Examples of functional modeling. NCSU GO Workshop 29 October 2009. Tools and materials from this workshop will be available online at the AgBase database Educational Resources link. For continuing support and assistance please contact: [email protected]. - PowerPoint PPT PresentationTRANSCRIPT
Examples of functional modeling.
NCSU GO Workshop
29 October 2009
Tools and materials from this workshop will be available online at the AgBase database Educational Resources link.
For continuing support and assistance please contact:
This workshop is supported by USDA CSREES grant number MISV-329140.
"Today’s challenge is to realise greater knowledge and understanding from the data-rich opportunities provided by modern high-throughput genomic technology."
Professor Andrew Cossins,
Consortium for Post-Genome Science, Chairman.
Bio-ontologies Bio-ontologies are used to capture biological
information in a way that can be read by both humans and computers.necessary for high-throughput “omics” datasetsallows data sharing across databases
Objects in an ontology (eg. genes, cell types, tissue types, stages of development) are well defined.
The ontology shows how the objects relate to each other.
What is the Gene Ontology?“a controlled vocabulary that can be applied to all organisms even as knowledge of gene and protein roles in cells is accumulating and changing”
the de facto standard for functional annotation assign functions to gene products at different levels, depending on how much is known about a gene product is used for a diverse range of species structured to be queried at different levels, eg:
find all the chicken gene products in the genome that are involved in signal transduction
zoom in on all the receptor tyrosine kinases human readable GO function has a digital tag to allow computational analysis of large datasets
COMPUTATIONALLY AMENABLE ENCYCLOPEDIA OF GENE FUNCTIONS AND THEIR RELATIONSHIPS
Who uses GO? http://www.ebi.ac.uk/GOA/users.html
Use GO for…….1. Determining which classes of gene
products are over-represented or under-represented.
2. Grouping gene products.
3. Relating a protein’s location to its function.
4. Focusing on particular biological pathways and functions (hypothesis-testing).
Global mRNA and protein expression was measured from quadruplicate samples of control, X- and Y-treated tissue.
Differentially-expressed mRNA’s and proteins identified from Affymetrix microarray data and DDF shotgun proteomics using Monte-Carlo resampling*. * Nanduri, B., P. Shah, M. Ramkumar, E. A. Allen, E. Swaitlo, S. C. Burgess*, and M. L. Lawrence*. 2008. Quantitative analysis of Streptococcus Pneumoniae TIGR4 response to in vitro iron restriction by 2-D LC ESI MS/MS. Proteomics 8, 2104-14.
Using network and pathway analysis as well as Gene Ontology-based hypothesis testing, differences in specific phyisological processes between X- and Y-treated were quantified and reported as net effects.
Translation to clinical research: Pig
Bindu Nanduri
Proportional distribution of mRNA functions differentially-expressed by X- and Y-treated tissues
Treatment X
immunity (primarily innate)
inflammation
Wound healing
Lipid metabolism
response to thermal injury
angiogenesis
Total differentially-expressed mRNAs: 4302
Total differentially-expressed mRNAs: 1960
Treatment Y
35 30 25 20 15 10 5 0 5
immunity (primarily innate)
Wound healing
Lipid metabolism
response to thermal injury
angiogenesis
X Y
Net functional distribution of differentially-expressed mRNAs: X- vs. Y-Treatment
Relative bias
classical inflammation(heat, redness, swelling, pain, loss of function)
sensory response to pain
immunity (primarily innate)
inflammation
Wound Healing
Lipid metabolism
response to Thermal Injury
Angiogenesis
hemorrhage
Total differentially-expressed proteins: 509
Total differentially-expressed proteins: 433
Proportional distribution of protein functions differentially-expressed by X- and Y-treated tissues
Treatment X Treatment Y
8 6 4 2 0 2 4 6
immunity (primarily innate)
classical inflammation(heat, redness, swelling, pain, loss of function)
Wound healing
lipid metabolism
response to thermal injury
angiogenesis
sensory response to pain
hemorrhage
Relative bias
Treatment X Treatment Y
Net functional distribution of differentially-expressed Proteins: X- vs. Y-Treatment
B-cells Stroma
immune response
apoptosis
cell-cell signaling
(Looking at function, not gene.)
Relating a protein’s location to its function.
Shyamesh Kumar BVSc
Focusing on particular biological pathways and functions (hypothesis-testing).
days post infection
mea
n to
tal l
esi
on
scor
e
0
2
4
6
8
10
12
14
16
18
0 20 40 60 80 100
Susceptible (L72)
Resistant (L61)
Genotype
Non-MHC associated resistance and susceptibility
Resistant ( L61)
Burgess et al,Vet Pathol 38:2,2001
The critical time point in MD lymphomagenesis
Susceptible (L72)
CD30 mab CD8 mab
Tissue
CD30 lo/- hyperplastic
CD30hi, Neoplastically-transformed
Marek’s Disease Lymphoma Model : Chicken
The neoplastically-transformed (CD30hi) cells in Marek’s disease lymphoma cell phenotype most closely resembles T-regulatory cells. LA Shack, T. Buza, SC Burgess. Cancer Immunology and Immunotherapy, 2008
0
5
10
15
20
25
L6 (R)
L7 (S)* *
* *
*IL
-4
IL-1
0
IL-1
2
IL-1
8
IFNγ
TGFβ
GPR-8
3
SMAD-7
CTLA-4
mRNA
40 –
mea
n C
t val
ueWhole tissue mRNA expression
0
5
10
15
20
25
IL-4 IL-12 IL-18 TGFβ GPR-83 SMAD-7 CTLA-4
**
**
40 –
mea
n C
t val
ue
mRNA
*
Microscopic lesion mRNA expression
L6 (R)
L7 (S)
Th-1 Th-2
NAIVE CD4+ T CELL
CYTOKINES AND T HELPER CELL DIFFERENTIATION
APC T reg
Th-1 Th-2
NAIVE CD4+ T CELL
IFN γ IL 12 IL 18
Macrophage
NK Cell
IL 12 IL 4
IL 4 IL10
APC
CTL
TGFβ
T regSmad 7
L6 Whole
L7 Whole
L7 Micro
Th-1, Th-2, T-reg ?
Inflammatory?
Step I. GO-based Phenotype Scoring.
Gene product Th1 Th2 Treg Inflammation
IL-2 1.58 1.58 -1.58
IL-4 0.00 0.00 0.00 0.00
IL-6 0.00 -1.20 1.20 -1.20
IL-8 0.00 0.00 1.18 1.18
IL-10 0.00 0.00 0.00 0.00
IL-12 0.00 0.00 0.00 0.00
IL-13 1.51 -1.51 0.00 0.00
IL-18 0.91 0.91 0.91 0.91
IFN- 0.00 0.00 0.00 0.00
TGF- -1.71 0.00 1.71 -1.71
CTLA-4 -1.89 -1.89 1.89 -1.89
GPR-83 -1.69 -1.69 1.69 -1.69
SMAD-7 0.00 0.00 0.00 0.00
Net Effect -1.29 -5.38 10.15 -5.98
Step III. Inclusion of quantitative data to the phenotype scoring table and calculation of net affect.
1-111SMAD-7
-11-1-1GPR-83
-11-1-1CTLA-4
-110-1TGF-
11-11IFN-
1111IL-18
NDND1-1IL-13
NDND-11IL-12
011-1IL-10
11NDNDIL-8
1-11IL-6
ND11-1IL-4
-11ND1IL-2
InflammationTregTh2Th1Gene product
ND = No data
Step II. Multiply by quantitative data for each gene product.
-20
0
20
40
60
80
100
120
Th-1 Th-2 T-reg Inflammation
Net
Eff
ect
-40
Whole Tissue L6 (R)L7 (S)
- 20
- 10
0
10
20
30
40
50
60
Th-1 Th-2 T-regInflammation
Phenotype
Net
Eff
ect
5mm
Microscopic lesions
L6 (R)
L7 (S)
Key points
• Modeling is subordinate to the biological questions/hypotheses.
•Together the Gene Ontology and canonical genetic networks/pathways provide the central and complementary foundation for modeling functional genomics data.
• The strategy you use to model your data will depend upon
• what information is readily available for your species of interest• what biological system you are studying