viewing and interpreting data within a biological context€¦ · easy download/consumption of data...
TRANSCRIPT
Viewing and Interpreting
Data within a Biological
Context
Samuel Payne
Pacific Northwest National Laboratory
Goals
Biodiversity Library and Plugin – Expose public data
Easy download/consumption of data on proteomeXchange
Planning experiments from a biological perspective
Active Data Canvas – Provide visual data analysis
Getting away from spreadsheets
Collaborating on data analysis
May 31, 2015 2
Navigation – Choose Organism
Navigation – Choose Pathways
Review Pathway Coverage
Export Data to Skyine
May 31, 2015 7
Library/Plugin Uses
May 31, 2015 8
Designing SRM assays
Spectrum library searches
DIA scoring
Bioinformatics data mining Proteotypic machine learning
LC elution prediction
Scoring functions
112 organisms
3 million peptides @ FDR ~ 0.00009
All data publicly available at MassIVE
For ANY organism
A Meaningful Context
I have data, what now?
1
Raw Data Identification Hypotheses Browse & Share
2 3
May 31, 2015 9
Heatmap View
May 31, 2015 10
1,608 proteins
174 tumor samples Ovarian Cancer Data
Heatmap View
May 31, 2015 11
Heatmap View
May 31, 2015 12
KEGG Overlay
May 31, 2015 13
Acknowledgements
Biodiversity Library and Plugin
Grant Fujimoto
Michael Degan, Chris Overall, Matt Monroe,
Lillian Ryadinskiy
Active Data Canvas
Joon-Yong Lee, Nick Cramer
Ryan Wilson, Gary Kiebel, Grant Fujimoto
Dick Smith
Poster Wednesday 312 (Biodiversity Library)
Poster Thursday 466 (Active Data Canvas)