viewing and interpreting data within a biological context€¦ · easy download/consumption of data...

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)