Viewing and Interpreting Data within a Biological Context€¦ · Easy download/consumption of data...
Transcript of Viewing and Interpreting Data within a Biological Context€¦ · Easy download/consumption of data...
![Page 1: Viewing and Interpreting Data within a Biological Context€¦ · Easy download/consumption of data on proteomeXchange Planning experiments from a biological perspective Active Data](https://reader034.fdocuments.us/reader034/viewer/2022051806/60003ea9e914ee27ea436075/html5/thumbnails/1.jpg)
Viewing and Interpreting
Data within a Biological
Context
Samuel Payne
Pacific Northwest National Laboratory
![Page 2: Viewing and Interpreting Data within a Biological Context€¦ · Easy download/consumption of data on proteomeXchange Planning experiments from a biological perspective Active Data](https://reader034.fdocuments.us/reader034/viewer/2022051806/60003ea9e914ee27ea436075/html5/thumbnails/2.jpg)
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
![Page 3: Viewing and Interpreting Data within a Biological Context€¦ · Easy download/consumption of data on proteomeXchange Planning experiments from a biological perspective Active Data](https://reader034.fdocuments.us/reader034/viewer/2022051806/60003ea9e914ee27ea436075/html5/thumbnails/3.jpg)
![Page 4: Viewing and Interpreting Data within a Biological Context€¦ · Easy download/consumption of data on proteomeXchange Planning experiments from a biological perspective Active Data](https://reader034.fdocuments.us/reader034/viewer/2022051806/60003ea9e914ee27ea436075/html5/thumbnails/4.jpg)
Navigation – Choose Organism
![Page 5: Viewing and Interpreting Data within a Biological Context€¦ · Easy download/consumption of data on proteomeXchange Planning experiments from a biological perspective Active Data](https://reader034.fdocuments.us/reader034/viewer/2022051806/60003ea9e914ee27ea436075/html5/thumbnails/5.jpg)
Navigation – Choose Pathways
![Page 6: Viewing and Interpreting Data within a Biological Context€¦ · Easy download/consumption of data on proteomeXchange Planning experiments from a biological perspective Active Data](https://reader034.fdocuments.us/reader034/viewer/2022051806/60003ea9e914ee27ea436075/html5/thumbnails/6.jpg)
Review Pathway Coverage
![Page 7: Viewing and Interpreting Data within a Biological Context€¦ · Easy download/consumption of data on proteomeXchange Planning experiments from a biological perspective Active Data](https://reader034.fdocuments.us/reader034/viewer/2022051806/60003ea9e914ee27ea436075/html5/thumbnails/7.jpg)
Export Data to Skyine
May 31, 2015 7
![Page 8: Viewing and Interpreting Data within a Biological Context€¦ · Easy download/consumption of data on proteomeXchange Planning experiments from a biological perspective Active Data](https://reader034.fdocuments.us/reader034/viewer/2022051806/60003ea9e914ee27ea436075/html5/thumbnails/8.jpg)
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
![Page 9: Viewing and Interpreting Data within a Biological Context€¦ · Easy download/consumption of data on proteomeXchange Planning experiments from a biological perspective Active Data](https://reader034.fdocuments.us/reader034/viewer/2022051806/60003ea9e914ee27ea436075/html5/thumbnails/9.jpg)
A Meaningful Context
I have data, what now?
1
Raw Data Identification Hypotheses Browse & Share
2 3
May 31, 2015 9
![Page 10: Viewing and Interpreting Data within a Biological Context€¦ · Easy download/consumption of data on proteomeXchange Planning experiments from a biological perspective Active Data](https://reader034.fdocuments.us/reader034/viewer/2022051806/60003ea9e914ee27ea436075/html5/thumbnails/10.jpg)
Heatmap View
May 31, 2015 10
1,608 proteins
174 tumor samples Ovarian Cancer Data
![Page 11: Viewing and Interpreting Data within a Biological Context€¦ · Easy download/consumption of data on proteomeXchange Planning experiments from a biological perspective Active Data](https://reader034.fdocuments.us/reader034/viewer/2022051806/60003ea9e914ee27ea436075/html5/thumbnails/11.jpg)
Heatmap View
May 31, 2015 11
![Page 12: Viewing and Interpreting Data within a Biological Context€¦ · Easy download/consumption of data on proteomeXchange Planning experiments from a biological perspective Active Data](https://reader034.fdocuments.us/reader034/viewer/2022051806/60003ea9e914ee27ea436075/html5/thumbnails/12.jpg)
Heatmap View
May 31, 2015 12
![Page 13: Viewing and Interpreting Data within a Biological Context€¦ · Easy download/consumption of data on proteomeXchange Planning experiments from a biological perspective Active Data](https://reader034.fdocuments.us/reader034/viewer/2022051806/60003ea9e914ee27ea436075/html5/thumbnails/13.jpg)
KEGG Overlay
May 31, 2015 13
![Page 14: Viewing and Interpreting Data within a Biological Context€¦ · Easy download/consumption of data on proteomeXchange Planning experiments from a biological perspective Active Data](https://reader034.fdocuments.us/reader034/viewer/2022051806/60003ea9e914ee27ea436075/html5/thumbnails/14.jpg)
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)