Using ADAGE for pathway-style analyses
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The document discusses advancements in data-driven pathway analysis, particularly using the ADAGE technique, to explore gene expression related to Pseudomonas aeruginosa. It outlines the significance of unsupervised learning and the development of ensemble methods to enhance pathway capture. Additionally, it describes the Research Parasite Awards criteria for recognizing independent replicative research in the scientific community.
Using ADAGE for pathway-style analyses
- 1. Research is to see what everybody else has seen and to think what nobody else has thought. - Albert Szent-Györgyi Image by J.W. McGuire/NIH
- 2. Image from You Don’t Know Jack. Vol 3.
- 3. Data-driven pathway analysis with ADAGE Casey Greene @GreeneScientist Calvin and Hobbes. Bill Watterson
- 4. If you showed 16,000 computers 10 million images from youtube, what would they see? Le et al. 2012
- 5. Analysis with Denoising Autoencoders of Gene Expression (ADAGE) Tan et al. Pac Sym Bio 2015; Tan et al. mSystems 2016.
- 6. LeCun, Bengio, and Hinton. Nature 2015. “Although we have not focused on it in this Review, we expect unsupervised learning to become far more important in the longer term.”
- 8. • Pseudomonas aeruginosa compendium • > 100 different experiments • Many different labs
- 10. HW relationships capture genes’ pathways Assign Pathway Tan et al. mSystems. 2016.
- 11. ADAGE analysis of publicly available gene expression data collections illuminates Pseudomonas aeruginosa- host interactions bioRxiv: http://dx.doi.org/10.1101/030650 github: http://github.com/greenelab/adage Tan, Hammond, Hogan, and Greene. mSystems. 2016
- 12. Bigger models generally find more pathways. Tan et al. in prep.
- 13. The pathways captured by ADAGE change with model size. Tan et al. in prep.
- 14. We can measure gene-gene similarity with ADAGE weights. … …
- 15. ADAGE similarity captures functional similarity. Tan et al. in prep.
- 17. ensemble ADAGE (eADAGE) Tan et al. in prep.
- 18. eADAGE captures more pathways than ADAGE. Tan et al. in prep.
- 19. eADAGE captures more pathways than ICA/PCA Tan et al. in prep.
- 20. I didn’t want to just know the names of things. I remember really wanting to know how it all worked. - Elizabeth Blackburn Image: US Embassy Sweden
- 21. Activity volcano plot Fold Change -log(p)
- 22. Pareto activity selection Fold Change -log(p)
- 23. volcano + networks = pathway-style analysis
- 24. ADAGE-based pathway analysis reveals transcriptomic changes Tan et al. in prep.
- 25. Where do we have (enough) data? Greene et al. Pac Sym Bio. 2016
- 26. ADAGE webserver coming soon! http://www.greenelab.com/webservers
- 28. Research Parasite Awards (The “Parasites”) Selection criteria for the work in question: • Not involved the design of the experiments that generated the data. • Published independently of the original investigators • May have extended, replicated or disproved what the original investigators had posited. • Provided source code and intermediate or final results in a manner that enhances reproducibility.
- 29. Research Parasite Awards (The “Parasites”) Additional selection criteria for the Junior Parasite award: • The award is based on work described in a single manuscript. • Must have published the work at the training stage of their career (postdoctoral, graduate, or undergraduate). • Should not have been in an independent investigator position for more than 2 years.
- 30. Research Parasite Awards (The “Parasites”) Additional selection criteria for the Sustained Parasitism award: • Must be an independent investigator in academia, industry or public sector. • Based on three manuscripts. • Must be last or corresponding author on each manuscript. • At least a five-year period must have elapsed between the publication of the first manuscript and the final manuscript.
- 31. It ain’t what you don’t know that gets you into trouble. It’s what you know for sure that just ain’t so. - Attributed to Mark Twain
- 32. Greene Lab: Jie Tan (Grad Student) Gregory Way (Grad Student) Brett Beaulieu-Jones (Grad Student) René Zelaya (Programmer) Matt Huyck (Programmer) Dongbo Hu (Programmer) Kathy Chen (Undergrad) Mulin Xiong (Undergrad) Tim Chang (Undergrad) Collaborators: Deb Hogan & Jack Hammond Data: All investigators who publicly release their gene expression data. Images: Artists who release their work under a Creative Commons license. Funding: Gordon and Betty Moore Foundation National Science Foundation Cystic Fibrosis Foundation National Institutes of Health American Cancer Society Find us online: http://www.greenelab.com Twitter: @GreeneScientist Calvin and Hobbes. Bill Watterson