the art of connectivity mapping - acm-bcb.org€¦ · the art of connectivity mapping avi...
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The Art of Connectivity Mapping
Avi Ma’ayan, PhDProfessor, Department of Pharmacological Sciences
Director, Mount Sinai Center for BioinformaticsIcahn School of Medicine at Mount Sinai, New York, NY
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2011
$$$$$+
Data+
Statistics+
Wiz Kid
$$$$$+
Expert Knowledge
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https://www.datanami.com
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The Variety of Sources for Mammalian Molecular Data Collected from Cells, Tissues, Model Organisms and Patients
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Genes,
Proteins,
Targets
Cells,
Tissues
Diseases,
Phenotypes,
Adverse
Events
Gene-Sets,
Modules,
Pathways
Drugs,
Small
molecules
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Ma’ayan et al. Trends Pharmacol Sci. 2014 Sep;35(9):450-60.
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The Harmonizome Project
http://amp.pharm.mssm.edu/Harmonizome/Rouillard et al. Database (Oxford). 2016 Jul 3;2016.
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Harmonizome Google Analytics
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Enrichr: a search
engine for gene sets…
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Enrichr Google Analytics
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Transcriptomics Proteomics Pathways
Genes
?
Knockout
Phenotypes
Observed
+
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+f (T, P, I)
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Gene Expression Single−Organism Cellular Localization Protein Localization To Organelle Cellular Component Disassembly Nuclear−Transcribed Mrna Catabolic Process Translation Protein Targeting To Membrane Protein Localization To Endoplasmic Reticulum Establishment Of Protein Localization To Endoplasmic Reticulum Srp−Dependent Cotranslational Protein Targeting To Membrane Protein Targeting To Er Cotranslational Protein Targeting To Membrane Establishment Of Protein Localization To Organelle Protein Localization To Membrane Protein Targeting Establishment Of Protein Localization To Membrane Nuclear−Transcribed Mrna Catabolic Process, Nonsense−Mediated Decay Protein Complex Disassembly Cellular Protein Complex Disassembly Viral Life Cycle Translational Elongation Translational Termination Viral Transcription
0 100 200 300 400
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0100200300400
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Machine Learning is the Obvious Next Step
Deep Learning(ANN with many layers)
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Predicting Side Effects with LINCS L1000 Data
Wang Z, Clark NR, Ma'ayan A. Bioinformatics. 2016 Aug 1;32(15):2338-45.
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3,713 drugs/compounds63 cell lines
3 time points51 dosages
17,041 significant drug induced signatures
http://amp.pharm.mssm.edu/L1000FWD
Fireworks Visualization of
17,041 Drug-Induced
Signatures
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3,713 drugs/compounds63 cell lines
3 time points51 dosages
17,041 significant drug induced signatures
http://amp.pharm.mssm.edu/L1000FWD
Fireworks Visualization of
17,041 Drug-Induced
Signatures
![Page 21: The Art of Connectivity Mapping - acm-bcb.org€¦ · The Art of Connectivity Mapping Avi Ma’ayan, PhD Professor, Department of Pharmacological Sciences Director, Mount Sinai Center](https://reader034.vdocuments.us/reader034/viewer/2022052015/602c9f36c446e3000808e662/html5/thumbnails/21.jpg)
3,713 drugs/compounds63 cell lines
3 time points51 dosages
17,041 significant drug induced signatures
http://amp.pharm.mssm.edu/L1000FWD
Fireworks Visualization of
17,041 Drug-Induced
Signatures
![Page 22: The Art of Connectivity Mapping - acm-bcb.org€¦ · The Art of Connectivity Mapping Avi Ma’ayan, PhD Professor, Department of Pharmacological Sciences Director, Mount Sinai Center](https://reader034.vdocuments.us/reader034/viewer/2022052015/602c9f36c446e3000808e662/html5/thumbnails/22.jpg)
3,713 drugs/compounds63 cell lines
3 time points51 dosages
17,041 significant drug induced signatures
http://amp.pharm.mssm.edu/L1000FWD
Fireworks Visualization of
17,041 Drug-Induced
Signatures
![Page 23: The Art of Connectivity Mapping - acm-bcb.org€¦ · The Art of Connectivity Mapping Avi Ma’ayan, PhD Professor, Department of Pharmacological Sciences Director, Mount Sinai Center](https://reader034.vdocuments.us/reader034/viewer/2022052015/602c9f36c446e3000808e662/html5/thumbnails/23.jpg)
3,713 drugs/compounds63 cell lines
3 time points51 dosages
17,041 significant drug induced signatures
http://amp.pharm.mssm.edu/L1000FWD
Fireworks Visualization of
17,041 Drug-Induced
Signatures
![Page 24: The Art of Connectivity Mapping - acm-bcb.org€¦ · The Art of Connectivity Mapping Avi Ma’ayan, PhD Professor, Department of Pharmacological Sciences Director, Mount Sinai Center](https://reader034.vdocuments.us/reader034/viewer/2022052015/602c9f36c446e3000808e662/html5/thumbnails/24.jpg)
3,713 drugs/compounds63 cell lines
3 time points51 dosages
17,041 significant drug induced signatures
http://amp.pharm.mssm.edu/L1000FWD
Fireworks Visualization of
17,041 Drug-Induced
Signatures
![Page 25: The Art of Connectivity Mapping - acm-bcb.org€¦ · The Art of Connectivity Mapping Avi Ma’ayan, PhD Professor, Department of Pharmacological Sciences Director, Mount Sinai Center](https://reader034.vdocuments.us/reader034/viewer/2022052015/602c9f36c446e3000808e662/html5/thumbnails/25.jpg)
3,713 drugs/compounds63 cell lines
3 time points51 dosages
17,041 significant drug induced signatures
http://amp.pharm.mssm.edu/L1000FWD
Fireworks Visualization of
17,041 Drug-Induced
Signatures
![Page 26: The Art of Connectivity Mapping - acm-bcb.org€¦ · The Art of Connectivity Mapping Avi Ma’ayan, PhD Professor, Department of Pharmacological Sciences Director, Mount Sinai Center](https://reader034.vdocuments.us/reader034/viewer/2022052015/602c9f36c446e3000808e662/html5/thumbnails/26.jpg)
3,713 drugs/compounds63 cell lines
3 time points51 dosages
17,041 significant drug induced signatures
http://amp.pharm.mssm.edu/L1000FWD
Fireworks Visualization of
17,041 Drug-Induced
Signatures
![Page 27: The Art of Connectivity Mapping - acm-bcb.org€¦ · The Art of Connectivity Mapping Avi Ma’ayan, PhD Professor, Department of Pharmacological Sciences Director, Mount Sinai Center](https://reader034.vdocuments.us/reader034/viewer/2022052015/602c9f36c446e3000808e662/html5/thumbnails/27.jpg)
3,713 drugs/compounds63 cell lines
3 time points51 dosages
17,041 significant drug induced signatures
http://amp.pharm.mssm.edu/L1000FWD
Fireworks Visualization of
17,041 Drug-Induced
Signatures
![Page 33: The Art of Connectivity Mapping - acm-bcb.org€¦ · The Art of Connectivity Mapping Avi Ma’ayan, PhD Professor, Department of Pharmacological Sciences Director, Mount Sinai Center](https://reader034.vdocuments.us/reader034/viewer/2022052015/602c9f36c446e3000808e662/html5/thumbnails/33.jpg)
Predicting Patient Age from Vital Signs and Lab Tests with Deep Learning
J Biomed Inform. 2017 Dec;76:59-68.
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Network Analysis in Systems Biology Course on Coursera
https://class.coursera.org/netsysbio-002
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GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions
Bioinformatics. 2015 Sep 15;31(18):3060-2.
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GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions
Bioinformatics. 2015 Sep 15;31(18):3060-2.
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GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions
Bioinformatics. 2015 Sep 15;31(18):3060-2.
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Microtask Signature Extraction Project: Using GEO2Enrichr to Extract and
Annotate Signatures from GEO
- Single Gene Perturbations (n=2225)- Drug/Toxin Perturbations (n=1319)- Disease vs. Normal Signatures (n=1105)
Nature Communications 7, 12846 (2016)
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http://amp.pharm.mssm.edu/CREEDS Nature Communications 7, 12846 (2016)
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http://archs4.cloud
ARCHS4: >300K Processed RNA-seq Samples from GEO for Human and Mouse
Nat Commun. 2018 Apr 10;9(1):1366.
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ARCHS4: >177K Processed RNA-seq Samples from GEO for Human and Mouse
http://archs4.cloud Nat Commun. 2018 Apr 10;9(1):1366.
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ARCHS4 Chrome Extension
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BioJupies Chrome Extension
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BioJupies
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Summary•Data abstraction for data integration• The Harmonizome and Enrichr resources•Next step is Machine Learning• L1000 data processing and visualization•Predicting MOA for L1000 small molecules•Predicting the predictability of novel small molecules• Integration with EMR based on drugs and vital signs•Predicting gene function with ARCHS4•ARCHS4 and BioJupies to facilitate data reuse, data
integration, and signature extraction
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NIH Support U54-HL127624 (LINCS-DCIC), U24-CA224260 (IDG-KMC), and OT3-OD025467 (NIH Data Commons)