Pathway Informatics
July 6, 2015
Ansuman Chattopadhyay, PhD
ansuman@pitt.edu
Databases:
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KEGG: http://www.genome.jp/kegg/kegg2.html
BioGRID: http://thebiogrid.org/
STRING: http://string-db.org/
NCBI Biosystems: http://www.ncbi.nlm.nih.gov/biosystems
Wiki-PI: http://severus.dbmi.pitt.edu/wiki-pi/
International Molecular Exchange Consortium: http://www.imexconsortium.org/
Pathway Commons: http://www.pathwaycommons.org/pc/
Millipore Pathways: http://www.millipore.com/pathways/pw/pathways
Applied Biosystems Pathways: http://www5.appliedbiosystems.com/tools/pathway/
HSLS OBRC listings on Pathway Databases: http://goo.gl/cbmzy
Gene Expression data search:
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NextBio registration: http://www.hsls.pitt.edu/molbio/nextbio
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HSLS-NextBio log-in: https://hsls.nextbio.com/c/authentication/login.nb:
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GEO: http://www.ncbi.nlm.nih.gov/geo/
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Array Express: http://www.ebi.ac.uk/arrayexpress/
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GEO2R: http://www.ncbi.nlm.nih.gov/geo/info/geo2r.html
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inSilico DB: https://insilicodb.org/app/
Pathway Analysis Tools:
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NIH DAVID: http://david.abcc.ncifcrf.gov/
NCBI FLINK: http://www.ncbi.nlm.nih.gov/Structure/flink/flink.cgi
Ingenuity IPA: http://www.ingenuity.com/
GeneGo Metacore: http://www.genego.com/
Pathway Drawing Tool:
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ePath3D- Registration: http://hsls.libguides.com/molbio/epath3d
ePath3D Sign-in: http://www.epath3d.com/SignIn
ChemBio Draw: http://technology.pitt.edu/software/chembiodraw-for-students
Pathway InfoBooster:
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http://www.hsls.pitt.edu/molbio/infobooster
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Pathway Informatics
July 6, 2015
Ansuman Chattopadhyay, PhD
ansuman@pitt.edu
Video Tutorial:
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Retrieve interacting partners of a protein of your interest (BioGrid and STRING):
http://media.hsls.pitt.edu/media/molbiovideos/ppi.swf
Hands-on:
Gene list- Resveratrol data
http://files.hsls.pitt.edu/files/molbio/bioinfogen/resveratrol.txt
http://files.hsls.pitt.edu/files/molbio/pathway_analysis/Resv-Nextbio.xlsx
Gene list-1
http://files.hsls.pitt.edu/files/molbio/bioinfogen/genelist-1.txt
Suggested Readings:
Plos Computational Biology Translational Bioinformatics:
http://www.ploscollections.org/article/browseIssue.action?issue=info:doi/10.1371/issue.pcol.v03.i11
Chapter 5: Network Biology Approach to Complex Diseases
Dong-Yeon Cho, Yoo-Ah Kim, Teresa M. Przytycka
PLOS Computational Biology: published 27 Dec 2012 | info:doi/10.1371/journal.pcbi.1002820
http://www.ploscollections.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002820
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub
TR, Lander ES, Mesirov JP.
Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50. Epub 2005 Sep 30.
http://www.ncbi.nlm.nih.gov/pubmed/16199517
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.
Huang da W, Sherman BT, Lempicki RA.
Nat Protoc. 2009;4(1):44-57. doi: 10.1038/nprot.2008.211.
http://www.nature.com/nprot/journal/v4/n1/pdf/nprot.2008.211.pdf
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