Network resources, human, (in progress)

*** GeneSigDB (used by Li14BMC, should contain disease genes). This site provide download for R analysis.   http://compbio.dfci.harvard.edu/genesigdb/

List of human disease genes in gene Card
http://www.genecards.org/cgi-bin/listdiseasecards.pl?type=full
(not sure whether this includes haploid type association)

Genome Research Genome-wide map of regulatory interactions in the human genome,

http://genome.cshlp.org/content/early/2014/09/15/gr.176586.114.abstract

Farmington study
http://videocast.nih.gov/Summary.asp?File=18760&bhcp=1

Network analysis of GWAS data, 2013 Current Opinion in Genetics and Development

Mark DM Leiserson1,2, Jonathan V Eldridge1,2, Sohini Ramachandran2,3 and Benjamin J Raphael1,2 

http://www.psidev.info/index.php?q=node/60#tools

MIF Parsers


The human protein interaction network data can be found from http://www.hprd.org/download

Reference: Peri S, Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK,
Surendranath V, Niranjan V, Muthusamy B, Gandhi TKB, GronborgM,
Ibarrola N, Deshpande N, Shanker K, Shivashankar HN, Rashmi BP,
Ramya MA, Zhao ZX, Chandrika KN, Padma N, Harsha HC et al
(2003) Development of human protein reference database as an initial
platform for approaching systems biology in humans. Genome Res 13:
2363–237

Gerstein lab's human networks
  human multinet 
http://homes.gersteinlab.org/Khurana-PLoSCompBio-2013/
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002886#s4

http://encodenets.gersteinlab.org/


dbCline
UChicago

peptieAtlas
http://www.nature.com/embor/journal/v9/n5/pdf/embor200856.pdf

ensemble

human twin aging expression
http://genomebiology.com/2013/14/7/R75?utm_campaign=10_12_13_genomebiol_Article_Mailing_Reg&utm_content=7387379393&utm_medium=BMCemail&utm_source=Emailvision


http://hongqinlab.blogspot.com/2013/10/mutation-tolerance-in-human-genes-data.html

http://hongqinlab.blogspot.com/2013/03/candidate-rojects-for-r-based-data.html

expression, aging, human, kidny,
http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0020427

9. Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A et al.: Human Protein Reference Database- 2009 update. [Internet]. Nucleic Acids Res 2009, 37: D767-D772. 

10. Stark C, Breitkreutz B-J, Reguly T, Boucher L, Breitkreutz A, Tyers M: BioGRID: a general repository for interaction datasets. [Internet]. Nucleic Acids Res 2006, 34:D535-D539. 

11. Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C et al.: STRING v9.1: protein–protein interaction networks, with increased coverage and integration. [Internet]. Nucleic Acids Res 2013, 41:D808-D815. 

12. Razick S, Magklaras G, Donaldson IM: iRefIndex: a consolidated protein interaction database with provenance. [Internet]. BMC Bioinformatics 2008, 9:405. 

13. Croft D, O’Kelly G, Wu G, Haw R, Gillespie M, Matthews L, Caudy M, Garapati P, Gopinath G, Jassal B et al.: Reactome: a database of reactions, pathways and biological processes. [Internet]. Nucleic Acids Research 2011, 39:D691-D697. 

14. Ewing RM et al.: Large-scale mapping of human protein– protein interactions by mass spectrometry. Molecular Systems Biology 2007, 3:89. 

15. Hutchins JRa et al.: Systematic analysis of human protein complexes identifies chromosome segregation proteins. Science 2010, 328:593-599. 

16. Rual J-F et al.: Towards a proteome-scale map of the human protein–protein interaction network. Nature 2005, 437:1173-1178. 

17. Stelzl U et al.: A human protein–protein interaction network: a resource for annotating the proteome. Cell 2005, 122:957-968. 

18. Yu H et al.: Next-generation sequencing to generate interactome datasets. Nat Methods 2011, 8:478-480. 608 Genetics of system biology Current Opinion 

From Gilman 2011 Neuron, netbag on autism

Downloaded Information

The data described in previous sections was downloaded from the following public

resources:

 GeneOntology annotations from NCBI (01/2009 – ftp://ftp.ncbi.nlm.nih.gov/gene/)

 Pathways and enzyme codes from Kyoto Encyclopedia of Genes and Genomes (KEGG)

database (01/2009 – ftp://ftp.genome.jp/pub/kegg/genes/organisms/hsa/)

 Domains from InterPro database (01/2009 – ftp://ftp.ebi.ac.uk/pub/databases/interpro/)

 Tissue indicators from the TiGER database (09/2009 – http://bioinfo.wilmer.jhu.edu/tiger/)

 Protein-protein Interactions:

o BIND with protein complexes (08/2009 – http://bond.unleashedinformatics.com/)

o BioGRID interactions (08/2009 – http://www.thebiogrid.org/downloads.php)

o DIP interactions (10/2009 – http://dip.doe-mbi.ucla.edu/dip/)

o HPRD interactions (10/2009 – http://www.hprd.org/)

o InNetDB interactions (05/2009 – http://hanlab.genetics.ac.cn/sys/intnetdb)

o IntAct (10/2009 – http://www.ebi.ac.uk/intact/)

o BiGG metabolic interactions (04/2009 – http://gcrg.ucsd.edu/Downloads )

o MINT (05/2009 – http://mint.bio.uniroma2.it/mint/)

o MIPS (05/2009 – http://mips.gsf.de/proj/ppi/)

gene expression between human and mouse, PNAS, mike snyder lab, Standford
http://www.pnas.org/content/111/48/17224.full