Protein Interactions

Description Usage Arguments Details Value Note Author(s) References See Also Examples

Conveiently combines some or all of the databases in the data dolder of the ganet package.

1 2	ganet.combine(BIOGRID=1,CORUM=1,DIP=1,HPRD=1, INNATEDB=1,INTACT=1,MINT=1,MPI=1,NAT=0,REACT=0)

`BIOGRID`	BioGrid: Biological General Repository for Interaction Datasets. 515421 unique links. (Downloaded from http://thebiogrid.org/ by January 2015)
`CORUM`	CORUM: the Comprehensive Resource of Mammalian protein complexes. 44666 unique links. (Downloaded from http://mips.helmholtz-muenchen.de/genre/proj/corum by January 2015)
`DIP`	DIP: Database of Interacting Proteins. 37945 unique links. (Downloaded from http://dip.doe-mbi.ucla.edu/dip/Main.cgi by January 2015)
`HPRD`	Human Protein Reference Database (HPRD). 44376 unique links. Downloaded from http://www.hprd.org/download by January 2015
`INNATEDB`	A knowledge resource for innate immunity interactions & pathways. 16665 unique links. Downloaded from http://www.innatedb.com/redirect.do?go=downloadImported by January 2015
`INTACT`	IntAct provides protein interaction data. 136605 unique links. Downloaded from https://www.ebi.ac.uk/intact/ by January 2015
`MINT`	Molecular INTeraction database (MINT). 296806 links. Downloaded from http://www.pathwaycommons.org by Nov 2011
`MPI`	MIPS Mammalian Protein-Protein Interaction Database. 807 unique links. Downloaded from http://mips.helmholtz-muenchen.de/proj/ppi/ by January 2015
`NAT`	Nature Pathway Interaction Database. 12944 links. Downloaded from http://www.pathwaycommons.org by Nov 2011
`REACT`	Reactome: a knowledgebase of biological processes. 642272 links. Downloaded from http://www.reactome.org/pages/download-data/ by January 2015

All the self interactions removed. Mutual interactions are unified. Please cite the reference of each database seperately for the ones you have used along with ganet references.

CombinedDatabases

Combined and unified databases of the selected databases.

This package is intended to be updated with respect to feedbacks and also with updates of the current databases.

Gokmen Altay

1. G. Altay, N. Altay, D.E. Neal, Global assessment of network inference algorithms based on available literature of gene/protein interactions, Turk J Biol, 37:547-555, 2013. 2. G. Altay, J Zapardel, B Peters, "Determining preprocessing combinations and sample size for Gene Network Inference over ...", bioArxiv, 2017.

3. Ruepp A, Waegele B, Lechner M, Brauner B, Dunger-Kaltenbach I, Fobo G, Frishman G, Montrone C, Mewes HW: CORUM: the comprehensive resource of mammalian protein complexes-2009. Nucleic Acids Research 2010, 38:D497-D501

4. Breuer K, Foroushani AK, Laird MR, Chen C, Sribnaia A, Lo R, Winsor GL, Hancock REW, Brinkman FSL, Lynn DJ: InnateDB: systems biology of innate immunity and beyond-recent updates and continuing curation. Nucleic Acids Research 2013, 41:D1228-D1233

5. Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D: The Database of Interacting Proteins: 2004 update. Nucleic Acids Research 2004, 32:D449-D451

6. Wang K, Nemenman I, Banerjee N, Margolin AA, Califano A: Genome-wide discovery of modulators of transcriptional interactions in human B lymphocytes. Research in Computational Molecular Biology, Proceedings 2006, 3909:348-362.

7. Kerrien S, Aranda B, Breuza L, Bridge A, Broackes-Carter F, Chen C, Duesbury M, Dumousseau M, Feuermann M, Hinz U, et al: The IntAct molecular interaction database in 2012. Nucleic Acids Research 2012, 40:D841-D846.

8. Licata L, Briganti L, Peluso D, Perfetto L, Iannuccelli M, Galeota E, Sacco F, Palma A, Nardozza AP, Santonico E, et al: MINT, the molecular interaction database: 2012 update. Nucleic Acids Research 2012, 40:D857-D861.

9. Prasad TSK, 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. Nucleic Acids Research 2009, 37:D767-D772.

10. Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M: BioGRID: a general repository for interaction datasets. Nucleic Acids Research 2006, 34:D535-D539.

ganet.ComLinks, ganet.FEtest, ganet.UniqNetSimp

#data(ganet.ex.net)

#CombinedDatabases <- ganet.combine(BIOGRID=1,CORUM=1,DIP=0,HPRD=0,
#INNATEDB=0, INTACT=0, MINT=0, MPI=0, NAT=0,REACT=0) 

## BIOGRID and CORUM databases are selected and  the other databases 
#are already zero by default.

## if you want to combine all the interactions then: alldatabases <- ganet.combine()

#see the example of ganet.FEtest for the use of this combined database