ScISI: The In Silico Interactome for Saccharomyces cerevisiae
In ScISI: In Silico Interactome

Description Usage Format Details Source References Examples

This is the incidence sparse-matrix representatin for the bi-partite graph for the in silico interactome given by Saccharomyces cerevisiae. The rows are indexed by the systematic gene names and the colunmns are indexed by the protein complexes. This matrix contains a 1 in the (i,j) postion if the protein in indexed in the i-th row is a member of the protein complex of the j-th column; it contains a 0 otherwise.

ScISIC is a sub-interactome of ScISI which consists of protein complexes derived from small scale experiments and have been curated by Gene Ontology (GO) or MIPS. While these complexes have been curated, not all of them have been completely verified to be true. Periodic changes to GO and MIPS will percolate through the protein complexes or protein complex composition and so the ScISIC will need to be rebuilt. A script located in the inst/Scripts/ entitled createScISIC.R creates an updated ScISIC if the GO and MIPS's files are up to date. GO 2.0.0 and complexcat-data-2006 (MIPS) were used to build ScISIC for Bioconductor 2.1 release of the package ScISI. Both are the most up to date versions of the repository as of 9 October 2007. In addition to MIPS and GO, we have also incorporated protein complexes curated by the IntAct repository. The IntAct protein complexes are obtained from the complex data XML file obtained from IntAct via Rintact.

In addition to the protein complexes found within MIPS and GO, ScISIC also contains manually curated protein complexes obtained from IntAct. Because IntAct has yet to version its release, the protein complexes were obtained on 25 May 2007.

ScISIC replaces ScISIverified which has been deprecated.

ScISI combines ScISIC with protein complex estimates on the datasets derived by Gavin et al (2002), Ho et al (2002), and Krogan et al (2004) using the penalized algorithm found with apComplex developed by Scholtens et al (2004).

1	data(ScISI)

The format of both the ScISI and ScISIC is a binary incidence matrix. The rows are indexed by the gene locus names and the columns are indexed by the identification codes for the protein complexes based on the repository from where they are obtained.

This is the working in silico interactome built for computational experimentation. The data from which this interactome is built is from the Intact, Gene Ontology, Mips, and estimated protein complexes from apComplex.

http://www.geneontology.org

http://www/bioconductor.org