Prioritizing functional modules mediating genetic perturbations and their phenotypic effects: a global strategy

doi:10.1186/gb-2008-9-12-r174

Genome Biology

Volume 9
Issue 12

Viewing options:

Abstract
Full text
PDF (649KB)
Additional files

Associated material:

PubMed record

Related literature:

Articles citing this article
on Google Scholar
on ISI Web of Science
on PubMed Central
Other articles by authors
on Google Scholar

Wang L
Sun F
Chen T

on PubMed

Wang L
Sun F
Chen T
Related articles/pages
on Google

on Google Scholar

on PubMed

Tools:

Post to:

Method

Prioritizing functional modules mediating genetic perturbations and their phenotypic effects: a global strategy

Li Wang¹ , Fengzhu Sun¹^,2 and Ting Chen¹

¹Molecular and Computational Biology, Department of Biology Sciences, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089-2910, USA

²MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, PR China

author email corresponding author email

Genome Biology 2008, 9:R174doi:10.1186/gb-2008-9-12-r174


Published:	16 December 2008

Subject areas: Bioinformatics, Genetics, Genome studies

Additional files

Additional data file 1:

Table S1: 94 curated lethal protein complexes identified by the BN model. The complex ID starting with 'GO', 'MIPS' and 'EBI' represents GO, MIPS and Intact ID, respectively. Total # denotes the total number of genes whose lethality is known. Lethal # denotes the number of genes that are lethal. Figure S1: genes in S. cerevisiae are classified into four groups according to their lethality and the lethality of protein complexes to which they belong. Within each group, the pie chart represents the distribution of genes with respect to the lethality of their orthologs in D. melanogaster. The lethal protein complexes were identified as in Figure 1b. Figure S2: simulation results. The performance of the BN model and the HG method in identifying lethal complexes given different degrees of overlap among protein complexes and different distributions of the proportion of lethal genes in a lethal complex.

Format: PDF Size: 176KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional data file 2:

The 27 GO CAN-processes prioritized by the BN model (yellow) and their offspring and ancestor nodes (blue). The nodes with red circles represent 23 out of 27 GO CAN-processes prioritized by the HG enrichment test. The size of the nodes is proportional to the minus log p-value of the HG enrichment test for the cancer genes. Those nodes with size zero are insignificant nodes by the HG enrichment test (p-value > 0.05).

Format: PDF Size: 464KB Download file

This file can be viewed with: Adobe Acrobat Reader