Sriganesh Srihari1, Piyush B. Madhamshettiwar1, Sarah Song1, Chao Liu1, Peter T. Simpson2, Kum Kum Khanna3 and Mark A. Ragan1
1Institute for Molecular Bioscience, The University of Queensland, St. Lucia QLD 4072, Australia
2The University of Queensland Centre for Clinical Research, Brisbane, QLD 4006, Australia
3QIMR-Berghofer Institute of Medical Research, Brisbane QLD 4006 Australia
Workflow for CONTOURv2: Linking changes in expression levels of protein complexes to their regulation by transcription factors.
The pipeline here obtains complexes extracted from protein interaction networks using our earlier published CONTOURv1 (Srihari & Ragan, Bioinformatics 2013, 29(12):1553-61)
21 July 2014: Accepted to BMC Systems Biology
04 July 2014: Updated website. Uploaded corrections to manuscript
20 Jan 2014: Created this website
Differential expression analysis of (individual) genes is often used to study their roles in diseases. However, diseases such as cancer are a result of the combined effect of multiple genes. Gene products such as proteins seldom act in isolation, but instead constitute stable multi-protein complexes performing dedicated functions. Therefore, complexes aggregate the effect of individual genes (proteins) and can be used to gain a better understanding of cancer mechanisms. Here, we observe that complexes show considerable changes in their expression, in turn directed by the concerted action of transcription factors (TFs), across cancer conditions. We seek to gain novel insights into cancer mechanisms through a systematic analysis of complexes and their transcriptional regulation.
Supplementary materialsDownload here
Cite: Srihari S et al., Complex-based analysis of dysregulated cellular processes in cancer, BMC Systems Biology 2014, to appear [PDF].
Funding: Australian NHMRC grant 1028742 to PTS and MAR.