Integrating protein family sequence similarities with gene expression to find signature gene networks in breast cancer metastasis

Sepideh Babaei, Erik Van Den Akker, Jeroen De Ridder*, Marcel J T Reinders

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contributionAcademicpeer-review

3 Citations (Scopus)

Abstract

Finding robust marker genes is one of the key challenges in breast cancer research. Significant signatures identified in independent datasets often show little to no overlap, possibly due to small sample size, noise in gene expression measurements, and heterogeneity across patients. To find more robust markers, several studies analyzed the gene expression data by grouping functionally related genes using pathways or protein interaction data. Here we pursue a protein similarity measure based on Pfam protein family information to aid the identification of robust subnetworks for prediction of metastasis. The proposed protein-to-protein similarities are derived from a protein-to-family network using family HMM profiles. The gene expression data is overlaid with the obtained protein-protein sequence similarity network on six breast cancer datasets. The results indicate that the captured protein similarities represent interesting predictive capacity that aids interpretation of the resulting signatures and improves robustness.

Original languageEnglish
Title of host publicationPattern Recognition in Bioinformatics - 6th IAPR International Conference, PRIB 2011, Proceedings
Pages247-259
Number of pages13
Volume7036 LNBI
DOIs
Publication statusPublished - 2011
Externally publishedYes
Event6th IAPR International Conference on Pattern Recognition in Bioinformatics, PRIB 2011 - Delft, Netherlands
Duration: 2 Nov 20114 Nov 2011

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume7036 LNBI
ISSN (Print)03029743
ISSN (Electronic)16113349

Conference

Conference6th IAPR International Conference on Pattern Recognition in Bioinformatics, PRIB 2011
Country/TerritoryNetherlands
CityDelft
Period2/11/114/11/11

Keywords

  • breast cancer markers
  • concordant signature
  • protein-to-family distance matrix
  • protein-to-protein sequence similarity

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