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Identification of Deregulated Transcription Factors Involved in Specific Bladder Cancer Subtypes

10 pagesPublished: March 11, 2020

Abstract

Comparison between tumoral and healthy cells may reveal abnormal regulation behaviors between a transcription factor and the genes it regulates, without exhibiting differential expression of the former genes. We propose a methodology for the identification of transcription factors involved in the deregulation of genes in tumoral cells. This strategy is based on the inference of a reference gene regulatory network that connects transcription factors to their downstream targets using gene expression data. Gene expression levels in tumor samples are then carefully compared to this reference network to detect deregulated target genes. A linear model is finally used to measure the ability of each transcription factor to explain these deregulations. We assess the performance of our method by numerical experiments on a public bladder cancer data set derived from the Cancer Genome Atlas project. We identify genes known for their implication in the development of specific bladder cancer subtypes as well as new potential biomarkers.

Keyphrases: cancer systems biology, deregulation, gene regulatory networks

In: Qin Ding, Oliver Eulenstein and Hisham Al-Mubaid (editors). Proceedings of the 12th International Conference on Bioinformatics and Computational Biology, vol 70, pages 1-10.

BibTeX entry
@inproceedings{BICOB2020:Identification_Deregulated_Transcription_Factors,
  author    = {Magali Champion and Julien Chiquet and Pierre Neuvial and Mohamed Elati and François Radvanyi and Etienne Birmelé},
  title     = {Identification of Deregulated Transcription Factors Involved in Specific Bladder Cancer Subtypes},
  booktitle = {Proceedings of the 12th International Conference on Bioinformatics and Computational Biology},
  editor    = {Qin Ding and Oliver Eulenstein and Hisham Al-Mubaid},
  series    = {EPiC Series in Computing},
  volume    = {70},
  publisher = {EasyChair},
  bibsource = {EasyChair, https://easychair.org},
  issn      = {2398-7340},
  url       = {/publications/paper/PX7P},
  doi       = {10.29007/v7qj},
  pages     = {1-10},
  year      = {2020}}
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