Statistical assessment of MSigDB gene sets in colon cancer

Angela Distaso, Luca Abatangelo, Rosalia Maglietta, Teresa Maria Creanza, Ada Piepoli, Massimo Carella, Annarita D'Addabbo, Sayan Mukherjee, Nicola Ancona

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Gene expression profiling offers a great opportunity for understanding the key role of genes in alterations which drive a normal cell to a cancer state. A deep understanding of the mechanisms of tumorigenesis can be reached focusing on deregulation of gene sets or pathways. We measure the amount of deregulation and assess the statistical significance of predefined pathways belonging to MSigDB collection in a colon cancer data set. To measure the relevance of the pathways we use two well-established methods: Gene Set Enrichment Analysis (GSEA) [7] and Gene List Analysis with Prediction Accuracy (GLAPA) [8]. We found that pathways associated to different diseases are strictly connected with colon cancer. Our study highlights the importance of using gene sets genes for understanding the main biological processes and pathways involved in colorectal cancer. Our analysis shows that many of the genes involved in these pathways are strongly associated to colorectal tumorigenesis.

Original languageEnglish
Title of host publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Pages206-213
Number of pages8
Volume5178 LNAI
EditionPART 2
DOIs
Publication statusPublished - 2008
Event12th International Conference on Knowledge-Based Intelligent Information and Engineering Systems, KES 2008 - Zagreb, Croatia
Duration: Sep 3 2008Sep 5 2008

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
NumberPART 2
Volume5178 LNAI
ISSN (Print)03029743
ISSN (Electronic)16113349

Other

Other12th International Conference on Knowledge-Based Intelligent Information and Engineering Systems, KES 2008
CountryCroatia
CityZagreb
Period9/3/089/5/08

Keywords

  • Machine learning
  • Microarray
  • Pathway analysis
  • Prediction accuracy

ASJC Scopus subject areas

  • Computer Science(all)
  • Theoretical Computer Science

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  • Cite this

    Distaso, A., Abatangelo, L., Maglietta, R., Creanza, T. M., Piepoli, A., Carella, M., D'Addabbo, A., Mukherjee, S., & Ancona, N. (2008). Statistical assessment of MSigDB gene sets in colon cancer. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (PART 2 ed., Vol. 5178 LNAI, pp. 206-213). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 5178 LNAI, No. PART 2). https://doi.org/10.1007/978-3-540-85565-1-26