Integer programming-based method for completing signaling pathways and its application to analysis of colorectal cancer.

Takeyuki Tamura, Yoshihiro Yamanishi, Mao Tanabe, Susumu Goto, Minoru Kanehisa, Katsuhisa Horimoto, Tatsuya Akutsu

    Research output: Contribution to journalArticle

    1 Citation (Scopus)

    Abstract

    Signaling pathways are often represented by networks where each node corresponds to a protein and each edge corresponds to a relationship between nodes such as activation, inhibition and binding. However, such signaling pathways in a cell may be affected by genetic and epigenetic alteration. Some edges may be deleted and some edges may be newly added. The current knowledge about known signaling pathways is available on some public databases, but most of the signaling pathways including changes upon the cell state alterations remain largely unknown. In this paper, we develop an integer programming-based method for inferring such changes by using gene expression data. We test our method on its ability to reconstruct the pathway of colorectal cancer in the KEGG database.

    Original languageEnglish
    Pages (from-to)193-203
    Number of pages11
    JournalGenome informatics. International Conference on Genome Informatics
    Volume24
    DOIs
    Publication statusPublished - 2010

    All Science Journal Classification (ASJC) codes

    • Medicine(all)

    Fingerprint Dive into the research topics of 'Integer programming-based method for completing signaling pathways and its application to analysis of colorectal cancer.'. Together they form a unique fingerprint.

  • Cite this