TY - JOUR
T1 - Integer programming-based method for completing signaling pathways and its application to analysis of colorectal cancer.
AU - Tamura, Takeyuki
AU - Yamanishi, Yoshihiro
AU - Tanabe, Mao
AU - Goto, Susumu
AU - Kanehisa, Minoru
AU - Horimoto, Katsuhisa
AU - Akutsu, Tatsuya
PY - 2010
Y1 - 2010
N2 - 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.
AB - 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.
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U2 - 10.1142/9781848166585_0016
DO - 10.1142/9781848166585_0016
M3 - Article
C2 - 22081600
AN - SCOPUS:84870175276
VL - 24
SP - 193
EP - 203
JO - Genome informatics. International Conference on Genome Informatics
JF - Genome informatics. International Conference on Genome Informatics
SN - 0919-9454
ER -