TY - JOUR
T1 - Network-based approach reveals Y chromosome influences prostate cancer susceptibility
AU - Khosravi, Pegah
AU - Gazestani, Vahid H.
AU - Asgari, Yazdan
AU - Law, Brian
AU - Sadeghi, Mehdi
AU - Goliaei, Bahram
N1 - Publisher Copyright:
© 2014 Elsevier Ltd.
PY - 2014/11/1
Y1 - 2014/11/1
N2 - The human Y chromosome contains a small number of genes that play a critical role in the determination of male-specific organs. Today's advances have provided valuable resources for defining the functions of this chromosome in both normal and cancerous prostates. Despite the fact that generation of high-throughput expression data is becoming usual; the systematic methods of data analysis in a biological context are still an impediment.Here we have shown that constructing co-expression networks using Y-chromosome genes provides an alternative strategy for the detection of new candidate genes involved in prostate cancer. In our approach, independent co-expression networks from normal and cancerous stages are reconstructed using a reverse engineering approach. We then highlight crucial pathways, biological processes, and genes involved in the prostate cancer by analyzing each network individually and in concert. Thus, we have identified 18 critical pathways and processes related to prostate cancer, many of which have previously been shown to be involved in cancer. In particular, we identify 22 Y-chromosome genes putatively linked to prostate cancer, 13 of which have been already verified experimentally.Our novel network-based approach is useful for accurate inference of processes and essential regulators that mediate molecular changes during cancer progression.
AB - The human Y chromosome contains a small number of genes that play a critical role in the determination of male-specific organs. Today's advances have provided valuable resources for defining the functions of this chromosome in both normal and cancerous prostates. Despite the fact that generation of high-throughput expression data is becoming usual; the systematic methods of data analysis in a biological context are still an impediment.Here we have shown that constructing co-expression networks using Y-chromosome genes provides an alternative strategy for the detection of new candidate genes involved in prostate cancer. In our approach, independent co-expression networks from normal and cancerous stages are reconstructed using a reverse engineering approach. We then highlight crucial pathways, biological processes, and genes involved in the prostate cancer by analyzing each network individually and in concert. Thus, we have identified 18 critical pathways and processes related to prostate cancer, many of which have previously been shown to be involved in cancer. In particular, we identify 22 Y-chromosome genes putatively linked to prostate cancer, 13 of which have been already verified experimentally.Our novel network-based approach is useful for accurate inference of processes and essential regulators that mediate molecular changes during cancer progression.
KW - Co-expression networks
KW - Expression data
KW - Prostate cancer
KW - Reverse engineering approach
KW - Y-chromosome genes
UR - http://www.scopus.com/inward/record.url?scp=84908509275&partnerID=8YFLogxK
U2 - 10.1016/j.compbiomed.2014.08.020
DO - 10.1016/j.compbiomed.2014.08.020
M3 - Article
C2 - 25199846
AN - SCOPUS:84908509275
SN - 0010-4825
VL - 54
SP - 24
EP - 31
JO - Computers in Biology and Medicine
JF - Computers in Biology and Medicine
ER -