Construction and analysis of protein-protein interaction networks based on proteomics data of prostate cancer.
Currently, using human prostate cancer (PCa) tissue samples to conduct proteomics research has generated a large amount of data; however, only a very small amount has been thoroughly investigated. In this study, we manually carried out the mining of the full text of proteomics literature that involved comparisons between PCa and normal or benign tissue and identified 41 differentially expressed proteins verified or reported more than 2 times from different research studies. We regarded these proteins as seed proteins to construct a protein-protein interaction (PPI) network. The extended network included one giant network, which consisted of 1,264 nodes connected via 1,744 edges, and 3 small separate components. The backbone network was then constructed, which was derived from key nodes and the subnetwork consisting of the shortest path between seed proteins. Topological analyses of these networks were conducted to identify proteins essential for the genesis of PCa. Solute carrier family 2 (facilitated glucose transporter), member 4 (SLC2A4) had the highest closeness centrality located in the center of each network, and the highest betweenness centrality and largest degree in the backbone network. Tubulin, beta 2C (TUBB2C) had the largest degree in the giant network and subnetwork. In addition, using module analysis of the whole PPI network, we obtained a densely connected region. Functional annotation indicated that the Ras protein signal transduction biological process, mitogen-activated protein kinase (MAPK), neurotrophin and the gonadotropin-releasing hormone (GnRH) signaling pathway may play an important role in the genesis and development of PCa. Further investigation of the SLC2A4, TUBB2C proteins, and these biological processes and pathways may therefore provide a potential target for the diagnosis and treatment of PCa.
Department of Urology, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei 063000, P.R. China.
Chen
C
Chen
Department of Modern Technology and Education Center, North China University of Science and Technology and International Science and Technology Cooperation Base of Geriatric Medicine, Tangshan, Hebei 063000, P.R. China.
Hong
H
Shen
Department of Urology, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei 063000, P.R. China.
Li-Guo
LG
Zhang
Department of Urology, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei 063000, P.R. China.
Jian
J
Liu
Tianjin Binhai New Area Hangu No. 1 High School, Tianjin 300480, P.R. China.
Xiao-Ge
XG
Cao
Department of Urology, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei 063000, P.R. China.
An-Liang
AL
Yao
Department of Urology, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei 063000, P.R. China.
Shao-San
SS
Kang
Department of Urology, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei 063000, P.R. China.
Wei-Xing
WX
Gao
Department of Urology, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei 063000, P.R. China.
Hui
H
Han
Department of Urology, North China University of Science and Technology Affiliated Hospital, Tangshan, Hebei 063000, P.R. China.
Feng-Hong
FH
Cao
Medical Research Center, North China University of Science and Technology and International Science and Technology Cooperation Base of Geriatric Medicine, Tangshan, Hebei 063000, P.R. China.
Zhi-Guo
ZG
Li
D016022:Case-Control Studies; D057225:Data Mining; D030541:Databases, Genetic; D015972:Gene Expression Regulation, Neoplastic; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D051275:Glucose Transporter Type 4 / Q000235:genetics / Q000378:metabolism; D007987:Gonadotropin-Releasing Hormone / Q000235:genetics / Q000378:metabolism; D006801:Humans; D008297:Male; D020928:Mitogen-Activated Protein Kinases / Q000235:genetics / Q000378:metabolism; D058977:Molecular Sequence Annotation; D009414:Nerve Growth Factors / Q000235:genetics / Q000378:metabolism; D011467:Prostate / Q000378:metabolism / Q000473:pathology; D011471:Prostatic Neoplasms / Q000175:diagnosis* / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D025941:Protein Interaction Mapping; D020033:Protein Isoforms / Q000235:genetics / Q000378:metabolism; D040901:Proteomics; D015398:Signal Transduction; D014404:Tubulin / Q000235:genetics / Q000378:metabolism; D018631:ras Proteins / Q000235:genetics / Q000378:metabolism
D051275:Glucose Transporter Type 4; D009414:Nerve Growth Factors; D020033:Protein Isoforms; C495692:SLC2A4 protein, human; D014404:Tubulin; D007987:Gonadotropin-Releasing Hormone; D020928:Mitogen-Activated Protein Kinases; D018631:ras Proteins