Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online)
Resource
Bmc Bioinformatics, vol.8(66), 2007
Journal
BMC Bioinformatics
Pages
66
Date Issued
2007
Date
2007
Author(s)
Chun-Nan Hsu
Jin-Mei Lai
Chia-Hung Liu
Huei-Hun Tseng
Chih-Yun Lin
Kuan-Ting Lin
Hsu-Hua Yeh
Ting-Yi Sung
Wen-Lian Hsu
Li-Jen Su
Sheng-An Lee
Chang-Han Chen
Gen-Cher Lee
D. T. Lee
Yow-Ling Shiue
Chang-Wei Yeh
Chao-Hui Chang
Cheng-Yan Kao
Chi-Ying Huang
Abstract
Background: The significant advances in microarray and proteomics analyses have resulted in an exponential increase in potential new targets and have promised to shed light on the identification of disease markers and cellular pathways. We aim to collect and decipher the HCC-related genes at the systems level. Results: Here, we build an integrative platform, the Encyclopedia of Hepatocellular Carcinoma genes Online, dubbed EHCO http://ehco.iis.sinica.edu.tw, to systematically collect, organize and compare the pileup of unsorted HCC-related studies by using natural language processing and softbots. Among the eight gene set collections, ranging across PubMed, SAGE, microarray, and proteomics data, there are 2,906 genes in total; however, more than 77% genes are only included once, suggesting that tremendous efforts need to be exerted to characterize the relationship between HCC and these genes. Of these HCC inventories, protein binding represents the largest proportion (?25%) from Gene Ontology analysis. In fact, many differentially expressed gene sets in EHCO could form interaction networks (e.g. HBV-associated HCC network) by using available human protein-protein interaction datasets. To further highlight the potential new targets in the inferred network from EHCO, we combine comparative genomics and interactomics approaches to analyze 120 evolutionary conserved and overexpressed genes in HCC. 47 out of 120 queries can form a highly interactive network with 18 queries serving as hubs. Conclusion: This architectural map may represent the first step toward the attempt to decipher the hepatocarcinogenesis at the systems level. Targeting hubs and/or disruption of the network formation might reveal novel strategy for HCC treatment. ? 2007 Hsu et al; licensee BioMed Central Ltd.
SDGs
Other Subjects
Comparative genomics; Differentially expressed gene; Exponential increase; Hepatocellular carcinoma; Integrative platforms; Interaction networks; NAtural language processing; Protein-protein interactions; Active networks; Biochemistry; Molecular biology; Natural language processing systems; Proteins; Genes; book; DNA microarray; gene expression profiling; gene expression regulation; gene regulatory network; genetics; human; liver cell carcinoma; liver tumor; procedures; Carcinoma, Hepatocellular; Encyclopedias as Topic; Gene Expression Profiling; Gene Expression Regulation, Neoplastic; Gene Regulatory Networks; Humans; Liver Neoplasms; Oligonucleotide Array Sequence Analysis
Type
journal article
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