title: Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online).
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Institute of Information Science, Academia Sinica, Taipei 115, Taiwan, ROC. chunnan@iis.sinica.edu.tw <chunnan@iis.sinica.edu.tw>
authors.forename: Chun-Nan
authors.initials: CN
authors.lastname: Hsu
authors.forename: Jin-Mei
authors.initials: JM
authors.lastname: Lai
authors.forename: Chia-Hung
authors.initials: CH
authors.lastname: Liu
authors.forename: Huei-Hun
authors.initials: HH
authors.lastname: Tseng
authors.forename: Chih-Yun
authors.initials: CY
authors.lastname: Lin
authors.forename: Kuan-Ting
authors.initials: KT
authors.lastname: Lin
authors.forename: Hsu-Hua
authors.initials: HH
authors.lastname: Yeh
authors.forename: Ting-Yi
authors.initials: TY
authors.lastname: Sung
authors.forename: Wen-Lian
authors.initials: WL
authors.lastname: Hsu
authors.forename: Li-Jen
authors.initials: LJ
authors.lastname: Su
authors.forename: Sheng-An
authors.initials: SA
authors.lastname: Lee
authors.forename: Chang-Han
authors.initials: CH
authors.lastname: Chen
authors.forename: Gen-Cher
authors.initials: GC
authors.lastname: Lee
authors.forename: D T
authors.initials: DT
authors.lastname: Lee
authors.forename: Yow-Ling
authors.initials: YL
authors.lastname: Shiue
authors.forename: Chang-Wei
authors.initials: CW
authors.lastname: Yeh
authors.forename: Chao-Hui
authors.initials: CH
authors.lastname: Chang
authors.forename: Cheng-Yan
authors.initials: CY
authors.lastname: Kao
authors.forename: Chi-Ying F
authors.initials: CY
authors.lastname: Huang
mesh_terms: D006528:Carcinoma, Hepatocellular / Q000235:genetics*; D004690:Encyclopedias as Topic; D020869:Gene Expression Profiling / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics; D053263:Gene Regulatory Networks / Q000235:genetics*; D006801:Humans; D008113:Liver Neoplasms / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods