Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online).
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.
Hsu
Chun-Nan
CN
Institute of Information Science, Academia Sinica, Taipei 115, Taiwan, ROC. chunnan@iis.sinica.edu.tw <chunnan@iis.sinica.edu.tw>
Lai
Jin-Mei
JM
Liu
Chia-Hung
CH
Tseng
Huei-Hun
HH
Lin
Chih-Yun
CY
Lin
Kuan-Ting
KT
Yeh
Hsu-Hua
HH
Sung
Ting-Yi
TY
Hsu
Wen-Lian
WL
Su
Li-Jen
LJ
Lee
Sheng-An
SA
Chen
Chang-Han
CH
Lee
Gen-Cher
GC
Lee
D T
DT
Shiue
Yow-Ling
YL
Yeh
Chang-Wei
CW
Chang
Chao-Hui
CH
Kao
Cheng-Yan
CY
Huang
Chi-Ying F
CY
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