title: Integration of gene chip and topological network techniques to screen a candidate biomarker gene (CBG) for predication of the source water carcinogenesis risks on mouse Mus musculus.
abstract: Screening of a candidate biomarker gene (CBG) to predicate the carcinogenesis risks in the Yangtze River source of drinking water in Nanjing area (YZR-SDW-NJ) on mouse (Mus musculus) was conducted in this research. The effects of YZR-SDW-NJ on the genomic transcriptional expression levels were measured by the GeneChip(®) Mouse Genome and data treated by the GO database analysis. The 298 genes discovered as the differently expressed genes (DEGs) were down-regulated and their values were ≤-1.5-fold. Of the 298 DEGs, 25 were cancer-related genes selected as the seed genes to build a topological network map with Genes2Networks software, only 7 of them occurred at the constructed map. Smad2 gene was at the constructed map center and could be identified as a candidate biomarker gene (CBG) primarily which involves the genesis and development of colorectal, leukemia, lung and prostate cancers directly. Analysis of the gene signal pathway further approved that smad2 gene had the relationships closely to other 16 cancer-related genes and could be used as a CBG to indicate the carcinogenic risks in YZR-SDW-NJ. The data suggest that integration of gene chip and network techniques may be a way effectively to screen a CBG. And the parameter values for further judgment of the CBG through signal pathway relationship analysis also will be discussed.
authors.affiliation: State Key Laboratory of Pollution Control & Resource Reuse and School of the Environment, Nanjing University, 163# Xianlindadao, Nanjing, 210046, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Sun
authors.forename: Shupei
authors.initials: S
authors.lastname: Cheng
authors.forename: Aimin
authors.initials: A
authors.lastname: Li
authors.forename: Rui
authors.initials: R
authors.lastname: Zhang
authors.forename: Bing
authors.initials: B
authors.lastname: Wu
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhang
authors.forename: Xuxiang
authors.initials: X
authors.lastname: Zhang
mesh_terms: D000818:Animals; D015415:Biomarkers / Q000378:metabolism*; D002274:Carcinogens, Environmental / Q000633:toxicity*; D004784:Environmental Monitoring; D005618:Fresh Water / Q000737:chemistry; D015870:Gene Expression / Q000187:drug effects; D020869:Gene Expression Profiling / Q000379:methods*; D008297:Male; D051379:Mice; D008813:Mice, Inbred ICR; D020411:Oligonucleotide Array Sequence Analysis; D018570:Risk Assessment / Q000379:methods; D051899:Smad2 Protein / Q000235:genetics; D014874:Water Pollutants, Chemical / Q000032:analysis / Q000633:toxicity*; D014881:Water Supply / Q000032:analysis
chemical_list: D015415:Biomarkers; D002274:Carcinogens, Environmental; D051899:Smad2 Protein; D014874:Water Pollutants, Chemical