A transcriptome anatomy of human colorectal cancers

BMC Cancer
Bingjian LüJian Chen

Abstract

Accumulating databases in human genome research have enabled integrated genome-wide study on complicated diseases such as cancers. A practical approach is to mine a global transcriptome profile of disease from public database. New concepts of these diseases might emerge by landscaping this profile. In this study, we clustered human colorectal normal mucosa (N), inflammatory bowel disease (IBD), adenoma (A) and cancer (T) related expression sequence tags (EST) into UniGenes via an in-house GetUni software package and analyzed the transcriptome overview of these libraries by GOTree Machine (GOTM). Additionally, we downloaded UniGene based cDNA libraries of colon and analyzed them by Xprofiler to cross validate the efficiency of GetUni. Semi-quantitative RT-PCR was used to validate the expression of beta-catenin and. 7 novel genes in colorectal cancers. The efficiency of GetUni was successfully validated by Xprofiler and RT-PCR. Genes in library N, IBD and A were all found in library T. A total of 14,879 genes were identified with 2,355 of them having at least 2 transcripts. Differences in gene enrichment among these libraries were statistically significant in 50 signal transduction pathways and Pfam protein domains by GOTM analys...Continue Reading

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Citations

Aug 24, 2011·Journal of Gastroenterology·Miho Sashikawa KimuraKentaro Sugano
Oct 15, 2011·American Journal of Physiology. Gastrointestinal and Liver Physiology·S RamalingamS T Magness
Sep 28, 2013·Gut and Liver·Hirotsugu SakamotoKentaro Sugano
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Sep 25, 2018·European Journal of Cancer Prevention : the Official Journal of the European Cancer Prevention Organisation (ECP)·Weisong XuZhenming Ge
Jan 13, 2019·Head & Neck·Antoine SchernbergYungan Tao
Jul 1, 2008·Journal of Nuclear Medicine : Official Publication, Society of Nuclear Medicine·Robert J GilliesRobert A Gatenby

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Methods Mentioned

BETA
profiler
PCR

Software Mentioned

Biocarta
Linux
Prodomains
GEne SeT AnaLysis Toolkit
UniGene
Xprofiler
GOTree
GeneOntology
Excel
GetUni

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