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 Uni Genes via an in-house Get Uni software package and analyzed the transcriptome overview of these libraries by GOTree Machine (GOTM).
Four precursor lesions of colorectal cancers, adenoma, inflammatory bowel disease (ulcerous colitis and Crohn's disease), juvenile polyp and hyperplastic polyp, were mentioned in the latest edition of WHO tumour classification of digestive tract .
Human Uni Gene database (hs.data, build#181) was also downloaded from NCBI Uni Gene repository .
Get Uni software package (available upon request), an in-house potent computational approach for clustering non-redundant nucleotide into Uni Genes, was written in Perl6.0 and run under Linux (Redhat 9.0) operating system.
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.
Transcriptome maps of these four tissues were constructed via an in-house Get Uni software package.
To our knowledge, the current study is the first transcriptome map of colorectal cancers mining from NCBI EST database (db EST) up to now.This also suggests that the interactions among genes or transcription level of genes really matters in both physiological and pathological processes including carcinogenesis.Hence, an integrated study on the genome-wide gene expression profile is necessary to build the corresponding gene networks underlying complicated diseases, such as colorectal cancers .Each Uni Gene cluster might represent one gene or at least one gene transcript.Thus, Uni Gene was widely applied in gene mapping, large scale gene expression, and gene alternative splicing variants identification.A molecular genetic model of multiple genes and steps was proposed by Vogelstein in 1990 .