Exhaustive mining of EST libraries for genes differentially expressed in normal and tumour tissues.
AUTOR(ES)
Schmitt, A O
RESUMO
A four-step procedure for the efficient and systematic mining of whole EST libraries for differentially expressed genes is presented. After eliminating redundant entries from the EST library under investigation (step 1), contigs of maximal length are built upon each remaining EST using about 4 000 000 public and proprietary ESTs (step 2). These putative genes are compared against a database comprising ESTs from 16 different tissues (both normal and tumour affected) to determine whether or not they are differentially expressed (step 3; electronic northern). Fisher's exact test is used to assess the significance of differential expression. In step 4, an attempt is made to characterise the contigs obtained in the assembly through database comparison. A case study of the CGAP library NCI_CGAP_Br1.1, a library made from three (well, moderately, and poorly differentiated) invasive ductal breast tumours (2126 ESTs in total) was carried out. Of the maximal contigs, 139 were found to be significantly (alpha = 0.05) over-expressed in breast tumour tissue, while 13 appeared to be down-regulated.
ACESSO AO ARTIGO
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=148701Documentos Relacionados
- Subtractive libraries for prospecting differentially expressed genes in the soybean under water deficit
- The three mouse multidrug resistance (mdr) genes are expressed in a tissue-specific manner in normal mouse tissues.
- Cloning of the mammalian type II iodothyronine deiodinase. A selenoprotein differentially expressed and regulated in human and rat brain and other tissues.
- Library subtraction of in vitro cDNA libraries to identify differentially expressed genes in scrapie infection.
- Chromogranin A expression in normal and malignant human tissues.
