Exhaustive mining of EST libraries for genes differentially expressed in normal and tumour tissues

A four-step procedure for the efficient and systematic mining of whole EST libraries for differentially expressed genes is presented. After eliminatin g redundant entries from the EST library under investigation (step 1), cont igs of maximal length are built upon each remaining EST using about 4000000 public and proprietary ESTs (step 2), These putative genes are compared ag ainst a database comprising ESTs from 16 different tissues (both normal and tumour affected) to determine whether or not they are differentially expre ssed (step 3; electronic northern). Fisher's exact test is used to assess t he significance of differential expression. In step 4, an attempt is made t o characterise the contigs obtained in the assembly through database compar ison. 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 w ere found to be significantly (alpha = 0.05) overexpressed in breast tumour tissue, while 13 appeared to be down-regulated.