Nucleic Acids Research, Vol 27, Issue 21 4251-4260, Copyright © 1999 by Oxford University Press
AO Schmitt, T Specht, G Beckmann, E Dahl, CP Pilarsky, B Hinzmann and A Rosenthal
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.
ARTICLES
Exhaustive mining of EST libraries for genes differentially expressed in normal and tumour tissues
metaGen Gesellschaft fur Genomforschung mbH, Ihnestrasse 63, D-14195 Berlin, Germany. armin.schmitt@metagen.de
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