Significance Test Of Gene Expression Profiles (SoGEP)
Significance test of gene expression profiles between a pair of the cDNA libraries was performed using Audic¡¯s (
Audic and Claverie, 1997) and Susko¡¯s test (
Susko and Roger, 2004) program. Since there was a multiple test problem, Bonferroni and Benjamini corrections were applied for the Audic¡¯s and Susko¡¯s test, respectively. As described in the previous papers (Shin et al., 2005, Shin et al., 2005, Han et al.,in preperation), the chicken EST data of each library were processed and assembled using mainly Phred (
Ewing & Green, 1998) and CAP3 (
Huang & Madan, 1999) programs. Number of a set of ESTs assembled into a contig is considered as the number of read of the gene. A singlet is considered as single read of the gene. Expression comparison of the gene was performed with the number of reads of the gene of two libraries. The stand alone Blast program, blastn, was used to cluster a pair of sequences between two library sequences with minimum 200 bp and 95% identity.
*SEE method of Statistical analysis of gene expression profiles
About corrected significance level
We have different significance level for each pair of library and two kind of test. It is because of different number of multiple test for each pair of library and different correction method for each test, Bonferroni and Benjamini corrections for the Audic's and Susko's test.