Simple Shared Motifs (SSM) in conserved region of promoters: a new approach to identify co-regulation patterns

BMC Bioinformatics

Table 3 Comparison between co-expressed genes and not co-expressed genes in CEXlists.

cp-value threshold	0.05	0.01	0.005	0.001
ACTA1	1.601	1.168	1.187	2.215
DES	1.366*	1.285	0.659	0.000
SPG7_HUMAN	2.078*	1.957*	1.846*	2.078*
SMAD2	1.877*	1.414*	1.297	1.361
SMAD3	1.363*	1.354	1.206	0.000
ADAM12	0.803	0.965	1.003	0.777
C9orf3	1.662*	1.400*	1.443*	1.381
APLP1	0.879	1.228	1.380	0.525
WISP2	1.311	0.559	0.000	0.000
SLC9A3R2	1.079	1.083	1.380	2.673
MNT	1.789*	1.893*	1.426	0.855
ALDOA_HUMAN	1.008	0.986	0.759	0.000
DEFA3	0.974	1.576	0.000	0.000
AURKA	1.274	1.247	0.687	1.145
AURKB	1.999*	2.263*	2.249*	2.353*
FSHR	0.000	0.000	0.000	0.000
LRRTM1	0.871	0.000	0.000	0.000
AURKC_HUMAN	0.556*	0.515	1.180	0.000
MRGPRF	1.559	1.697	1.300	0.000
Q658L9_HUMAN	0.000	0.000	0.000	0.000
DUSP12	1.446*	2.139*	1.555	1.993
EEF1D	1.649*	1.515*	1.634*	1.348
ALB	1.953*	1.877*	1.769*	0.972
C6orf62	1.930*	1.756*	1.926*	1.626
CLK3	0.759*	0.970	0.558	1.953

For four cp-value thresholds, t, the table compares Gemma genes present in CEXlists (cp-value <t) and Gemma genes not present in CEXlists (cp-value >t). For genes present or not in CEXlists, the ratio of genes in Gemma per gene is computed. The final value in the Table is the ratio of the result obtained for a CEXlist and the genes out of it. Thus, a value above one indicates an enrichment of co-expressed genes in a CEXlist. Fisher tests were used to compare the distribution of Gemma genes in and out of CEXlists, a "*" indicates a distribution significantly different (p < 0.05).

ISSN: 1471-2105