Table 2

Genome-wide occurrences of each candidate motif within coding and upstream regions

Upstream

Coding



Motif

Number of genes

Number of motifs

Number of motifs/10 kb

Number of genes

Number of motifs

Number of motifs/10 kb

p-value


GLYCA

885

2608

2.23

956

3618

2.14

0.0538

GLYCB

418

982

0.84

201

531

0.31

< 0.001

MICA

734

2010

1.72

435

1019

0.6

< 0.001

MICB

223

637

0.54

290

769

0.46

0.0026

NTBA

658

1959

1.67

418

1495

0.89

< 0.001

NTBB

1100

2548

2.18

359

852

0.5

< 0.001

RPA

368

581

0.49

145

262

0.15

< 0.001

RPB

1311

4030

3.45

810

2648

1.57

< 0.001


The number of occurrences of each motif and the genes containing them in the whole genome Motif density (number of motifs per 10 kb) was computed using MAST to search position weight matrix profiles of each motif against custom built databases (upstream regions (11,685,162 bp) and coding regions (16,862,741 bp)).

Mullapudi et al. Genome Biology 2009 10:R34   doi:10.1186/gb-2009-10-4-r34

Open Data