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Table 3 Interpretation of over-represented motifs with respect to published evidence. (See footnote for definition of the categories.)

From: Predictive screening for regulators of conserved functional gene modules (gene batteries) in mammals

I: Expected cases

Number

Function / expression

Transcription factors

4

lymphocytes

Irf1/Irf2/ISRE, NFKB [34-36]

6

liver

HNF-1 alpha and beta, HNF4 alpha [32, 59-61]

9,12

cardiac and skeletal muscle

MyoD/E47, MEF2 family factors, SRF [4, 6, 48]

15

erythroid cells

GATA-1 [62]

16

B lymphocytes

Spi-B, Oct-I* [37, 40, 63]

22

cell cycle

E2F family factors [49, 50]

40

smooth muscle

SRF [5, 64]

II: Extended

3

neural tissue

NRSF [65]

5

testis

SOX17, RFX2 (RFX1-RFX3) [41-43]

6

liver

ARP-1/COUP-TF, PPARγ [66, 67]

13

ER

XBP-1 [68]

15,16

erythroid cells/ B cells

AREB6* [38]

17

kidney

HNF-4alpha, HNF-1-alpha/beta [69, 70]

III: Unexpected

1

protein synthesis

NRF and ETS family factors

2

oocyte

E2F and ETS family factors

6

liver

ROR-alpha

8

ECM

Pax4

9

cardiac muscle

TALE family factors TGIF and MEIS1

13

ER

NRF and ETS family factors

24

pancreas

E47

30

small intestine

HNF4-alpha and GATA factors

44

retina/eye

Ik-2

45

testis

cap

  1. Criteria for inclusion in the different groups: I. Existing evidence of co-regulation of cluster member by the factor, and/or a mutant mouse phenotype that affects differentiation of the cell type. II. Evidence of the factor acting on a limited number of genes in the tissue. Evidence of the transcription factor being expressed in the tissue. III. No or limited evidence in the literature. * = Detected at 20% FDR.