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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.