Table 1

Major functional groups overrepresented among state-change genes and corresponding overrepresented TREs. The groups are presented according to the order of significance identified by DAVID. Overrepresented TREs marked in bold are either "off-on" TFs or increased their level; regular – not present in Panomics set; italics – not present under either condition.

Functional group

Number of genes

Major Gene Ontologies

Overrepresented TREs

Gene expression, RNA processing and protein synthesis

12

73

Transcription factors

7

5

Translation initiation factors

v-Maf, SOX-9, FOXJ2, CP2, HFH-3, Elk-1, NRF-2, AREB6

9

6

RNA processing – ribosome biogenesis

NGFI-C, GR, HNF-4, YY1, Elk-1, NRF-2, v-Myb, NF-κB, TATA, c-Myc

11

8

Zinc binding

MIF-1, Tax/CREB

Cell signaling proteins

3

16

G-protein receptor

2

7

GABA receptor/ion channels

N-Myc

6

9

Ion channels, K

Post-translational modification and regulatory control

8

5

Glycosyltransferases

10

28

Kinases

CDP, CR3+HD, CRE-BP1, CCAAT

Cell-ECM adhesion

4

4

Cadherins

HNF-3β, CDP CR3+HD, E2, NF-κB, USF

Immune function associated with suppression of effector T-cells

1

15

Transmembrane immunoglobulin-like proteins

NF-κB, v-Maf, RSRFC4, FOXJ2, AP-1, Pax-4, USF, CDP, Brn-2

Transmembrane proteins of unknown significance

5

14

Transmembrane proteins

AP-1

Dozmorov et al. BMC Bioinformatics 2008 9(Suppl 9):S4   doi:10.1186/1471-2105-9-S9-S4