Table 3.
Enrichment of conserved cis-regulatory motifs for genes in the FFDF cluster1
| Gene motif (number of genes) | Description | Genes in overlap | p-value2 |
|---|---|---|---|
| CTTTGT_V$LEF1_Q (22036) | Genes with promoter regions [-2 kb, 2 kb] around transcription start site containing the motif CTTTGT which matches annotation for LEF1: lymphoid enhancer-binding factor 1 | 185 | 7.12E-11 |
| TTTGTAG,MIR-520D (337) | Targets of MicroRNA TTTGTAG, MIR-520D | 48 | 5.19E-09 |
| GTACTGT,MIR-101 (257) | Targets of MicroRNA GTACTGT, MIR-101 | 38 | 7.22E-08 |
| GTGCCAA,MIR-96 (304) | Targets of MicroRNA GTGCCAA,MIR-96 | 42 | 1.04E-07 |
| ACCAAAG,MIR-9 (501) | Targets of MicroRNA ACCAAAG, MIR-9 | 59 | 1.05E-07 |
| AACTTT_UNKNOWN (1963) | Genes with promoter regions [-2 kb, 2 kb] around transcription start site containing motif AACTTT. Motif does not match any known transcription factor | 166 | 1.06E-07 |
| CTTTGTA,MIR-52 (437) | Targets of MicroRNA CTTTGTA, MIR-524 | 52 | 4.17E-07 |
| ACACTGG,MIR-199A,MIR-199B (160) | Targets of MicroRNA ACACTGG, MIR-199A, MIR-199B | 26 | 1.29E-06 |
| CATTGTYY_V$SOX9_B1 (370) | Genes with promoter regions [-2 kb, 2 kb] around transcription start site containing the motif CATTGTYY which matches annotation for SOX9: SRY (sex determining region Y)-box 9 (campomelic dysplasia, autosomal sex-reversal) | 45 | 1.32E-06 |
| CAGTATT,MIR-200B,MIR-200C,MIR-429 (470) | Targets of MicroRNA CAGTATT, MIR-200B, MIR-200C, MIR-429 | 53 | 1.60E-06 |
| TGCCTTA,MIR-124A (556) | Targets of MicroRNA TGCCTTA, MIR-124A | 59 | 2.91E-06 |
| ATACTGT,MIR-144 (199) | Targets of MicroRNA ATACTGT, MIR-144 | 29 | 3.05E-06 |
| ATATGCA,MIR-448 (212) | Targets of MicroRNA ATATGCA, MIR-448 | 30 | 3.77E-06 |
| TGTTTAC,MIR-30A-5P,MIR-30C,MIR-30D,MIR-30B,MIR-30E-5P (582) | Targets of MicroRNA TGTTTAC, MIR-30A-5P, MIR-30C, MIR-30D, MIR-30B, MIR-30E-5P | 60 | 5.75E-06 |
| V$SOX9_B1 (241) | Genes with promoter regions [-2 kb, 2 kb] around transcription start site containing the motif NNNNAACAATRGNN which matches annotation for SOX9: SRY (sex determining region Y)-box 9 (campomelic dysplasia, autosomal sex-reversal) | 32 | 6.91E-06 |
| GTGCAAT,MIR-25,MIR-32,MIR-92,MIR-363,MIR-367 (311) | Targets of MicroRNA GTGCAAT, MIR-25, MIR-32, MIR-92, MIR-363, MIR-367 | 38 | 7.23E-06 |
| TTGTTT_V$FOXO4_01 (2149) | Genes with promoter regions [-2 kb, 2 kb] around transcription start site containing the motif TTGTTT which matches annotation for MLLT7: myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 7 | 168 | 8.87E-06 |
| TGAGATT,MIR-216 (107) | Targets of MicroRNA TGAGATT, MIR-216 | 19 | 8.87E-06 |
| GCACCTT,MIR-18A,MIR-18B (119) | Targets of MicroRNA GCACCTT, MIR-18A, MIR-18B | 20 | 1.20E-05 |
1The FFDF gene expression cluster was examined for enrichment of conserved cis-acting regulatory motifs using the Molecular Signatures Database (MSigDB) [14]. The conserved transcription factor binding sites and anonymous conserved motifs were restricted to a sequence window corresponding to ± 2 kb of the transcription start site while the conserved miRNA recognition sites were restricted to the 3' untranslated regions of the genes in this cluster.
2P-values are uncorrected for multiple testing and were calculated as described [14]. Only motifs with p-values < 0.05 after Bonferonni correction for multiple testing are shown.