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Table 3 Enrichment of conserved cis-regulatory motifs for genes in the FFDF cluster1

From: A gene network switch enhances the oxidative capacity of ovine skeletal muscle during late fetal development

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
  1. 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.
  2. 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.