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Table 2 Enrichment of conserved cis-regulatory motifs for genes in the FFUF 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
TGACCTY_V$ERR1_Q2 (1081) Genes with promoter regions [-2 kb, 2 kb] around transcription start site containing the motif TGACCTY which matches annotation for ESRRA: estrogen-related receptor alpha 76 1.08E-10
TGACCTTG_V$SF1_Q6 (258) Genes with promoter regions [-2 kb, 2 kb] around transcription start site containing the motif TGRCCTTG which matches annotation for SF1: splicing factor 1 26 2.91E-7
V$SF1_Q6 (264) Genes with promoter regions [-2 kb, 2 kb] around transcription start site containing the motif TGRCCTTG which matches annotation for SF1: splicing factor 1 25 1.49E-6
V$ER_Q6_02 (261) Genes with promoter regions [-2 kb, 2 kb] around transcription start site containing the motif NAGGTCANNNY which matches annotation for ESR1: estrogen receptor 1 22 3.48E-5
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 43 4.31E-5
  1. 1The FFUF gene expression cluster was examined for enrichment of conserved cis-acting regulatory motifs by using the Molecular Signatures Database (MSigDB) and its associated analysis procedures [14]. The database contained motifs conserved in the human, mouse rat and dog genomes. 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 region 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.
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BMC Genomics

ISSN: 1471-2164

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