Database
TFCONES: A database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements
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* Corresponding author: Byrappa Venkatesh mcbbv@imcb.a-star.edu.sg
Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
BMC Genomics 2007, 8:441 doi:10.1186/1471-2164-8-441
Published: 29 November 2007Additional files
Additional data file 1:
Human TF-encoding genes with more than one ortholog in fugu genome.
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Additional data file 2:
Clusters of TF-encoding genes in the human genome.
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Additional data file 3:
Clusters of TF-encoding genes in the mouse genome.
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Additional data file 4:
Clusters of TF-encoding genes in the fugu genome.
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Additional data file 5:
Conserved clusters of human, mouse and fugu TF-encoding genes. An asterisk indicates a human TF-encoding gene that has no ortholog in fugu but is located in a Hox conserved syntenic block.
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Additional data file 6:
Distribution of lengths of (A) human-mouse and (B) human-fugu CNEs.
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Additional data file 7:
Top twenty TF-encoding genes associated with the highest density of human-fugu CNEs. For genes that are part of conserved clusters, we averaged out the number or length of CNEs present in the whole cluster over the number of genes in that cluster. CNE density is defined as the number of bases located in CNEs per 100 bp of non-repetitive noncoding sequence in the longest orthologous fugu gene locus.
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Additional data file 8:
Significantly over-represented and under-represented Gene Ontology terms (P < 0.01) of CNE-associated human TF-encoding genes. Group A denotes 385 of 389 CNE-associated TF-encoding genes with Gene Ontology annotation, while Group B denotes 804 of 816 orthologous TF-encoding genes with Gene Ontology annotation. P-values marked with a negative sign denote significant depletion. The analysis was carried out using GOstat (Beissbarth and Speed 2004).
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