RegulonDB Gene Evolutionary Conservation
Evolutionary conservation of the TrpR regulatory interaction in mtr orthologous genes

In general an interaction is conserved if there is a significant overrepresentation of TFBSs in the set of orthologous promoters of the target gene. The set of orthologous promoter for mtr was scanned with the annotated matrix for TrpR. In order to avoid bias due to an excessive representation of close genomes (i.e. several E. coli genomes) we masked the regulatory sequences that were too similar. Overrepresentation is calculated based on the binomial distribution, comparing the observed scores vs. the expected ones for the masked sequence set.


Ortholog predicted binding sitesmtr_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_TrpR_sites.tab
Ortholog predicted binding sites graphmtr_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_TrpR_sites.jpg
genesmtr_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_query_genes.tab
Query sequencemtr_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_query_seq.fasta
Orthologsmtr_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_ortho_bbh.tab
ortho sequencesmtr_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_ortho_seq.fasta
Purged sequencesmtr_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_ortho_seq_purged.fasta
Occ sigmtr_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_TrpR_occ_sig.tab
Occ sig graphmtr_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_TrpR_occ_sig.jpg
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Occ freq graphmtr_Escherichia_coli_K_12_substr__MG1655_uid57779_Gammaproteobacteria_TrpR_occ_freq.jpg
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