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RegTransBase specifications

Information


Unique identifier OMICS_03210
Name RegTransBase
Restrictions to use None
Maintained No
Wikipedia https://en.wikipedia.org/wiki/RegTransBase

Maintainer


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Publications for RegTransBase

RegTransBase citations

 (11)
call_split

Lactobacillus oligofermentans glucose, ribose and xylose transcriptomes show higher similarity between glucose and xylose catabolism induced responses in the early exponential growth phase

2016
BMC Genomics
PMCID: 4972977
PMID: 27487841
DOI: 10.1186/s12864-016-2840-x
call_split See protocol

[…] uite. Selected enriched motifs were used to query the TFBS database using the tomtom tool (genome background HMM was taken into account). The database comprised the combination of the PRODORIC [] and RegTransBase [] databases that contain literature-based and manually-curated prokaryotic TFBS. For verification, Lactobacillaceae-specific TFBS profiles of CcpA, XylR, RbsR and Rex, as well as the Bac […]

library_books

A Bioinformatics Analysis Reveals a Group of MocR Bacterial Transcriptional Regulators Linked to a Family of Genes Coding for Membrane Proteins

2016
PMCID: 4944035
PMID: 27446613
DOI: 10.1155/2016/4360285

[…] ments. Candidate DNA-binding sites were submitted to the TOMTOM and FIMO tools of the MEME suite []. TOMTOM compares TFBSs with the known motifs contained in the databases Prodoric release 8.9 [] and RegTransBase release version 7 [] and displays the alignments to significant matches (E-value threshold < 0.01). With the aim of checking whether the TFBSs are present in single copy through the genom […]

library_books

Cis regulatory motifs and antisense transcriptional control in the apicomplexan Theileria parva

2016
BMC Genomics
PMCID: 4761415
PMID: 26896950
DOI: 10.1186/s12864-016-2444-5

[…] prehensive eukaryotic motif databases JASPAR [] and TRANSFAC [], FLY [], FlyReg [] and Agris [], AthaMap [], PLACE [], Uniprobe [], other yeast motifs [, ], as well as the prokaryotic motif databases RegTransBase [] and DPInteract []. The Smith-Waterman local alignment method with a similarity score defined by Pearson’s correlation coefficient estimated motif similarity. The STAMP motif phylogenet […]

library_books

Transcription factor MrpC binds to promoter regions of hundreds of developmentally regulated genes in Myxococcus xanthus

2014
BMC Genomics
PMCID: 4320627
PMID: 25515642
DOI: 10.1186/1471-2164-15-1123

[…] nding sites if present. The top 500 ranked peaks and the smaller dataset partitions were searched using MEME [] to detect any overrepresented motifs. The motif of interest was compared with motifs in RegTransBase [] using TOMTOM [] to identify similarity to known transcription factor binding motifs. […]

library_books

A comparison of key aspects of gene regulation in Streptomyces coelicolor and Escherichia coli using nucleotide resolution transcription maps produced in parallel by global and differential RNA sequencing

2014
Mol Microbiol
PMCID: 4681348
PMID: 25266672
DOI: 10.1111/mmi.12810

[…] s I sites (see ). The finding that not all TSSs identified previously by RNA-seq (Vockenhuber et al., ) or indeed conventional mapping approaches, such as S1 mapping and primer extension (recorded in RegTransBase) (Cipriano et al., ), were identified here is not surprising given the physiological and regulatory complexity of streptomycetes (Strohl, ; Chater, ; van Wezel and McDowall, ). There are […]

library_books

A high resolution network model for global gene regulation in Mycobacterium tuberculosis

2014
Nucleic Acids Res
PMCID: 4191388
PMID: 25232098
DOI: 10.1093/nar/gku777

[…] Motifs (e-value < 1) from the cholesterol utilization biclusters were run against the ‘Prokaryotes–RegTransBase v4′ database using TOMTOM (). The regulators with significant P-values (P ≤ 0.01) were searched for sequence similarity against the MTB genome using blastn (nucleotide query/nucleotide da […]

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RegTransBase institution(s)
Institute for Information Transmission Problems, RAS. Bolshoi Karetny pereulok, Moscow, Russia; Lawrence Berkeley National Laboratory, CA, USA; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA; Howard Hughes Medical Institute, MD, USA; Department of Bioengineering, University of California Berkeley, CA, USA; Virtual Institute of Microbial Stress and Survival, Berkeley CA, USA; Faculty of Bioengineering and Bioinformatics, Moscow State University Vorobievy, Moscow, Russia; State Research Center GosNIIGenetika.Dorozhny proezd, Moscow, Russia; Department of Energy Joint Genome Institute,Walnut Creek, CA, USA

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