Literature DB >> 26013488

Every Site Counts: Submitting Transcription Factor-Binding Site Information through the CollecTF Portal.

Ivan Erill1.   

Abstract

Experimentally verified transcription factor-binding sites represent an information-rich and highly applicable data type that aptly summarizes the results of time-consuming experiments and inference processes. Currently, there is no centralized repository for this type of data, which is routinely embedded in articles and extremely hard to mine. CollecTF provides the first standardized resource for submission and deposition of these data into the NCBI RefSeq database, maximizing its accessibility and prompting the community to adopt direct submission policies.
Copyright © 2015, American Society for Microbiology. All Rights Reserved.

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Year:  2015        PMID： 26013488      PMCID： PMC4518829          DOI： 10.1128/JB.00031-15

Source DB:  PubMed          Journal:  J Bacteriol        ISSN： 0021-9193            Impact factor:   3.490


  30 in total

1.  The EMBL nucleotide sequence database.

Authors:  W Baker; A van den Broek; E Camon; P Hingamp; P Sterk; G Stoesser; M A Tuli
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

3.  Network motifs in the transcriptional regulation network of Escherichia coli.

Authors:  Shai S Shen-Orr; Ron Milo; Shmoolik Mangan; Uri Alon
Journal:  Nat Genet       Date:  2002-04-22       Impact factor: 38.330

4.  The GenBank nucleic acid sequence database.

Authors:  C Burks; J W Fickett; W B Goad; M Kanehisa; F I Lewitter; W P Rindone; C D Swindell; C S Tung; H S Bilofsky
Journal:  Comput Appl Biosci       Date:  1985-12

5.  RegTransBase--a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes.

Authors:  Michael J Cipriano; Pavel N Novichkov; Alexey E Kazakov; Dmitry A Rodionov; Adam P Arkin; Mikhail S Gelfand; Inna Dubchak
Journal:  BMC Genomics       Date:  2013-04-02       Impact factor: 3.969

6.  Analysis of the SOS response of Vibrio and other bacteria with multiple chromosomes.

Authors:  Neus Sanchez-Alberola; Susana Campoy; Jordi Barbé; Ivan Erill
Journal:  BMC Genomics       Date:  2012-02-03       Impact factor: 3.969

7.  ArrayExpress update--simplifying data submissions.

Authors:  Nikolay Kolesnikov; Emma Hastings; Maria Keays; Olga Melnichuk; Y Amy Tang; Eleanor Williams; Miroslaw Dylag; Natalja Kurbatova; Marco Brandizi; Tony Burdett; Karyn Megy; Ekaterina Pilicheva; Gabriella Rustici; Andrew Tikhonov; Helen Parkinson; Robert Petryszak; Ugis Sarkans; Alvis Brazma
Journal:  Nucleic Acids Res       Date:  2014-10-31       Impact factor: 16.971

8.  Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima.

Authors:  Dmitry A Rodionov; Irina A Rodionova; Xiaoqing Li; Dmitry A Ravcheev; Yekaterina Tarasova; Vasiliy A Portnoy; Karsten Zengler; Andrei L Osterman
Journal:  Front Microbiol       Date:  2013-08-23       Impact factor: 5.640

9.  LASAGNA: a novel algorithm for transcription factor binding site alignment.

Authors:  Chih Lee; Chun-Hsi Huang
Journal:  BMC Bioinformatics       Date:  2013-03-24       Impact factor: 3.169

10.  CollecTF: a database of experimentally validated transcription factor-binding sites in Bacteria.

Authors:  Sefa Kiliç; Elliot R White; Dinara M Sagitova; Joseph P Cornish; Ivan Erill
Journal:  Nucleic Acids Res       Date:  2013-11-14       Impact factor: 16.971
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  3 in total

Review 1.  Databases for Microbiologists.

Authors:  Igor B Zhulin
Journal:  J Bacteriol       Date:  2015-05-26       Impact factor: 3.490

2.  From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF.

Authors:  Sefa Kılıç; Dinara M Sagitova; Shoshannah Wolfish; Benoit Bely; Mélanie Courtot; Stacy Ciufo; Tatiana Tatusova; Claire O'Donovan; Marcus C Chibucos; Maria J Martin; Ivan Erill
Journal:  Database (Oxford)       Date:  2016-04-25       Impact factor: 3.451

3.  Transcription profile of Escherichia coli: genomic SELEX search for regulatory targets of transcription factors.

Authors:  Akira Ishihama; Tomohiro Shimada; Yukiko Yamazaki
Journal:  Nucleic Acids Res       Date:  2016-02-03       Impact factor: 16.971
  3 in total

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