MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations

Keilwagen J, Baumbach J, Kohl TA, Grosse I (2009)
Genome Biology 10(5): R46.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Keilwagen, Jens; Baumbach, Jan; Kohl, Thomas A.; Grosse, Ivo
Abstract / Bemerkung
Valuable binding-site annotation data are stored in databases. However, several types of errors can, and do, occur in the process of manually incorporating annotation data from the scientific literature into these databases. Here, we introduce MotifAdjuster http://dig.ipk-gatersleben.de/MotifAdjuster.html webcite, a tool that helps to detect these errors, and we demonstrate its efficacy on public data sets.
Erscheinungsjahr
2009
Zeitschriftentitel
Genome Biology
Band
10
Ausgabe
5
Seite(n)
R46
ISSN
1465-6906
Page URI
https://pub.uni-bielefeld.de/record/1783197

Zitieren

Keilwagen J, Baumbach J, Kohl TA, Grosse I. MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations. Genome Biology. 2009;10(5):R46.
Keilwagen, J., Baumbach, J., Kohl, T. A., & Grosse, I. (2009). MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations. Genome Biology, 10(5), R46. https://doi.org/10.1186/gb-2009-10-5-r46
Keilwagen, Jens, Baumbach, Jan, Kohl, Thomas A., and Grosse, Ivo. 2009. “MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations”. Genome Biology 10 (5): R46.
Keilwagen, J., Baumbach, J., Kohl, T. A., and Grosse, I. (2009). MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations. Genome Biology 10, R46.
Keilwagen, J., et al., 2009. MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations. Genome Biology, 10(5), p R46.
J. Keilwagen, et al., “MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations”, Genome Biology, vol. 10, 2009, pp. R46.
Keilwagen, J., Baumbach, J., Kohl, T.A., Grosse, I.: MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations. Genome Biology. 10, R46 (2009).
Keilwagen, Jens, Baumbach, Jan, Kohl, Thomas A., and Grosse, Ivo. “MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations”. Genome Biology 10.5 (2009): R46.
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77 References

Daten bereitgestellt von Europe PubMed Central.

Evolution of transcription factors and the gene regulatory network in Escherichia coli.
Madan Babu M, Teichmann SA., Nucleic Acids Res. 31(4), 2003
PMID: 12582243
Transcription factors: structural families and principles of DNA recognition.
Pabo CO, Sauer RT., Annu. Rev. Biochem. 61(), 1992
PMID: 1497306
Nonisotopic quantitative analysis of protein-DNA interactions at equilibrium.
Benotmane AM, Hoylaerts MF, Collen D, Belayew A., Anal. Biochem. 250(2), 1997
PMID: 9245437
Seed-specific transcription factors ABI3 and FUS3: molecular interaction with DNA.
Monke G, Altschmied L, Tewes A, Reidt W, Mock HP, Baumlein H, Conrad U., Planta 219(1), 2004
PMID: 14767767
Protein-DNA interaction mapping using genomic tiling path microarrays in Drosophila.
Sun LV, Chen L, Greil F, Negre N, Li TR, Cavalli G, Zhao H, Van Steensel B, White KP., Proc. Natl. Acad. Sci. U.S.A. 100(16), 2003
PMID: 12876199
Fitting a mixture model by expectation maximization to discover motifs in biopolymers.
Bailey TL, Elkan C., Proc Int Conf Intell Syst Mol Biol 2(), 1994
PMID: 7584402
Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment.
Lawrence CE, Altschul SF, Boguski MS, Liu JS, Neuwald AF, Wootton JC., Science 262(5131), 1993
PMID: 8211139
Gibbs Recursive Sampler: finding transcription factor binding sites.
Thompson W, Rouchka EC, Lawrence CE., Nucleic Acids Res. 31(13), 2003
PMID: 12824370
Environmentally induced foregut remodeling by PHA-4/FoxA and DAF-12/NHR.
Ao W, Gaudet J, Kent WJ, Muttumu S, Mango SE., Science 305(5691), 2004
PMID: 15375261
A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length.
Favorov AV, Gelfand MS, Gerasimova AV, Ravcheev DA, Mironov AA, Makeev VJ., Bioinformatics 21(10), 2005
PMID: 15728117
PRODORIC: prokaryotic database of gene regulation.
Munch R, Hiller K, Barg H, Heldt D, Linz S, Wingender E, Jahn D., Nucleic Acids Res. 31(1), 2003
PMID: 12519998
RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation.
Gama-Castro S, Jimenez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Penaloza-Spinola MI, Contreras-Moreira B, Segura-Salazar J, Muniz-Rascado L, Martinez-Flores I, Salgado H, Bonavides-Martinez C, Abreu-Goodger C, Rodriguez-Penagos C, Miranda-Rios J, Morett E, Merino E, Huerta AM, Trevino-Quintanilla L, Collado-Vides J., Nucleic Acids Res. 36(Database issue), 2007
PMID: 18158297
AGRIS and AtRegNet. a platform to link cis-regulatory elements and transcription factors into regulatory networks.
Palaniswamy SK, James S, Sun H, Lamb RS, Davuluri RV, Grotewold E., Plant Physiol. 140(3), 2006
PMID: 16524982
AthaMap, integrating transcriptional and post-transcriptional data.
Bulow L, Engelmann S, Schindler M, Hehl R., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18842622
CTCFBSDB: a CTCF-binding site database for characterization of vertebrate genomic insulators.
Bao L, Zhou M, Cui Y., Nucleic Acids Res. 36(Database issue), 2007
PMID: 17981843
JASPAR: an open-access database for eukaryotic transcription factor binding profiles.
Sandelin A, Alkema W, Engstrom P, Wasserman WW, Lenhard B., Nucleic Acids Res. 32(Database issue), 2004
PMID: 14681366
ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation.
Montgomery SB, Griffith OL, Sleumer MC, Bergman CM, Bilenky M, Pleasance ED, Prychyna Y, Zhang X, Jones SJ., Bioinformatics 22(5), 2006
PMID: 16397004
SCPD: a promoter database of the yeast Saccharomyces cerevisiae.
Zhu J, Zhang MQ., Bioinformatics 15(7-8), 1999
PMID: 10487868
TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes.
Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre-Dirrie A, Reuter I, Chekmenev D, Krull M, Hornischer K, Voss N, Stegmaier P, Lewicki-Potapov B, Saxel H, Kel AE, Wingender E., Nucleic Acids Res. 34(Database issue), 2006
PMID: 16381825
TRED: a transcriptional regulatory element database, new entries and other development.
Jiang C, Xuan Z, Zhao F, Zhang MQ., Nucleic Acids Res. 35(Database issue), 2007
PMID: 17202159
Transcription Regulatory Regions Database (TRRD): its status in 2002.
Kolchanov NA, Ignatieva EV, Ananko EA, Podkolodnaya OA, Stepanenko IL, Merkulova TI, Pozdnyakov MA, Podkolodny NL, Naumochkin AN, Romashchenko AG., Nucleic Acids Res. 30(1), 2002
PMID: 11752324
MATCH: A tool for searching transcription factor binding sites in DNA sequences.
Kel AE, Gossling E, Reuter I, Cheremushkin E, Kel-Margoulis OV, Wingender E., Nucleic Acids Res. 31(13), 2003
PMID: 12824369
Assessing computational tools for the discovery of transcription factor binding sites.
Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, Regnier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z., Nat. Biotechnol. 23(1), 2005
PMID: 15637633
Fast index based algorithms and software for matching position specific scoring matrices.
Beckstette M, Homann R, Giegerich R, Kurtz S., BMC Bioinformatics 7(), 2006
PMID: 16930469
Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes.
Munch R, Hiller K, Grote A, Scheer M, Klein J, Schobert M, Jahn D., Bioinformatics 21(22), 2005
PMID: 16109747
Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli.
Stormo GD, Schneider TD, Gold L, Ehrenfeucht A., Nucleic Acids Res. 10(9), 1982
PMID: 7048259
Computer methods to locate signals in nucleic acid sequences.
Staden R., Nucleic Acids Res. 12(1 Pt 2), 1984
PMID: 6364039

Bernardo JM, Smith AFM., 1994
Accelerated quantification of Bayesian networks with incomplete data.
Thiesson B., 1995
Choice of basis for Laplace approximation.
MacKay DJ., 1998

Heckerman D., 1995
Learning with mixtures of trees.
Meila M, Jordan MI., 2000
A Bayesian method for the induction of probabilistic networks from data.
Cooper GF, Herskovits E., 1992
Operations for learning with graphical models.
Buntine WL., 1994

Heckerman D, Geiger D, Chickering D., 1995
Maximum likelihood from incomplete data via the EM algorithm.
Dempster AP, Laird NM, Rubin DB., 1977
A weight array method for splicing signal analysis.
Zhang MQ, Marr TG., Comput. Appl. Biosci. 9(5), 1993
PMID: 8293321
On comparing classifiers: pitfalls to avoid and a recommended approach.
Salzberg SL., 1997
A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling.
Thijs G, Lescot M, Marchal K, Rombauts S, De Moor B, Rouze P, Moreau Y., Bioinformatics 17(12), 2001
PMID: 11751219
Identifying transcription factor binding sites through Markov chain optimization.
Ellrott K, Yang C, Sladek FM, Jiang T., Bioinformatics 18 Suppl 2(), 2002
PMID: 12385991
Modeling dependencies in protein-DNA binding sites.
Barash Y, Elidan G, Friedman N, Kaplan T., 2003
Splice site identification by idlBNs.
Castelo R, Guigo R., Bioinformatics 20 Suppl 1(), 2004
PMID: 15262783
A universal data compression system.
Rissanen J., 1983
The power of amnesia: learning probabilistic automata with variable memory length.
Ron D, Singer Y, Tishby N., 1996
Context-specific Independence in Bayesian networks.
Boutilier C, Friedman N, Goldszmidt M, Koller D., 1996

Bühlmann P., 1997
Finding short DNA motifs using permuted Markov models.
Zhao X, Huang H, Speed TP., J. Comput. Biol. 12(6), 2005
PMID: 16108724
Identification of transcription factor binding sites with variable-order Bayesian networks.
Ben-Gal I, Shani A, Gohr A, Grau J, Arviv S, Shmilovici A, Posch S, Grosse I., Bioinformatics 21(11), 2005
PMID: 15797905
Sequence logos: a new way to display consensus sequences.
Schneider TD, Stephens RM., Nucleic Acids Res. 18(20), 1990
PMID: 2172928
WebLogo: a sequence logo generator.
Crooks GE, Hon G, Chandonia JM, Brenner SE., Genome Res. 14(6), 2004
PMID: 15173120
Recognition of DNA by Fur: a reinterpretation of the Fur box consensus sequence.
Baichoo N, Helmann JD., J. Bacteriol. 184(21), 2002
PMID: 12374814
A consensus sequence for binding of Lrp to DNA.
Cui Y, Wang Q, Stormo GD, Calvo JM., J. Bacteriol. 177(17), 1995
PMID: 7665463
Primary and secondary modes of DNA recognition by the NarL two-component response regulator.
Maris AE, Kaczor-Grzeskowiak M, Ma Z, Kopka ML, Gunsalus RP, Dickerson RE., Biochemistry 44(44), 2005
PMID: 16262254
PRODORIC URL of the Matrix of NarL
AUTHOR UNKNOWN, 0
Microarray analysis of gene regulation by oxygen, nitrate, nitrite, FNR, NarL and NarP during anaerobic growth of Escherichia coli: new insights into microbial physiology.
Overton TW, Griffiths L, Patel MD, Hobman JL, Penn CW, Cole JA, Constantinidou C., Biochem. Soc. Trans. 34(Pt 1), 2006
PMID: 16417494
Identification and characterization of the caiF gene encoding a potential transcriptional activator of carnitine metabolism in Escherichia coli.
Eichler K, Buchet A, Lemke R, Kleber HP, Mandrand-Berthelot MA., J. Bacteriol. 178(5), 1996
PMID: 8631699
Regulation of the ubiquinone (coenzyme Q) biosynthetic genes ubiCA in Escherichia coli.
Kwon O, Druce-Hoffman M, Meganathan R., Curr. Microbiol. 50(4), 2005
PMID: 15902464
TMAO anaerobic respiration in Escherichia coli: involvement of the tor operon.
Mejean V, Iobbi-Nivol C, Lepelletier M, Giordano G, Chippaux M, Pascal MC., Mol. Microbiol. 11(6), 1994
PMID: 8022286
Jstacs: A Java Framework for Statistical Analysis and Classification of Biological Sequences
AUTHOR UNKNOWN, 0
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