The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
MatInspector and beyond: promoter analysis based on transcription factor binding sites
Open accessAbstract
Motivation: Promoter analysis is an essential step on the way to identify regulatory networks. A prerequisite for successful promoter analysis is the prediction of potential transcription factor binding sites (TFBS) with reasonable accuracy. The next steps in promoter analysis can be tackled only with reliable predictions, e.g. finding phylogenetically conserved patterns or identifying higher order combinations of sites in promoters of co-regulated genes. Results: We present a new version of the program MatInspector that identifies TFBS in nucleotide sequences using a large library of weight matrices. By introducing a matrix family concept, optimized thresholds, and comparative analysis, the enhanced program produces concise results avoiding redundant and false-positive matches. We describe a number of programs based on MatInspector allowing in-depth promoter analysis (DiAlignTF, FrameWorker) and targeted design of regulatory sequences (SequenceShaper). Availability: MatInspector and the other programs described here can be used online at http://www.genomatix.de/matinspector.html. Access is free after registration within certain limitations (e.g. the number of analysis per month is currently limited to 20 analyses of arbitrary sequences). Contact: cartharius@genomatix.de Supplementary information: http://www.genomatix.de/matinspector.html
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The sequence of the human genome
Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) · Science · doi:10.1126/science.1058040 · Cited by 13,909
Complete sequencing and characterization of 21,243 full-length human cDNAs
Ota, T., Suzuki, Y., Nishikawa, T., Otsuki, T., Sugiyama, T., Irie, R., Wakamatsu, A., Hayashi, K., Sato, H., Nagai, K., et al. (2004) · Nature Genetics · doi:10.1038/ng1285 · Cited by 925
Cited by
Oberlander, T. F., Weinberg, J., Papsdorf, M., Grunau, R., Misri, S., & Devlin, A. M. (2008) · Epigenetics · doi:10.4161/epi.3.2.6034 · Cited by 1,432
Yu, J., Yu, J., Mani, R.-S., Cao, Q., Brenner, C. J., Cao, X., Wang, X., Wu, L., Li, J., Hu, M., et al. (2010) · Cancer Cell · doi:10.1016/j.ccr.2010.03.018 · Cited by 850
Readhead, B., Haure-Mirande, J.-V., Funk, C. C., Richards, M. A., Shannon, P., Haroutunian, V., Sano, M., Liang, W. S., Beckmann, N. D., Price, N. D., et al. (2018) · Neuron · doi:10.1016/j.neuron.2018.05.023 · Cited by 708
Santangelo, L., Giurato, G., Cicchini, C., Montaldo, C., Mancone, C., Tarallo, R., Battistelli, C., Alonzi, T., Weisz, A., & Tripodi, M. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.09.031 · Cited by 601
STAT3 mediates hepatic hepcidin expression and its inflammatory stimulation
Verga Falzacappa, M. V., Vujic Spasic, M., Kessler, R., Stolte, J., Hentze, M. W., & Muckenthaler, M. U. (2007) · Blood · doi:10.1182/blood-2006-07-033969 · Cited by 567
Metadata
- Authors
- Cartharius, K., Frech, K., Grote, K., Klocke, B., Haltmeier, M., Klingenhoff, A., Frisch, M., Bayerlein, M., & Werner, T.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2005-04-28
- Volume
- 21
- Issue
- 13
- Pages
- 2933-2942
- ISSN
- 0266-7061 (ISSN-L)
- 1367-4803
- 1460-2059
- OpenAlex
- W2153550523
- Cited by
- 1,979
- References
- 2
- FWCI
- 39.41
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Cartharius, K., Frech, K., Grote, K., Klocke, B., Haltmeier, M., Klingenhoff, A., Frisch, M., Bayerlein, M., & Werner, T. (2005). MatInspector and beyond: promoter analysis based on transcription factor binding sites. Bioinformatics. https://doi.org/10.1093/bioinformatics/bti473
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