Cargando…
Targetfinder.org: a resource for systematic discovery of transcription factor target genes
Targetfinder.org (http://targetfinder.org/) provides a web-based resource for finding genes that show a similar expression pattern to a group of user-selected genes. It is based on a large-scale gene expression compendium (>1200 experiments, >13 000 genes). The primary application of Targetfin...
Autores principales: | , , , |
---|---|
Formato: | Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2010
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896086/ https://www.ncbi.nlm.nih.gov/pubmed/20460454 http://dx.doi.org/10.1093/nar/gkq374 |
_version_ | 1782183306454892544 |
---|---|
author | Kiełbasa, Szymon M. Blüthgen, Nils Fähling, Michael Mrowka, Ralf |
author_facet | Kiełbasa, Szymon M. Blüthgen, Nils Fähling, Michael Mrowka, Ralf |
author_sort | Kiełbasa, Szymon M. |
collection | PubMed |
description | Targetfinder.org (http://targetfinder.org/) provides a web-based resource for finding genes that show a similar expression pattern to a group of user-selected genes. It is based on a large-scale gene expression compendium (>1200 experiments, >13 000 genes). The primary application of Targetfinder.org is to expand a list of known transcription factor targets by new candidate target genes. The user submits a group of genes (the ‘seed’), and as a result the web site provides a list of other genes ranked by similarity of their expression to the expression of the seed genes. Additionally, the web site provides information on a recovery/cross-validation test to check for consistency of the provided seed and the quality of the ranking. Furthermore, the web site allows to analyse affinities of a selected transcription factor to the promoter regions of the top-ranked genes in order to select the best new candidate target genes for further experimental analysis. |
format | Text |
id | pubmed-2896086 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-28960862010-07-02 Targetfinder.org: a resource for systematic discovery of transcription factor target genes Kiełbasa, Szymon M. Blüthgen, Nils Fähling, Michael Mrowka, Ralf Nucleic Acids Res Articles Targetfinder.org (http://targetfinder.org/) provides a web-based resource for finding genes that show a similar expression pattern to a group of user-selected genes. It is based on a large-scale gene expression compendium (>1200 experiments, >13 000 genes). The primary application of Targetfinder.org is to expand a list of known transcription factor targets by new candidate target genes. The user submits a group of genes (the ‘seed’), and as a result the web site provides a list of other genes ranked by similarity of their expression to the expression of the seed genes. Additionally, the web site provides information on a recovery/cross-validation test to check for consistency of the provided seed and the quality of the ranking. Furthermore, the web site allows to analyse affinities of a selected transcription factor to the promoter regions of the top-ranked genes in order to select the best new candidate target genes for further experimental analysis. Oxford University Press 2010-07-01 2010-05-11 /pmc/articles/PMC2896086/ /pubmed/20460454 http://dx.doi.org/10.1093/nar/gkq374 Text en © The Author(s) 2010. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Articles Kiełbasa, Szymon M. Blüthgen, Nils Fähling, Michael Mrowka, Ralf Targetfinder.org: a resource for systematic discovery of transcription factor target genes |
title | Targetfinder.org: a resource for systematic discovery of transcription factor target genes |
title_full | Targetfinder.org: a resource for systematic discovery of transcription factor target genes |
title_fullStr | Targetfinder.org: a resource for systematic discovery of transcription factor target genes |
title_full_unstemmed | Targetfinder.org: a resource for systematic discovery of transcription factor target genes |
title_short | Targetfinder.org: a resource for systematic discovery of transcription factor target genes |
title_sort | targetfinder.org: a resource for systematic discovery of transcription factor target genes |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896086/ https://www.ncbi.nlm.nih.gov/pubmed/20460454 http://dx.doi.org/10.1093/nar/gkq374 |
work_keys_str_mv | AT kiełbasaszymonm targetfinderorgaresourceforsystematicdiscoveryoftranscriptionfactortargetgenes AT bluthgennils targetfinderorgaresourceforsystematicdiscoveryoftranscriptionfactortargetgenes AT fahlingmichael targetfinderorgaresourceforsystematicdiscoveryoftranscriptionfactortargetgenes AT mrowkaralf targetfinderorgaresourceforsystematicdiscoveryoftranscriptionfactortargetgenes |