TRANSFAC (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "TRANSFAC" in English language version.

refsWebsite

Global rank English rank

31nih.gov

4^th place

17doi.org

2^nd place

6web.archive.org

1^st place

4archive.today

14^th place

3upenn.edu

702^nd place

520^th place

2gene-regulation.de

low place

2nju.edu.cn

low place

1gene-regulation.com

low place

1genexplain.com

low place

1edgar-wingender.de

low place

1kuleuven.be

4,725^th place

3,556^th place

1semanticscholar.org

11^th place

8^th place

1manchester.ac.uk

4,003^rd place

2,646^th place

1upc.es

low place

1lifl.fr

low place

1systemsbiology.net

low place

1ugent.be

3,695^th place

3,560^th place

1mpg.de

1,624^th place

1,592^nd place

1mcgill.ca

2,527^th place

1,840^th place

1tau.ac.il

4,464^th place

4,468^th place

1broadinstitute.org

low place

1harvard.edu

18^th place

17^th place

archive.today

TESS (Transcription Element Search System) at CBIL of the University of Pennsylvania
PMS Archived 2012-07-10 at archive.today, developed at the Nanjing University
T-Reg Comparator Archived 2012-07-18^{(Timestamp length)} at archive.today on the server of the Max Planck Institute for Molecular Genetics
MACO Archived 2012-07-10 at archive.today, developed at Nanjing University

broadinstitute.org

MSigDB: Mammalian transcription factor target gene sets; GSEA wiki server of Broad Institute of MIT and Harvard, Cambridge, MA

doi.org

Wingender E (July 2008). "The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation". Brief. Bioinformatics. 9 (4): 326–32. doi:10.1093/bib/bbn016. PMID 18436575.
Wingender E (March 1988). "Compilation of transcription regulating proteins". Nucleic Acids Res. 16 (5): 1879–902. doi:10.1093/nar/16.5.1879. PMC 338188. PMID 3282223.
Wingender E, Dietze P, Karas H, Knüppel R (January 1996). "TRANSFAC: a database on transcription factors and their DNA binding sites". Nucleic Acids Res. 24 (1): 238–41. doi:10.1093/nar/24.1.238. PMC 145586. PMID 8594589.
Heinemeyer T, Chen X, Karas H, Kel AE, Kel OV, Liebich I, Meinhardt T, Reuter I, Schacherer F, Wingender E (January 1999). "Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms". Nucleic Acids Res. 27 (1): 318–22. doi:10.1093/nar/27.1.318. PMC 148171. PMID 9847216.
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, Régnier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z (January 2005). "Assessing computational tools for the discovery of transcription factor binding sites". Nat. Biotechnol. 23 (1): 137–44. doi:10.1038/nbt1053. PMID 15637633. S2CID 3234451.
Narlikar L, Gordân R, Ohler U, Hartemink AJ (July 2006). "Informative priors based on transcription factor structural class improve de novo motif discovery". Bioinformatics. 22 (14): e384–92. doi:10.1093/bioinformatics/btl251. PMID 16873497.
Goemann B, Wingender E, Potapov AP (2009). "An approach to evaluate the topological significance of motifs and other patterns in regulatory networks". BMC Syst Biol. 3: 53. doi:10.1186/1752-0509-3-53. PMC 2694767. PMID 19454001.
Kozhenkov S, Dubinina Y, Sedova M, Gupta A, Ponomarenko J, Baitaluk M (2010). "BiologicalNetworks 2.0--an integrative view of genome biology data". BMC Bioinformatics. 11: 610. doi:10.1186/1471-2105-11-610. PMC 3019228. PMID 21190573.
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 (January 2006). "TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes". Nucleic Acids Res. 34 (Database issue): D108–10. doi:10.1093/nar/gkj143. PMC 1347505. PMID 16381825.
Boardman PE, Oliver SG, Hubbard SJ (July 2003). "SiteSeer: Visualisation and analysis of transcription factor binding sites in nucleotide sequences". Nucleic Acids Res. 31 (13): 3572–5. doi:10.1093/nar/gkg511. PMC 168918. PMID 12824368.
Kel AE, Gössling E, Reuter I, Cheremushkin E, Kel-Margoulis OV, Wingender E (July 2003). "MATCH: A tool for searching transcription factor binding sites in DNA sequences". Nucleic Acids Res. 31 (13): 3576–9. doi:10.1093/nar/gkg585. PMC 169193. PMID 12824369.
Messeguer X, Escudero R, Farré D, Núñez O, Martínez J, Albà MM (February 2002). "PROMO: detection of known transcription regulatory elements using species-tailored searches". Bioinformatics. 18 (2): 333–4. doi:10.1093/bioinformatics/18.2.333. PMID 11847087.
Tonon L, Touzet H, Varré JS (July 2010). "TFM-Explorer: mining cis-regulatory regions in genomes". Nucleic Acids Res. 38 (Web Server issue): W286–92. doi:10.1093/nar/gkq473. PMC 2896114. PMID 20522509.
Hooghe B, Hulpiau P, van Roy F, De Bleser P (July 2008). "ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species". Nucleic Acids Res. 36 (Web Server issue): W128–32. doi:10.1093/nar/gkn195. PMC 2447729. PMID 18453628.
Su G, Mao B, Wang J (2006). "A web server for transcription factor binding site prediction". Bioinformation. 1 (5): 156–7. doi:10.6026/97320630001156. PMC 1891680. PMID 17597879.
Su G, Mao B, Wang J (2006). "MACO: a gapped-alignment scoring tool for comparing transcription factor binding sites". In Silico Biol. (Gedrukt). 6 (4): 307–10. doi:10.3233/ISB-00243. PMID 16922693.
Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K, Lander ES, Kellis M (March 2005). "Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals". Nature. 434 (7031): 338–45. Bibcode:2005Natur.434..338X. doi:10.1038/nature03441. PMC 2923337. PMID 15735639.

edgar-wingender.de

Wingender, E: The classification of transcription factors

gene-regulation.com

TRANSFAC Public on the gene regulation portal of BIOBASE

gene-regulation.de

Patch on the free portal of BIOBASE
Match on the free portal of BIOBASE

genexplain.com

TRANSFAC taken over by geneXplain

harvard.edu

ui.adsabs.harvard.edu

Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K, Lander ES, Kellis M (March 2005). "Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals". Nature. 434 (7031): 338–45. Bibcode:2005Natur.434..338X. doi:10.1038/nature03441. PMC 2923337. PMID 15735639.

kuleuven.be

lirias.kuleuven.be

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, Régnier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z (January 2005). "Assessing computational tools for the discovery of transcription factor binding sites". Nat. Biotechnol. 23 (1): 137–44. doi:10.1038/nbt1053. PMID 15637633. S2CID 3234451.

lifl.fr

bioinfo.lifl.fr

TFM Explorer Archived 2011-09-19 at the Wayback Machine on the bioinformatics software server of the SEQUOIA group

manchester.ac.uk

chick.manchester.ac.uk

SiteSeer Archived 2011-06-25 at the Wayback Machine of the University of Manchester

mcgill.ca

genomequebec.mcgill.ca

PReMOD Archived 2008-12-28 at the Wayback Machine: Human and mouse genome of the years 2004 & 2005; IRCM / McGill University, Montreal

mpg.de

treg.molgen.mpg.de

T-Reg Comparator Archived 2012-07-18^{(Timestamp length)} at archive.today on the server of the Max Planck Institute for Molecular Genetics

nih.gov

pubmed.ncbi.nlm.nih.gov

Wingender E (July 2008). "The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation". Brief. Bioinformatics. 9 (4): 326–32. doi:10.1093/bib/bbn016. PMID 18436575.
Wingender E (March 1988). "Compilation of transcription regulating proteins". Nucleic Acids Res. 16 (5): 1879–902. doi:10.1093/nar/16.5.1879. PMC 338188. PMID 3282223.
Wingender E, Dietze P, Karas H, Knüppel R (January 1996). "TRANSFAC: a database on transcription factors and their DNA binding sites". Nucleic Acids Res. 24 (1): 238–41. doi:10.1093/nar/24.1.238. PMC 145586. PMID 8594589.
Wingender E (1997). "[Classification of eukaryotic transcription factors]". Mol. Biol. (Mosk.) (in Russian). 31 (4): 584–600. PMID 9340487.
Heinemeyer T, Chen X, Karas H, Kel AE, Kel OV, Liebich I, Meinhardt T, Reuter I, Schacherer F, Wingender E (January 1999). "Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms". Nucleic Acids Res. 27 (1): 318–22. doi:10.1093/nar/27.1.318. PMC 148171. PMID 9847216.
Stegmaier P, Kel AE, Wingender E (2004). "Systematic DNA-binding domain classification of transcription factors". Genome Inform. 15 (2): 276–86. PMID 15706513.
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, Régnier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z (January 2005). "Assessing computational tools for the discovery of transcription factor binding sites". Nat. Biotechnol. 23 (1): 137–44. doi:10.1038/nbt1053. PMID 15637633. S2CID 3234451.
Narlikar L, Gordân R, Ohler U, Hartemink AJ (July 2006). "Informative priors based on transcription factor structural class improve de novo motif discovery". Bioinformatics. 22 (14): e384–92. doi:10.1093/bioinformatics/btl251. PMID 16873497.
Goemann B, Wingender E, Potapov AP (2009). "An approach to evaluate the topological significance of motifs and other patterns in regulatory networks". BMC Syst Biol. 3: 53. doi:10.1186/1752-0509-3-53. PMC 2694767. PMID 19454001.
Kozhenkov S, Dubinina Y, Sedova M, Gupta A, Ponomarenko J, Baitaluk M (2010). "BiologicalNetworks 2.0--an integrative view of genome biology data". BMC Bioinformatics. 11: 610. doi:10.1186/1471-2105-11-610. PMC 3019228. PMID 21190573.
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 (January 2006). "TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes". Nucleic Acids Res. 34 (Database issue): D108–10. doi:10.1093/nar/gkj143. PMC 1347505. PMID 16381825.
Boardman PE, Oliver SG, Hubbard SJ (July 2003). "SiteSeer: Visualisation and analysis of transcription factor binding sites in nucleotide sequences". Nucleic Acids Res. 31 (13): 3572–5. doi:10.1093/nar/gkg511. PMC 168918. PMID 12824368.
Kel AE, Gössling E, Reuter I, Cheremushkin E, Kel-Margoulis OV, Wingender E (July 2003). "MATCH: A tool for searching transcription factor binding sites in DNA sequences". Nucleic Acids Res. 31 (13): 3576–9. doi:10.1093/nar/gkg585. PMC 169193. PMID 12824369.
Messeguer X, Escudero R, Farré D, Núñez O, Martínez J, Albà MM (February 2002). "PROMO: detection of known transcription regulatory elements using species-tailored searches". Bioinformatics. 18 (2): 333–4. doi:10.1093/bioinformatics/18.2.333. PMID 11847087.
Tonon L, Touzet H, Varré JS (July 2010). "TFM-Explorer: mining cis-regulatory regions in genomes". Nucleic Acids Res. 38 (Web Server issue): W286–92. doi:10.1093/nar/gkq473. PMC 2896114. PMID 20522509.
Hooghe B, Hulpiau P, van Roy F, De Bleser P (July 2008). "ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species". Nucleic Acids Res. 36 (Web Server issue): W128–32. doi:10.1093/nar/gkn195. PMC 2447729. PMID 18453628.
Su G, Mao B, Wang J (2006). "A web server for transcription factor binding site prediction". Bioinformation. 1 (5): 156–7. doi:10.6026/97320630001156. PMC 1891680. PMID 17597879.
Su G, Mao B, Wang J (2006). "MACO: a gapped-alignment scoring tool for comparing transcription factor binding sites". In Silico Biol. (Gedrukt). 6 (4): 307–10. doi:10.3233/ISB-00243. PMID 16922693.
Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K, Lander ES, Kellis M (March 2005). "Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals". Nature. 434 (7031): 338–45. Bibcode:2005Natur.434..338X. doi:10.1038/nature03441. PMC 2923337. PMID 15735639.

ncbi.nlm.nih.gov

Wingender E (March 1988). "Compilation of transcription regulating proteins". Nucleic Acids Res. 16 (5): 1879–902. doi:10.1093/nar/16.5.1879. PMC 338188. PMID 3282223.
Wingender E, Dietze P, Karas H, Knüppel R (January 1996). "TRANSFAC: a database on transcription factors and their DNA binding sites". Nucleic Acids Res. 24 (1): 238–41. doi:10.1093/nar/24.1.238. PMC 145586. PMID 8594589.
Heinemeyer T, Chen X, Karas H, Kel AE, Kel OV, Liebich I, Meinhardt T, Reuter I, Schacherer F, Wingender E (January 1999). "Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms". Nucleic Acids Res. 27 (1): 318–22. doi:10.1093/nar/27.1.318. PMC 148171. PMID 9847216.
Goemann B, Wingender E, Potapov AP (2009). "An approach to evaluate the topological significance of motifs and other patterns in regulatory networks". BMC Syst Biol. 3: 53. doi:10.1186/1752-0509-3-53. PMC 2694767. PMID 19454001.
Kozhenkov S, Dubinina Y, Sedova M, Gupta A, Ponomarenko J, Baitaluk M (2010). "BiologicalNetworks 2.0--an integrative view of genome biology data". BMC Bioinformatics. 11: 610. doi:10.1186/1471-2105-11-610. PMC 3019228. PMID 21190573.
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 (January 2006). "TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes". Nucleic Acids Res. 34 (Database issue): D108–10. doi:10.1093/nar/gkj143. PMC 1347505. PMID 16381825.
Boardman PE, Oliver SG, Hubbard SJ (July 2003). "SiteSeer: Visualisation and analysis of transcription factor binding sites in nucleotide sequences". Nucleic Acids Res. 31 (13): 3572–5. doi:10.1093/nar/gkg511. PMC 168918. PMID 12824368.
Kel AE, Gössling E, Reuter I, Cheremushkin E, Kel-Margoulis OV, Wingender E (July 2003). "MATCH: A tool for searching transcription factor binding sites in DNA sequences". Nucleic Acids Res. 31 (13): 3576–9. doi:10.1093/nar/gkg585. PMC 169193. PMID 12824369.
Tonon L, Touzet H, Varré JS (July 2010). "TFM-Explorer: mining cis-regulatory regions in genomes". Nucleic Acids Res. 38 (Web Server issue): W286–92. doi:10.1093/nar/gkq473. PMC 2896114. PMID 20522509.
Hooghe B, Hulpiau P, van Roy F, De Bleser P (July 2008). "ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species". Nucleic Acids Res. 36 (Web Server issue): W128–32. doi:10.1093/nar/gkn195. PMC 2447729. PMID 18453628.
Su G, Mao B, Wang J (2006). "A web server for transcription factor binding site prediction". Bioinformation. 1 (5): 156–7. doi:10.6026/97320630001156. PMC 1891680. PMID 17597879.
Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K, Lander ES, Kellis M (March 2005). "Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals". Nature. 434 (7031): 338–45. Bibcode:2005Natur.434..338X. doi:10.1038/nature03441. PMC 2923337. PMID 15735639.

nju.edu.cn

mcube.nju.edu.cn

PMS Archived 2012-07-10 at archive.today, developed at the Nanjing University
MACO Archived 2012-07-10 at archive.today, developed at Nanjing University

semanticscholar.org

api.semanticscholar.org

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, Régnier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z (January 2005). "Assessing computational tools for the discovery of transcription factor binding sites". Nat. Biotechnol. 23 (1): 137–44. doi:10.1038/nbt1053. PMID 15637633. S2CID 3234451.