TRANSFAC

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TRANSFAC
File:Database.png
Content
DescriptionTranscription Factor Database
Data types
captured		Eukaryotic transcription factors, their binding sites and binding profiles
Organismseukaryotes
Contact
Research centerHelmholtz Centre for Infection Research; BIOBASE GmbH; geneXplain GmbH
Primary citationWingender (2008)[1]
Release date1988
Access
WebsiteTRANSFAC 7.0 Public 2005

TRANSFAC (TRANScription FACtor database) is a manually curated database of eukaryotic transcription factors, their genomic binding sites and DNA binding profiles. The contents of the database can be used to predict potential transcription factor binding sites.

Introduction

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The origin of the database was an early data collection published 1988.[2] The first version that was released under the name TRANSFAC was developed at the former German National Research Centre for Biotechnology and designed for local installation (now: Helmholtz Centre for Infection Research).[3] In one of the first publicly funded bioinformatics projects, launched in 1993, TRANSFAC developed into a resource that became available on the Internet.[4]

In 1997, TRANSFAC was transferred to a newly established company, BIOBASE, in order to secure long-term financing of the database. Since then, the most up-to-date version has to be licensed, whereas older versions are free for non-commercial users.[5][6] Since July 2016, TRANSFAC is maintained and distributed by geneXplain GmbH, Wolfenbüttel, Germany.[7]

Content and features

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The content of the database is organized in a way that it is centered around the interaction between transcription factors (TFs) and their DNA binding sites (TFBS). TFs are described with regard to their structural and functional features, extracted from the original scientific literature. They are classified to families, classes and superclasses according to the features of their DNA binding domains.[8][9][10][11]

Binding of a TF to a genomic site is documented by specifying the localization of the site, its sequence and the experimental method applied. All sites that refer to one TF, or a group of closely related TFs, are aligned and used to construct a position-specific scoring matrix (PSSM), or count matrix. Many matrices of the TRANSFAC matrix library have been constructed by a team of curators, others were taken from scientific publications.

Applications

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The TRANSFAC database can be used as an encyclopedia of eukaryotic transcription factors. The target sequences and the regulated genes can be listed for each TF, which can be used as benchmark for TFBS recognition tools or as training sets for new transcription factor binding sites (TFBS) recognition algorithms.[12] The TF classification enables to analyze such data sets with regard to the properties of the DNA-binding domains.[13] Another application is to retrieve all TFs that regulate a given (set of) gene(s). In the context of systems-biological studies, the TF-target gene relations documented in TRANSFAC were used to construct and analyze transcription regulatory networks.[14][15] By far the most frequent use of TRANSFAC is the computational prediction of potential TFBS. A number of algorithms exist which either use the individual binding sites or the matrix library for this purpose:

  • Patch – analyzes sequence similarities with the binding sites documented in TRANSFAC; it is provided along with the database.[16][17]
  • SiteSeer – analyzes sequence similarities with the binding sites documented in TRANSFAC.[18][19]
  • Match – identifies potential TFBS using the matrix library; it is provided along with the database.[20][21]
  • TESS (Transcription Element Search System) – analyzes sequence similarities with binding sites of TRANSFAC as well as potential binding sites using the matrix libraries of TRANSFAC and three other sources.[22][23] TESS also provides a program for the identification of cis-regulatory modules (CRMs, characteristic combinations of TFBSs), which uses TRANSFAC matrices.[24]
  • PROMO – matrix-based prediction of TFBSs with aid of the commercial database version[25][26]
  • TFM Explorer – Identification of common potential TFBSs in a set of genes[27][28]
  • MotifMogul – matrix-based sequence analysis with a number of different algorithms[29]
  • ConTra – matrix-based sequence analysis in conserved promoter regions[30][31]
  • PMS (Poly Matrix Search) – matrix-based sequence analysis in conserved promoter regions [32][33]

Comparison of matrices with the matrix library of TRANSFAC and other sources:

  • T-Reg Comparator[34] to compare individual or groups of matrices with those of TRANSFAC or other libraries.
  • MACO (Poly Matrix Search)[35][36] – matrix comparison with matrix libraries.

A number of servers provide genomic annotations computed with the aid of TRANSFAC.[37][38] Others have used such analyses to infer target gene sets.[39][40]

See also

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References

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  1. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  2. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  3. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  4. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  5. ^ TRANSFAC Public on the gene regulation portal of BIOBASE
  6. ^ Access to TRANSFAC Public via TESS Archived 2012-07-24 at the Wayback Machine at the Computational Biology and Informatics Laboratory (CBIL) of University of Pennsylvania (Penn)
  7. ^ TRANSFAC taken over by geneXplain
  8. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  9. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  10. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  11. ^ Wingender, E: The classification of transcription factors
  12. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  13. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  14. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  15. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  16. ^ Patch on the free portal of BIOBASE
  17. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  18. ^ SiteSeer Archived 2011-06-25 at the Wayback Machine of the University of Manchester
  19. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  20. ^ Match on the free portal of BIOBASE
  21. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  22. ^ TESS (Transcription Element Search System) at CBIL of the University of Pennsylvania
  23. ^ Site Search bei TESS Archived 2012-07-24 at the Wayback Machine
  24. ^ AnGEL CRM Searches Archived 2012-07-24 at the Wayback Machine in the TESS system
  25. ^ PROMO on the ALGGEN server of the Polytechnic University of Catalonia (UPC)
  26. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  27. ^ TFM Explorer Archived 2011-09-19 at the Wayback Machine on the bioinformatics software server of the SEQUOIA group
  28. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  29. ^ MotifMogul of the Institute for Systems Biology in Seattle
  30. ^ ConTra of the Ghent University
  31. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  32. ^ PMS Archived 2012-07-10 at archive.today, developed at the Nanjing University
  33. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  34. ^ T-Reg Comparator Archived 2012-07-18(Timestamp length) at archive.today on the server of the Max Planck Institute for Molecular Genetics
  35. ^ MACO Archived 2012-07-10 at archive.today, developed at Nanjing University
  36. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  37. ^ PReMOD Archived 2008-12-28 at the Wayback Machine: Human and mouse genome of the years 2004 & 2005; IRCM / McGill University, Montreal
  38. ^ PRIMA: Human genome of 2004; Tel-Aviv University
  39. ^ MSigDB: Mammalian transcription factor target gene sets; GSEA wiki server of Broad Institute of MIT and Harvard, Cambridge, MA
  40. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
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