TRANSFAC

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TRANSFAC
Database.png
Content
Description Transcription Factor Database
Data types
captured		 Eukaryotic transcription factors, their binding sites and binding profiles
Organisms eukaryotes
Contact
Research center Helmholtz Centre for Infection Research; BIOBASE GmbH
Primary citation Wingender (2008)[1]
Release date 1988
Access
Website Lua error in package.lua at line 80: module 'strict' not found.

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

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]

Content and features

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.[7][8][9][10]

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.

Availability

The usage of an older version of TRANSFAC is free of charge for non-profit users. Access to the most up-to-date version requires a license.

Applications

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 TFBS recognition algorithms.[11] The TF classification enables to analyze such data sets with regard to the properties of the DNA-binding domains.[12] 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.[13][14] By far the most frequent use of TRANSFAC is the computational prediction of potential transcription factor binding sites (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.[15][16]
  • SiteSeer – analyzes sequence similarities with the binding sites documented in TRANSFAC.[17][18]
  • Match – identifies potential TFBS using the matrix library; it is provided along with the database.[19][20]
  • 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.[21][22] TESS also provides a program for the identification of cis-regulatory modules (CRMs, characteristic combinations of TFBSs), which uses TRANSFAC matrices.[23]
  • PROMO – matrix-based prediction of TFBSs with aid of the commercial database version[24][25]
  • TFM Explorer – Identification of common potential TFBSs in a set of genes[26][27]
  • MotifMogul – matrix-based sequence analysis with a number of different algorithms[28]
  • ConTra – matrix-based sequence analysis in conserved promoter regions[29][30]
  • PMS (Poly Matrix Search) – matrix-based sequence analysis in conserved promoter regions [31][32]

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

  • T-Reg Comparator[33] to compare individual or groups of matrices with those of TRANSFAC or other libraries.
  • MACO (Poly Matrix Search)[34][35] – matrix comparison with matrix libraries.

A number of servers provide genomic annotations computed with the aid of TRANSFAC.[36][37] Others have used such analyses to infer target gene sets.[38][39]

Similar data sources

The following resources offer contents that are related to or partially overlapping with TRANSFAC:

  • JASPAR – collection of transcription factor binding profiles (matrices) and sequence analysis program
  • PLACE – cis-regulatory DNA elements in plants; until February 2007
  • PlantCARE – cis-regulatory elements and transcription factors in plants (2002)
  • PRODORIC – a similar concept as TRANSFAC for prokaryotes
  • RegTransBase - transcription factor binding sites in a diverse set of bacteria.
  • RegulonDB – focus on the bacterium Escherichia coli
  • SCPD – specific collection of data- and tools for yeast (Saccharomyces cerevisiae) (1998)
  • TFe – the transcription factor encyclopedia
  • TRRD – Transcription Regulatory Regions Database, mainly about regulatory regions and TF-binding sites
  • PAZAR - Database with focus on experimentally validated transcription factor binding sites
  • HOCOMOCO - Homo Sapiens Comprehensive Model Collection[40]

References

  1. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  2. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  3. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  4. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  5. ↑ TRANSFAC Public on the gene regulation portal of BIOBASE
  6. ↑ Access to TRANSFAC Public via TESS at the Computational Biology and Informatics Laboratory (CBIL) of University of Pennsylvania (Penn)
  7. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  8. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  9. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  10. ↑ Wingender, E: The classification of transcription factors
  11. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  12. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  13. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  14. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  15. ↑ Patch on the free portal of BIOBASE
  16. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  17. ↑ SiteSeer of the University of Manchester
  18. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  19. ↑ Match on the free portal of BIOBASE
  20. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  21. ↑ TESS (Transcription Element Search System) at CBIL of the University of Pennsylvania
  22. ↑ Site Search bei TESS
  23. ↑ AnGEL CRM Searches in the TESS system
  24. ↑ PROMO on the ALGGEN server of the Polytechnic University of Catalonia (UPC)
  25. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  26. ↑ TFM Explorer on the bioinformatics software server of the SEQUOIA group
  27. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  28. ↑ MotifMogul of the Institute for Systems Biology in Seattle
  29. ↑ ConTra of the Ghent University
  30. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  31. ↑ PMS, developed at the Nanjing University
  32. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  33. ↑ T-Reg Comparator on the server of the Max Planck Institute for Molecular Genetics
  34. ↑ MACO, developed at Nanjing University
  35. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  36. ↑ PReMOD: Human and mouse genome of the years 2004 & 2005; IRCM / McGill University, Montreal
  37. ↑ PRIMA: Human genome of 2004; Tel-Aviv University
  38. ↑ MSigDB: Mammalian transcription factor target gene sets; GSEA wiki server of Broad Institute of MIT and Harvard, Cambridge, MA
  39. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  40. ↑ Lua error in package.lua at line 80: module 'strict' not found.

External links

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