TFBS: Computational Framework for Transcription Factor Binding Site Analysis

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2002 Aug 15

PMID 12176838

Citations 98

Authors

Boris Lenhard

Wyeth W Wasserman

Affiliations

Soon will be listed here.

Abstract

Motivation: TFBS is a set of integrated, object-oriented Perl modules for transcription factor binding site detection and analysis. It implements objects representing specificity profile matrices, binding sites and sets thereof, pattern generators, and pattern database interfaces. The modules are interoperable with the BioPerl open source system.

Availability And Supplementary Information: The module package with documentation and example scripts are available at http://forkhead.cgb.ki.se/TFBS/

Citing Articles

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Human granzyme B regulatory B cells prevent effector CD4+CD25- T cell proliferation through a mechanism dependent from lymphotoxin alpha.

Sailliet N, Mai H, Dupuy A, Tilly G, Fourgeux C, Braud M Front Immunol. 2023; 14:1183714.

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A gene expression profile for the lower osteogenic potent of bone-derived MSCs from osteoporosis with T2DM and the potential mechanism.

Xia S, Ma Z, Wang B, Gao F, Guo S, Chen X J Orthop Surg Res. 2022; 17(1):402.

PMID: 36050744 PMC: 9438120. DOI: 10.1186/s13018-022-03291-2.

Transcriptional Silencers in Drosophila Serve a Dual Role as Transcriptional Enhancers in Alternate Cellular Contexts.

Gisselbrecht S, Palagi A, Kurland J, Rogers J, Ozadam H, Zhan Y Mol Cell. 2019; 77(2):324-337.e8.

PMID: 31704182 PMC: 6980774. DOI: 10.1016/j.molcel.2019.10.004.

MANTA2, update of the Mongo database for the analysis of transcription factor binding site alterations.

Fornes O, Gheorghe M, Richmond P, Arenillas D, Wasserman W, Mathelier A Sci Data. 2018; 5:180141.

PMID: 30040077 PMC: 6057437. DOI: 10.1038/sdata.2018.141.