Ghent University Academic Bibliography

Advanced

TF2Network : predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information

Shubhada Rajabhau Kulkarni UGent, Dries Vaneechoutte UGent, Jan Van de Velde and Klaas Vandepoele UGent (2018) NUCLEIC ACIDS RESEARCH. 46(6).
abstract
A gene regulatory network (GRN) is a collection of regulatory interactions between transcription factors (TFs) and their target genes. GRNs control different biological processes and have been instrumental to understand the organization and complexity of gene regulation. Although various experimental methods have been used to map GRNs in Arabidop-sis thaliana, their limited throughput combined with the large number of TFs makes that for many genes our knowledge about regulating TFs is incomplete. We introduce TF2Network, a tool that exploits the vast amount of TF binding site information and enables the delineation of GRNs by detecting potential regulators for a set of co-expressed or functionally related genes. Validation using two experimental benchmarks reveals that TF2Network predicts the correct regulator in 75-92% of the test sets. Furthermore, our tool is robust to noise in the input gene sets, has a low false discovery rate, and shows a better performance to recover correct regulators compared to other plant tools. TF2Network is accessible through a web interface where GRNs are interactively visualized and annotated with various types of experimental functional information. TF2Network was used to perform systematic functional and regulatory gene annotations, identifying new TFs involved in circadian rhythm and stress response.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
COEXPRESSION NETWORKS, COMPARATIVE GENOMICS, PROMOTER SEQUENCES, DNA, ELEMENTS, PLANT GENE, THALIANA, EXPRESSION, DATABASE, TOOLS, IDENTIFICATION
journal title
NUCLEIC ACIDS RESEARCH
Nucleic Acids Res.
volume
46
issue
6
article number
e31
pages
15 pages
Web of Science type
Article
Web of Science id
000429009500001
ISSN
0305-1048
1362-4962
DOI
10.1093/nar/gkx1279
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
copyright statement
Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
id
8563189
handle
http://hdl.handle.net/1854/LU-8563189
date created
2018-05-28 12:55:26
date last changed
2018-06-07 12:43:58
@article{8563189,
  abstract     = {A gene regulatory network (GRN) is a collection of regulatory interactions between transcription factors (TFs) and their target genes. GRNs control different biological processes and have been instrumental to understand the organization and complexity of gene regulation. Although various experimental methods have been used to map GRNs in Arabidop-sis thaliana, their limited throughput combined with the large number of TFs makes that for many genes our knowledge about regulating TFs is incomplete. We introduce TF2Network, a tool that exploits the vast amount of TF binding site information and enables the delineation of GRNs by detecting potential regulators for a set of co-expressed or functionally related genes. Validation using two experimental benchmarks reveals that TF2Network predicts the correct regulator in 75-92\% of the test sets. Furthermore, our tool is robust to noise in the input gene sets, has a low false discovery rate, and shows a better performance to recover correct regulators compared to other plant tools. TF2Network is accessible through a web interface where GRNs are interactively visualized and annotated with various types of experimental functional information. TF2Network was used to perform systematic functional and regulatory gene annotations, identifying new TFs involved in circadian rhythm and stress response.},
  articleno    = {e31},
  author       = {Kulkarni, Shubhada Rajabhau and Vaneechoutte, Dries and Van de Velde, Jan and Vandepoele, Klaas},
  issn         = {0305-1048},
  journal      = {NUCLEIC ACIDS RESEARCH},
  keyword      = {COEXPRESSION NETWORKS,COMPARATIVE GENOMICS,PROMOTER SEQUENCES,DNA,ELEMENTS,PLANT GENE,THALIANA,EXPRESSION,DATABASE,TOOLS,IDENTIFICATION},
  language     = {eng},
  number       = {6},
  pages        = {15},
  title        = {TF2Network : predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information},
  url          = {http://dx.doi.org/10.1093/nar/gkx1279},
  volume       = {46},
  year         = {2018},
}

Chicago
Kulkarni, Shubhada Rajabhau, Dries Vaneechoutte, Jan Van de Velde, and Klaas Vandepoele. 2018. “TF2Network : Predicting Transcription Factor Regulators and Gene Regulatory Networks in Arabidopsis Using Publicly Available Binding Site Information.” Nucleic Acids Research 46 (6).
APA
Kulkarni, S. R., Vaneechoutte, D., Van de Velde, J., & Vandepoele, K. (2018). TF2Network : predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information. NUCLEIC ACIDS RESEARCH, 46(6).
Vancouver
1.
Kulkarni SR, Vaneechoutte D, Van de Velde J, Vandepoele K. TF2Network : predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information. NUCLEIC ACIDS RESEARCH. 2018;46(6).
MLA
Kulkarni, Shubhada Rajabhau, Dries Vaneechoutte, Jan Van de Velde, et al. “TF2Network : Predicting Transcription Factor Regulators and Gene Regulatory Networks in Arabidopsis Using Publicly Available Binding Site Information.” NUCLEIC ACIDS RESEARCH 46.6 (2018): n. pag. Print.