CMGRN – Constructing Multilevel Gene Regulatory Networks

CMGRN

:: DESCRIPTION

CMGRN is a web server for constructing multilevel gene regulatory networks using ChIP-seq and gene expression data.

::DEVELOPER

Systems bioinformatics lab , Hong Kong Baptist University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jan 21.
CMGRN: a web server for constructing multilevel gene regulatory networks using ChIP-seq and gene expression data.
Guan D1, Shao J, Deng Y, Wang P, Zhao Z, Liang Y, Wang J, Yan B.

jump3 – Inference of Gene Regulatory Networks

jump3

:: DESCRIPTION

Jump3 is based on a formal on/off model of gene expression, but uses a non-parametric procedure based on decision trees (called “jump trees”) to reconstruct the GRN topology, allowing the inference of networks of hundreds of genes.

::DEVELOPER

vân anh huynh-thu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • MatLab / R Package

:: DOWNLOAD

 jump3

:: MORE INFORMATION

Citation

Combining tree-based and dynamical systems for the inference of gene regulatory networks.
Huynh-Thu VA, Sanguinetti G.
Bioinformatics. 2015 Jan 7. pii: btu863.

MutaNET 1.1.2 – Automated analysis of Genomic Mutations in Gene Regulatory NETworks

MutaNET 1.1.2

:: DESCRIPTION

MutaNET provides a NGS mutation calling pipeline and an automated analysis tool for coding regions, protein domains, regulation and transcription factor binding site information to analyse the potential impact of mutations on genes of interest.

::DEVELOPER

Chair of Computational Biology at the Saarland University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Python

:: DOWNLOAD

MutaNET

:: MORE INFORMATION

Citation

Hollander M, Hamed M, Helms V, Neininger K.
MutaNET: a tool for automated analysis of genomic mutations in gene regulatory networks.
Bioinformatics. 2018 Mar 1;34(5):864-866. doi: 10.1093/bioinformatics/btx687. PMID: 29087464; PMCID: PMC6192214.

EhecRegNet v2 – Database of Pathogenic E. coli Transcriptional Gene Regulatory Networks

EhecRegNet v2

:: DESCRIPTION

EhecRegNet is a database of gene regulations conserved between E. coli K12 and human pathogenic EHEC strains.

::DEVELOPER

Baumbach lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Integr Biol (Camb). 2012 Jul;4(7):728-33. doi: 10.1039/c2ib00132b.
On the trail of EHEC/EAEC–unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria.
Pauling J1, Röttger R, Neuner A, Salgado H, Collado-Vides J, Kalaghatgi P, Azevedo V, Tauch A, Pühler A, Baumbach J.

Exit mobile version