INSECT 2.0 – Genome-wide Cis-regulatory Modules Prediction

INSECT 2.0

:: DESCRIPTION

INSECT (IN-silico SEarch for Co-occurring Transcription factors) is an easy-to-use and powerful web server for biologists analysing genomic sequence data for in silico cis-regulatory modules prediction and analysis.

::DEVELOPER

Biomedicine Research Institute of Buenos Aires

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

INSECT 2.0: a web-server for genome-wide cis-regulatory modules prediction.
Parra RG, Rohr CO, Koile D, Perez-Castro C, Yankilevich P.
Bioinformatics. 2015 Dec 12. pii: btv726.

MOPAT – Predict recurrent Cis-regulatory Modules from known Motif

MOPAT

:: DESCRIPTION

MOPAT (Motif Pair Tree) identifies CRMs through the identification of motif modules, groups of motifs co-ccurring in multiple CRMs. It can identify orthologous CRMs without multiple alignments. It can also find CRMs given a large number of known motifs.

::DEVELOPER

Jianfei Hu: rochujf@gmail.com, Haiyan Nancy Hu , Xiaoman Shawn Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows

:: DOWNLOAD

 MOPAT

:: MORE INFORMATION

Citation:

Hu J, Hu H, Li X.
MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs.
Nucleic Acids Res. 2008; 36(13):4488-97

i-cisTarget – Prediction of Regulatory Features and Cis-regulatory modules in Drosophila

i-cisTarget

:: DESCRIPTION

i-cisTarget is an integrative genomics method for the prediction of regulatory features (motifs and in vivo features), and cis-regulatory modules in Drosophila

::DEVELOPER

Laboratory of Computational Biology @ the Center for Human Genetics (CME), at the Faculty of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Aug;40(15):e114. doi: 10.1093/nar/gks543. Epub 2012 Jun 20.
i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules.
Herrmann C1, Van de Sande B, Potier D, Aerts S.

ModuleDigger – An Itemset Mining framework for the Detection of Cis-regulatory Modules

ModuleDigger

:: DESCRIPTION

ModuleDigger is an itemset mining based strategy for computationally detecting cis-regulatory modules (CRMs) in a set of genes.

::DEVELOPER

 Kathleen Marchal 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ModuleDigger

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S30.
ModuleDigger: an itemset mining framework for the detection of cis-regulatory modules.
Sun H, De Bie T, Storms V, Fu Q, Dhollander T, Lemmens K, Verstuyf A, De Moor B, Marchal K.

PhylCRM 1.1 – Cis-regulatory Module (CRM) Prediction

PhylCRM 1.1

:: DESCRIPTION

PhylCRM is a new cis-regulatory module (CRM) prediction algorithm. PhylCRM combines data for individual motif occurances scored on an alignment using previously described MONKEY scoring sheme (Moses et al., Genome Biology 5, R98, 2004) into a single CRM prediction. PhylCRM can scan very long genomic sequences for candidate CRMs by quantifying both motif clustering and conservation across arbitrarily many genomes using an evolutionary model consistent with the phylogeny of the genomes.

::DEVELOPER

The Bulyk Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  PhylCRM

:: MORE INFORMATION

Citation

Nat Methods. 2008 Apr;5(4):347-53. doi: 10.1038/nmeth.1188. Epub 2008 Mar 2.
Systematic identification of mammalian regulatory motifs’ target genes and functions.
Warner JB, Philippakis AA, Jaeger SA, He FS, Lin J, Bulyk ML.

EMMA 1.1 – Prediction & Alignment of Cis-regulatory Modules

EMMA 1.1

:: DESCRIPTION

EMMA (Evolutionary Model-based cis-regulatory Module Analysis) is meant for prediction of regulatory targets of a motif using two-species comparison. If you have a sequence window of length ~100 bp – 2000 bp, and its orthologous window from another species, use EMMA to score the window for matches to a given motif. EMMA is also useful for alignment of cis-regulatory modules (enhancers) between two species, if you have knowledge of the relevant transcription factor motifs.

::DEVELOPER

The Sinha Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

EMMA

:: MORE INFORMATION

Citation

LoS Comput Biol. 2009 Mar;5(3):e1000299. doi: 10.1371/journal.pcbi.1000299.
Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution.
He X, Ling X, Sinha S.

IntHmm – Identifying Cis-Regulatory Modules in the Human Genome

IntHmm

:: DESCRIPTION

IntHmm is an integrated approach to identify cis-regulatory modules in human genome.

::DEVELOPER

Wei Wang’s group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 IntHmm

:: MORE INFORMATION

Citation

Won K-J, Agarwal S, Shen L, Shoemaker R, Ren B, et al. (2009)
An Integrated Approach to Identifying Cis-Regulatory Modules in the Human Genome.
PLoS ONE 4(5): e5501.

ModuleMaster 1.1 – Identify Cis-regulatory Modules using Promoter Analysis and Microarray Expression data Regression

ModuleMaster 1.1

:: DESCRIPTION

ModuleMaster is a novel application for finding cis-regulatory modules (CRMs) in sets of co-expressed genes. The application comes with a newly developed method which not only considers transcription factor binding information but also multivariate functional relationships between regulators and target genes to improve the detection of CRMs. Given only the results of a microarray and a subsequent clustering experiment, the program includes all necessary data and algorithms to perform every step to find CRMs.

::DEVELOPER

the Center for Bioinformatics Tübingen (Zentrum für Bioinformatik Tübingen, ZBIT).

:: SCREENSHOTS

ModuleMaster

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • Java

:: DOWNLOAD

  ModuleMaster

:: MORE INFORMATION

Citation

Biosystems. 2010 Jan;99(1):79-81. doi: 10.1016/j.biosystems.2009.09.005. Epub 2009 Oct 9.
ModuleMaster: a new tool to decipher transcriptional regulatory networks.
Wrzodek C, Schröder A, Dräger A, Wanke D, Berendzen KW, Kronfeld M, Harter K, Zell A.

CisPlusFinder 1.0 – Predict Cis-regulatory modules

CisPlusFinder 1.0

:: DESCRIPTION

 CisPlusFinder predicts cis-regulatory modules based on perfect local ungapped sequences using comparative sequence data from multiple organisms.

::DEVELOPER

the Bergman lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 CisPlusFinder

:: MORE INFORMATION

Citation

Pierstorff, N., C.M. Bergman & T. Wiehe. (2006)
Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA.
Bioinformatics 22:2858-2864.

CisModule 20051205 – De novo Discovery of Cis-regulatory Modules

CisModule 20051205

:: DESCRIPTION

CisModule: A Bayesian module sampler by hierachical mixture modeling

::DEVELOPER

Qing Zhou

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

 CisModule

:: MORE INFORMATION

Citation

Zhou, Q. and Wong, W.H. (2004).
CisModule: De novo discovery of cis-regulatory modules by hierarchical mixture modeling.
Proceedings of the National Academy of Sciences USA, 101: 12114-12119.