:: DESCRIPTION
CONTOUR is a systematic tracking of dysregulated modules identifies novel genes in cancer
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Srihari S & Ragan MA (2013)
Systematic tracking of dysregulated modules identifies novel genes in cancer,
Bioinformatics 29(12):1553–1561. doi: 10.1093/bioinformatics/btt191
:: DESCRIPTION
ModuleAlign uses a novel scoring scheme that integrates sequence information and both local and global network topology. It computes a homology score between proteins based on a hierarchical clustering of the input networks. (a) shows the hierarchical structure of a network. Leaves represent the proteins and each cluster joins sets of proteins with similar interactions.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Hashemifar S, Ma J, Naveed H, Canzar S, Xu J.
ModuleAlign: module-based global alignment of protein-protein interaction networks.
Bioinformatics. 2016 Sep 1;32(17):i658-i664. doi: 10.1093/bioinformatics/btw447. PMID: 27587686.
:: DESCRIPTION
Stubb uses a probabilistic model and a maximum likelihood approach to efficiently detect cis-regulatory modules over genomic scales.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W555-9.
Stubb: a program for discovery and analysis of cis-regulatory modules.
Sinha S, Liang Y, Siggia E.
:: DESCRIPTION
Heinz is a tool for single-species active module discovery.
xHeinz is a software solver that searches for active subnetwork modules that are conserved between two species. It uses a branch-and-cut algorithm that finds provably optimal or near-optimal solutions.
::DEVELOPER
Algorithmic Bioinformatics, Heinrich-Heine-Universität Düsseldorf
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
xHeinz: An algorithm for mining cross-species network modules under a flexible conservation model.
El-Kebir M, Soueidan H, Hume T, Beisser D, Dittrich M, Müller T, Blin G, Heringa J, Nikolski M, Wessels LF, Klau GW.
Bioinformatics. 2015 May 27. pii: btv316
:: DESCRIPTION
MERLIN (Modular regulatory network learning with per gene information) is an algorithm for learning regulatory networks that strikes a balance between per-gene and per-module methods.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Roy S, Lagree S, Hou Z, Thomson JA, Stewart R, Gasch AP.
Integrated module and gene-specific regulatory inference implicates upstream signaling networks.
PLoS Comput Biol. 2013;9(10):e1003252. doi: 10.1371/journal.pcbi.1003252. Epub 2013 Oct 17. PMID: 24146602; PMCID: PMC3798279.
:: DESCRIPTION
PETModule is a software developed to find enhancer target gene (ETG) pairs through a motif module based approach. The output of the software is the enhancer target gene pairs with a probability score that measures how likely the predicted target gene is reliable. PETModule only needs enhancer locations to predict their target genes.
::DEVELOPER
Hu Lab – Data Integration and Knowledge Discovery @ UCF
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Sci Rep. 2016 Jul 20;6:30043. doi: 10.1038/srep30043.
PETModule: a motif module based approach for enhancer target gene prediction.
Zhao C, Li X, Hu H.
:: DESCRIPTION
GibbsModule is a software for de novo detection of cis-regulatory motifs and modules in eukaryote genomes. GibbsModule models the coexpressed genes within one species as sharing a core cis-regulatory motif and each homologous gene group as sharing a homologous cis-regulatory module (CRM), characterized by a similar composition of motifs.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Genome Res. 2008 Aug;18(8):1325-35. Epub 2008 May 15.
Cross-species de novo identification of cis-regulatory modules with GibbsModule: application to gene regulation in embryonic stem cells.
Xie D, Cai J, Chia NY, Ng HH, Zhong S.
:: DESCRIPTION
EgoNet is implemented by Python and it is designed to detecting disease related subnetwork from a large biological network (PPI, metabolic network) combined with gene expression data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Genomics. 2014 Apr 28;15:314. doi: 10.1186/1471-2164-15-314.
EgoNet: identification of human disease ego-network modules.
Yang R, Bai Y, Qin Z, Yu T
:: DESCRIPTION
MORPH is an algorithm for revealing missing genes in biological pathways, and demonstrate its capabilities
MORPH-R is Morph R package.
::DEVELOPER
Ron Shamir’s lab and Eleanore Wurtzel’s lab
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Tzfadia, O., Amar, D., Bradbury, L.M.T., Wurtzel, E.T., and Shamir, R. (2012)
The MORPH algorithm: ranking candidate genes for membership in Arabidopsis thaliana and Solanum lycopersicum pathways.
Plant Cell. 2012 Nov;24(11):4389-406. doi: 10.1105/tpc.112.104513.
Physiol Plant. 2015 Jan 27. doi: 10.1111/ppl.12326. [Epub ahead of print]
The MORPH-R web server and software tool for predicting missing genes in biological pathways.
Amar D, Frades I, Diels T, Zaltzman D, Ghatan N, Hedley PE, Alexandersson E, Tzfadia O, Shamir R.
