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CoMDP specifications

Information


Unique identifier OMICS_10916
Name CoMDP
Alternative name Co-occurring Mutated Driver Pathways
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Co-occurring Mutated Driver Pathways

CoMDP citations

 (5)
library_books

Integration of multiple networks and pathways identifies cancer driver genes in pan cancer analysis

2018
BMC Genomics
PMCID: 5756345
PMID: 29304754
DOI: 10.1186/s12864-017-4423-x

[…] ained by other well-validated computational methods used to identify cancer driver genes, such as ActiveDriver [], Dendrix [], MDPFinder [], Simon [], NetBox [], OncodriveFM [], MutsigCV [], MeMo [], CoMDP [], DawnRank [], DriverNet [], e-Driver [], iPAC [], MSEA [], and OncodriveCLUST [].We applied DriverDB [] to obtain results from all these algorithms and the cancer datasets considered by our c […]

library_books

Progression inference for somatic mutations in cancer

2017
PMCID: 5415494
PMID: 28492066
DOI: 10.1016/j.heliyon.2017.e00277

[…] ncers. DriverDB assembles together lists of the top ranked driver genes determined from the use of 15 packages, including ActiveDriver, Dendrix, MDPFinder, Simon, NetBox, OncodriveFM, MutSigCV, MEMo, CoMDP, DawnRank, DriverNet, e-Driver, iPAC, MSEA, and OncodriveCLUST. lists the cancer types, sample size, and descriptions of the driver genes used, including chromosome location, gene ontology nome […]

library_books

Identification of driver modules in pan cancer via coordinating coverage and exclusivity

2017
Oncotarget
PMCID: 5482642
PMID: 28415609
DOI: 10.18632/oncotarget.16433

[…] he trade-off between coverage and exclusivity []. Multi-Dendrix [] designed a new metric as the sum of Dendrix weights and adopted a new programming model to identify multiple modules simultaneously. CoMDP proposed an exact mathematical programming method to identify co-occurring mutated driver pathways []. However, the mutational landscape of cancer usually consists of genes of which some are mut […]

library_books

Discovery of cancer common and specific driver gene sets

2017
Nucleic Acids Res
PMCID: 5449640
PMID: 28168295
DOI: 10.1093/nar/gkx089

[…] s in cancer. More importantly, the collaboration among different pathways means these gene sets are likely simultaneously mutated in a large cohort of patients. To this end, Zhang et al. () developed CoMDP to de novo discover co-occurring mutated driver gene sets in cancer by introducing a novel weight function and a mathematical programming model; Melamed et al. () introduced an information theor […]

library_books

Membrane Topology and Structural Insights into the Peptide Pheromone Receptor ComD, A Quorum Sensing Histidine Protein Kinase of Streptococcus mutans

2016
Sci Rep
PMCID: 4873836
PMID: 27199267
DOI: 10.1038/srep26502

[…] alman-Gal) for β-galactosidase activity (LacZ) using the methods as described previously. The results showed that the strains expressing the ComDL38-Pho/Lac (L38), the ComDT110-Pho/Lac (T110) and the ComDP187-Pho/Lac (P187) exhibited the higher levels of phosphatase activities (blue color), indicating the periplasmic or extracellular location of these fusion points (). In contrast, the strains exp […]

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CoMDP institution(s)
National Center for Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China
CoMDP funding source(s)
This project was supported by the National Natural Science Foundation of China, No. 61379092 and 11131009, the Foundation for Members of Youth Innovation Promotion Association, CAS, The Outstanding Young Scientist Program of CAS, the Scientific Research Foundation for ROCS, SEM, and the Key Laboratory of Random Complex Structures and Data Science, CAS.

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