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CMA specifications


Unique identifier OMICS_18434
Name CMA
Alternative name Composite Module Analyst
Interface Web user interface
Restrictions to use None
Input data A set of co-regulated genes.
Output data A model providing the best discrimination between the two promoter sets at the last iteration.
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Alexander Kel

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Publication for Composite Module Analyst

CMA citations


Computational master regulator search reveals mTOR and PI3K pathways responsible for low sensitivity of NCI H292 and A427 lung cancer cell lines to cytotoxic action of p53 activator Nutlin 3

BMC Med Genomics
PMCID: 5836833
PMID: 29504919
DOI: 10.1186/s12920-018-0330-5

[…] the condition of the experiment. We denote the study and background sets briefly as Yes and No sets. The «Genome Enhancer» module uses two algorithms for TFBS enrichment analysis: F-Match [] and CMA (Composite Module Analyst) []. F-Match algorithm finds a critical value (a threshold) for the score of each PWM in the library that maximizes the Yes/No ratio under the constraint of statistical signif […]


Genome Wide Transcriptional Profiles during Temperature and Oxidative Stress Reveal Coordinated Expression Patterns and Overlapping Regulons in Rice

PLoS One
PMCID: 3397947
PMID: 22815860
DOI: 10.1371/journal.pone.0040899

[…] ing the three stress conditions. Two different time points were used in our experiments to score ‘primary’ (at early time points) and ‘secondary’ (at late time points) changes in the gene expression. Composite module analyst (CMA) analysis was employed to unravel the key transcription factors that may explain concerted expression changes of specific components in various signal transduction networ […]


Insights into p53 transcriptional function via genome wide chromatin occupancy and gene expression analysis

Cell Death Differ
PMCID: 3504713
PMID: 22790872
DOI: 10.1038/cdd.2012.89

[…] sitional weight matrices (PWMs) from the TRANSFAC database for vertebrate TFs. Overrepresentation of TF-binding sites and composite elements (TF site pairs) were computed by the F-Match algorithm and composite module analyst program (Composite Module Analysts) that is implemented in the geneXplain platform ( […]


Assessing Computational Methods of Cis Regulatory Module Prediction

PLoS Comput Biol
PMCID: 2996316
PMID: 21152003
DOI: 10.1371/journal.pcbi.1001020
call_split See protocol

[…] studies that search for tissue specific or stage specific CRMs based on a set of co-regulated genes. Some studies also include information from microarray expression data, such as LRA , ClusterScan , Composite Module Analyst , and ModuleMiner . Other methods scan only for regions where a small set of user defined transcription factors bind but do not predict novel CRMs, such as STORM & MODSTORM , […]


Target Genes of the MADS Transcription Factor SEPALLATA3: Integration of Developmental and Hormonal Pathways in the Arabidopsis Flower

PLoS Biol
PMCID: 2671559
PMID: 19385720
DOI: 10.1371/journal.pbio.1000090
call_split See protocol

[…] ng the CArG box matrices in the profile. Site frequencies were compared to a control sequence set consisting of randomly sampled Arabidopsis promoters, assuming a binomial distribution. The algorithm Composite Module Analyst (CMA, []) was used to identify transcription modules overrepresented in the query dataset, based on the binding site prediction by MATCH. CMA parameters were set to find modul […]


Assessment of composite motif discovery methods

BMC Bioinformatics
PMCID: 2311304
PMID: 18302777
DOI: 10.1186/1471-2105-9-123

[…] Using our assessment framework, we benchmarked eight published methods for module discovery: CisModule [], Cister [], Cluster-Buster [], Composite Module Analyst (CMA) [], MCAST [], ModuleSearcher [], MSCAN [] and Stubb []. See Table for brief descriptions of each of these methods. CisModule, CMA and ModuleSearcher process all the seq […]

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CMA institution(s)
A.P. Ershov’s Institute of Informatics Systems, Novosibirsk, Russia; Institute of Cytology and Genetics, Novosibirsk, Russia; BIOBASE GmbH, Wolfenbuttel, Germany; Department Bioinformatics, UKG/University Gottingen, Gottingen, Germany
CMA funding source(s)
Supported by grant of the German Ministry of Education and Research (BMBF) together with BioRegioN GmbH ‘BioProfil’, grant no. 0313092; by European Commission under FP6-‘Life sciences, genomics and biotechnology for health’ contract LSHG-CT-2004- 503568 ‘COMBIO’ and contract no. 518153 ‘EuroDia’; by European Commission under ‘Marie Curie research training networks’ contract MRTN-CT-2004-512285 ‘TRANSISTOR’, and by INTAS grant no. 03-51-5218.

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