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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

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

[…] using transfac® database of transcription factors and their binding sites in genome and using transpath® database of signal transduction network with associated software such as match™ and composite module analyst (cma)., using genome-wide gene expression profiling we compared several lung cancer cell lines and showed that expression programs executed in nutlin-3 insensitive cell lines […]


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

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

[…] 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 […]


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

PMCID: 3504713
PMID: 22790872
DOI: 10.1038/cdd.2012.89

[…] 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 (, expression profiling of mcf7 cells was performed using affymetrix […]


Assessing Computational Methods of Cis Regulatory Module Prediction

PMCID: 2996316
PMID: 21152003
DOI: 10.1371/journal.pcbi.1001020

[…] 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 & […]


Assessment of composite motif discovery methods

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

[…] expected from chance alone. the types of the binding motifs are irrelevant, however, and each potential module instance is analyzed independently from the rest. other tools, like modulesearcher [], composite module analyst [] and creme [], search for specific combinations of motifs that co-occur multiple times in regulatory regions of related genes., with an increasing number of programs […]


Genome wide prediction of HNF4α functional binding sites by the use of local and global sequence context

PMCID: 2374721
PMID: 18291023
DOI: 10.1186/gb-2008-9-2-r36

[…] the assumed false positive match of the hnf4 matrix (we chose at random 642 sequence fragments scattered through intergenic regions on all human chromosomes)., we analyzed these sets using the composite module analyst (cma) program (see materials and methods), which allowed us to study combinations of tfbss in the interrogated sequences. input for cma is a set of dna sequences under study […]

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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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