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GRAM specifications

Information


Unique identifier OMICS_28752
Name GRAM
Alternative name Genetic RegulAtory Modules
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Version 0.6
Stability Stable
Maintained Yes

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Maintainer


  • person_outline David Gifford

Publication for Genetic RegulAtory Modules

GRAM citations

 (3)
library_books

Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes

2015
PMCID: 4666684
PMID: 26446758
DOI: 10.3109/10409238.2015.1087961

[…] have been developed to correlate model organism or human TF ChIP-chip and ChIP-seq data with gene expression; such methods include partial least squares (PLS) regression (Boulesteix & Strimmer, ), a genetic regulatory modules (GRAM) algorithm (Bar-Joseph et al., ), a probabilistic model termed target identification from profiles (TIP) (Cheng et al., ), a support vector machine (SVMs) (Qian et al. […]

library_books

A systems biology approach to construct the gene regulatory network of systemic inflammation via microarray and databases mining

2008
BMC Med Genomics
PMCID: 2567339
PMID: 18823570
DOI: 10.1186/1755-8794-1-46

[…] ased on the expression profiles of microarray data. An approach of combining genome-wide expression analysis with a clustering method has been introduced to identify functional networks using a GRAM (Genetic Regulatory Modules) algorithm to provide biological insights into gene regulatory networks []. Because the clustering algorithms are employed to identify sets of co-expressed and potentially c […]

library_books

Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP chip data

2007
BMC Bioinformatics
PMCID: 1994961
PMID: 17683565
DOI: 10.1186/1471-2105-8-283

[…] analysis is conditional on co-expression of the two genes.Several heuristic algorithms have been developed for constructing TMs by integrated analysis of gene expression and binding (ChIP-chip) data. Genetic Regulatory Modules (GRAM) algorithm [] uses binding data to identify a gene set bound to common TFs (p-value < 0.001). It then searches for other genes at a lower level of significance (p-valu […]

Citations

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GRAM institution(s)
MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA, USA; MIT Department of Biology, Cambridge, MA, USA
GRAM funding source(s)
Supported by the Program in Mathematics and Molecular Biology at Florida State University through the Burroughs Wellcome Fund Interfaces Program, a National Defense Engineering and Science graduate fellowship, and partially funded by a US National Institutes of Health grant.

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