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|Alternative name||Genetic RegulAtory Modules|
|Interface||Command line interface|
|Restrictions to use||None|
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- person_outline David Gifford
Publication for Genetic RegulAtory Modules
Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes
[…] 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. […]
A systems biology approach to construct the gene regulatory network of systemic inflammation via microarray and databases mining
[…] 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 […]
Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP chip data
[…] 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 […]
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