ARACNE pipeline

ARACNE specifications

Information


Unique identifier OMICS_01851
Name ARACNE
Alternative names Algorithm for the Reconstruction of Accurate Cellular Networks, ARACNe-AP
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, Java
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Documentation


Maintainers


  • person_outline Artemis G. Hatzigeorgiou <>
  • person_outline Andrea Califano <>

Additional information


https://sourceforge.net/projects/aracne-ap/

Publications for Algorithm for the Reconstruction of Accurate Cellular Networks

ARACNE IN pipelines

 (11)
2014
PMCID: 4229886
PMID: 24885447
DOI: 10.1186/1471-2164-15-373

[…] (nā€‰=ā€‰21) placentas based on gestational age., gse10588 was previously analyzed with respect to global differential gene expression patterns. we conducted a novel analysis on this dataset by using the algorithm for the reconstruction of accurate cellular networks (aracne) [25] integrated into geworkbench (http://wiki.c2b2.columbia.edu/workbench) in order to infer transcriptional relationships and i […]

2014
PMCID: 4229886
PMID: 24885447
DOI: 10.1186/1471-2164-15-373

[…] analyzed with respect to global differential gene expression patterns. we conducted a novel analysis on this dataset by using the algorithm for the reconstruction of accurate cellular networks (aracne) [25] integrated into geworkbench (http://wiki.c2b2.columbia.edu/workbench) in order to infer transcriptional relationships and identify key gene regulators. aracne is an information-theory […]

2014
PMCID: 4229886
PMID: 24885447
DOI: 10.1186/1471-2164-15-373

[…] of accurate cellular networks (aracne) [25] integrated into geworkbench (http://wiki.c2b2.columbia.edu/workbench) in order to infer transcriptional relationships and identify key gene regulators. aracne is an information-theory based method developed to reconstruct gene regulatory networks in mammalian cellular context using gene expression profiles [25]. aracne calculates mutual information […]

2014
PMCID: 4229886
PMID: 24885447
DOI: 10.1186/1471-2164-15-373

[…] and identify key gene regulators. aracne is an information-theory based method developed to reconstruct gene regulatory networks in mammalian cellular context using gene expression profiles [25]. aracne calculates mutual information (mi) between every combination of genes. if interactions (edges) between more than two genes (nodes) are found, aracne uses the data processing inequality (dpi) […]

2014
PMCID: 4229886
PMID: 24885447
DOI: 10.1186/1471-2164-15-373

[…] context using gene expression profiles [25]. aracne calculates mutual information (mi) between every combination of genes. if interactions (edges) between more than two genes (nodes) are found, aracne uses the data processing inequality (dpi) algorithm to remove the weakest interaction. in our analyses, the threshold for mi was set at pā€‰=ā€‰10-7 and dpi was set at 0.15., further analysis […]

ARACNE institution(s)
Department of Biomedical Informatics, Columbia University, New York, NY, USA; Joint Centers for Systems Biology, Columbia University, New York, NY, USA; Institute for Cancer Genetics, Columbia University, New York, NY, USA; Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY, USA; IBM T.J. Watson Research Center, Yorktown Heights, NY; USA
ARACNE funding source(s)
Supported by the NCI (1R01CA109755-01A1) and the NIAID (1R01AI066116-01), the NLM Medical Informatics Research Training Program (5 T15 LM007079-13).

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