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TimeDelay-ARACNE specifications

Information


Unique identifier OMICS_10586
Name TimeDelay-ARACNE
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.30.0
Stability Stable
Requirements
Biobase, Rgraphviz, GenKern
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Michele Ceccarelli

Publication for TimeDelay-ARACNE

TimeDelay-ARACNE citations

 (5)
library_books

MapReduce Algorithms for Inferring Gene Regulatory Networks from Time Series Microarray Data Using an Information Theoretic Approach

2017
Biomed Res Int
PMCID: 5294223
PMID: 28243601
DOI: 10.1155/2017/6261802

[…] ne single-node server (denoted as MRS), the Java implementation of the M2 algorithm running on a single-node server, and the R implementation of the related time-delayed mutual information algorithm, TimeDelay-ARACNE []. In , it can be seen that MRC is highly scalable and that it outperforms the other three programs. Notably, due to Hadoop's overhead, MRS is even slower than the Java program. The […]

library_books

Inferring Weighted Directed Association Network from Multivariate Time Series with a Synthetic Method of Partial Symbolic Transfer Entropy Spectrum and Granger Causality

2016
PLoS One
PMCID: 5104482
PMID: 27832153
DOI: 10.1371/journal.pone.0166084

[…] the context likelihood of relatedness (CLR) algorithm, also used mutual information as a metric of similarity between the expression profiles of two genes. Zoppoli et al. [] proposed a method called TimeDelay-ARACNE. It tries to extract dependencies between two genes at different time delays, providing a measure of these dependencies in terms of mutual information. TimeDelay-ARACNE can infer smal […]

library_books

DTW MIC Coexpression Networks from Time Course Data

2016
PLoS One
PMCID: 4816347
PMID: 27031641
DOI: 10.1371/journal.pone.0152648

[…] figshare, at the URL https://figshare.com/articles/Gene_Net_Weaver_Dataset/2279628.In each of the three cases Yeast20, Ecoli20 and Ecoli50, a network is inferred by PCC, DTW-MIC, Transfer Entropy and TimeDelay ARACNE from each of the time course dataset {d1, …, d10}, and the obtained graph is compared via the HIM distance to the corresponding true network. As an example, in we show the true Yeast […]

library_books

Highly sensitive inference of time delayed gene regulation by network deconvolution

2014
BMC Syst Biol
PMCID: 4290726
PMID: 25521243
DOI: 10.1186/1752-0509-8-S4-S6

[…] layed GRN. In 2010, a dynamic version of ARACNE (Algorithm for the Reconstruction of Accurate Cellular Networks) was introduced to infer time-delayed dependencies among genes []. Their method, called TimeDelay ARACNE (or TD-ARACNE), is able to reconstruct time-delayed dependencies effectively. In 2012, Morshed et al. proposed a framework to infer instantaneous and time-delayed genetic interactions […]

library_books

A negative selection heuristic to predict new transcriptional targets

2013
BMC Bioinformatics
PMCID: 3548675
PMID: 23368951
DOI: 10.1186/1471-2105-14-S1-S3

[…] n a given pair of genes [-]. Those methods can be distinguished in: i) gene relevance network models, which detect gene-gene interactions with a similarity measure and a threshold, such as ARACNE [], TimeDelay-ARACNE [], and CLR [] that infer the network structure with a statistical score derived from the mutual information and a set of pruning heuristics; ii) boolean network models, which adopt a […]


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TimeDelay-ARACNE institution(s)
Department of Biological and Environmental Studies, University of Sannio, Benevento, Italy; Biogem scarl, Institute for Genetic Research "Gaetano Salvatore", Ariano Irpino (Avellino), Italy
TimeDelay-ARACNE funding source(s)
This work was supported by Italian Ministry MIUR (PRIN 20085CH22F).

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