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DDN specifications

Information


Unique identifier OMICS_08326
Name DDN
Alternative name Differential Dependency Network
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java, MATLAB
Computer skills Advanced
Stability Stable
Requirements
Cytoscape
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Yue Wang

Publications for Differential Dependency Network

DDN citations

 (7)
call_split

A transcriptome analysis of two grapevine populations segregating for tendril phyllotaxy

2017
PMCID: 5506248
PMID: 28713572
DOI: 10.1038/hortres.2017.32
call_split See protocol

[…] s were facilitated using the algorithm implemented by Plant RegMap.To assess changes in co-expression topology in the mutant and wild-type background, network-based analysis was carried out using the differential dependency network (DDN) algorithm as implemented in its Cytoscape-based version, knowledge-fused differential dependency network (KDDN), where the predicted cis-regulatory connections am […]

library_books

Biological Networks for Cancer Candidate Biomarkers Discovery

2016
Cancer Inform
PMCID: 5012434
PMID: 27625573
DOI: 10.4137/CIN.S39458

[…] d networks.The aim of GRNs is to mathematically capture the dependencies between transcriptional regulatory genes and their downstream targets. Zhang et al., proposed a local dependency method called differential dependency network (DDN) to find statistically significant topological changes in GRNs under two biological conditions, which provides an alternative mean for biomarker prediction. This m […]

library_books

Identifying Network Perturbation in Cancer

2016
PLoS Comput Biol
PMCID: 4856318
PMID: 27145341
DOI: 10.1371/journal.pcbi.1004888

[…] squares model to each gene, computes a connectivity scores between genes, and then calculates the L1 distance between score vectors to estimate network perturbation []. Zhang et al. (2009) proposed a differential dependency network (DDN) method that uses lasso regression to construct networks, followed by permutation tests to measure the significance of the network differences [].There have been a […]

library_books

A powerful score based statistical test for group difference in weighted biological networks

2016
BMC Bioinformatics
PMCID: 4751708
PMID: 26867929
DOI: 10.1186/s12859-016-0916-x

[…] pology information to carry out various biomedical tasks. Langfelder et al. [] provided several measures for comparing network topologies for weighted correlation networks. Zhang et al. [] proposed a differential dependency network analysis to detect topological changes in transcriptional networks between subclasses of breast cancer. Valcarcel et al. [] introduced a formal statistical method for t […]

library_books

Integrative network based approach identifies key genetic elements in breast invasive carcinoma

2015
BMC Genomics
PMCID: 4460623
PMID: 26040466
DOI: 10.1186/1471-2164-16-S5-S2

[…] In order to validate the proposed approach and the constructed network topology [TF-gene interactions only], we applied a peer knowledge-based differential network method, KDDN (Knowledge-Guided Differential Dependency Network) [] on the same dataset. The same prior was used for KDDN. The networks predicted by our approach showed 61% edges overlap with the inferred differential KDDN interacti […]

library_books

Pathway mapping and development of disease specific biomarkers: protein based network biomarkers

2015
J Cell Mol Med
PMCID: 4407592
PMID: 25560835
DOI: 10.1111/jcmm.12447

[…] nowledge-based networks via the combination of genomics, proteomics and bioinformatics, such as GRNInfer , MDCinfer , TRNInfer , Samo , MNAligner , PTG , PRNA , NOA , differential dependency network (DDN) , WGCNA , SurvNet or DiME , each of them has its own advantages and strength on basis of scientific needs and investigative goals, as summarized in Table.Methodologies for expression data integr […]

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DDN institution(s)
Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA, USA

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