Tag: Network Analysis

OCSANA – Optimal Combinations of Interventions from Network Analysis

OCSANA

:: DESCRIPTION

OCSANA is a new software designed to identify and prioritize optimal and minimal combinations of interventions to disrupt the paths between source nodes and target nodes

::DEVELOPER

U900 Institut Curie – INSERM/Mines ParisTech “Bioinformatics and Computational Systems Biology of Cancer

:: SCREENSHOTS

OCSANA

:: REQUIREMENTS

:: DOWNLOAD

 OCSANA

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jun 15;29(12):1571-3. doi: 10.1093/bioinformatics/btt195. Epub 2013 Apr 26.
OCSANA: optimal combinations of interventions from network analysis.
Vera-Licona P, Bonnet E, Barillot E, Zinovyev A.

GenCLiP 3 – Human Gene Function And Network Analysis

GenCLiP 3

:: DESCRIPTION

GenCLiP is a literature mining tool that can cluster a list of genes with keywords that are auto-extracted from their up-to-date related literature and then manually curated by the user. GenCLiP can also generate a group of negative control genes and a group of positive control genes for comparing the cluster results with the analyzed genes to filter out un-specific keywords.

::DEVELOPER

GenCLiP team

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Wang JH, Zhao LF, Wang HF, Wen YT, Jiang KK, Mao XM, Zhou ZY, Yao KT, Geng QS, Guo D, Huang ZX.
GenCLiP 3: mining human genes’ functions and regulatory networks from PubMed based on co-occurrences and natural language processing.
Bioinformatics. 2019 Nov 4:btz807. doi: 10.1093/bioinformatics/btz807. Epub ahead of print. PMID: 31681951.

Bioinformatics. 2014 Apr 23. pii: btu241. [Epub ahead of print]
GenCLiP 2.0: a web server for functional clustering of genes and construction of molecular networks based on free terms.
Wang JH, Zhao LF, Lin P, Su XR, Chen SJ, Huang LQ, Wang HF, Zhang H, Hu ZF, Yao KT, Huang ZX.

BMC Bioinformatics. 2008 Jul 13;9:308.
GenCLiP: a software program for clustering gene lists by literature profiling and constructing gene co-occurrence networks related to custom keywords.
Huang ZX, Tian HY, Hu ZF, Zhou YB, Zhao J, Yao KT.

NAIL 1.01 – Network Analysis in the Life Sciences

NAIL 1.01

:: DESCRIPTION

The NAIL (Network Analysis and Inference Library) project is a set of tools for solving problems in the life sciences using network (graph) approaches. NAIL includes methods for creating networks, analysing and comparing networks, and for visualising or presenting the results.

::DEVELOPER

NAIL team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • MaxLab

:: DOWNLOAD

  NAIL

:: MORE INFORMATION

Citation

NAIL, a software toolset for inferring, analyzing and visualizing regulatory networks.
Hurley DG, Cursons J, Wang YK, Budden DM, Print CG, Crampin EJ.
Bioinformatics. 2014 Sep 21. pii: btu612.

NeAT – Network Analysis Tools

NeAT

:: DESCRIPTION

NeAT is a toolbox for the analysis of biological networks, clusters, classes and pathways.

::DEVELOPER

NeAT Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 NeAT

:: MORE INFORMATION

Citation

Network Analysis Tools: from biological networks to clusters and pathways.
Brohée S, Faust K, Lima-Mendez G, Vanderstocken G, van Helden J.
Nat Protoc. 2008;3(10):1616-29. doi: 10.1038/nprot.2008.100.

SNPrank 0.1.0 – Network Analysis tool for GWAS

SNPrank 0.1.0

:: DESCRIPTION

SNPrank is an eigenvector centrality algorithm that ranks the importance of single nucleotide polymorphisms (SNPs) in a genetic association interaction network (GAIN). Each SNP is ranked according to its overall contribution to the phenotype, including its main effect and second- and higher-order gene-gene interactions.

::DEVELOPER

Insilico Research Group (McKinney Laboratory for Bioinformatics and In Silico Modeling)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python / Java / MatLab

:: DOWNLOAD

 pysnprank ,  matsnprank , jsnprank

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jan 15;27(2):284-5. doi: 10.1093/bioinformatics/btq638. Epub 2010 Nov 25.
Real-world comparison of CPU and GPU implementations of SNPrank: a network analysis tool for GWAS.
Davis NA, Pandey A, McKinney BA.

iDINGO 1.0.4 – Integrative Differential Network Analysis in Genomics

iDINGO 1.0.4

:: DESCRIPTION

iDINGO is an R package to estimate group-specific integrative networks and make inference on the integrative differential networks, considering the biological hierarchy among the platforms

::DEVELOPER

iDINGO team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R

:: DOWNLOAD

 iDINGO

:: MORE INFORMATION

Citation:

Class CA, Ha MJ, Baladandayuthapani V, Do KA.
iDINGO-integrative differential network analysis in genomics with Shiny application.
Bioinformatics. 2018 Apr 1;34(7):1243-1245. doi: 10.1093/bioinformatics/btx750. PMID: 29194470; PMCID: PMC6030922.

DINGO: Differential Network Analysis in Genomics.
Ha MJ, Baladandayuthapani V, Do KA.
Bioinformatics. 2015 Jul 6. pii: btv406.

PINBPA 1.1.9 – Cytoscape app for Network Analysis of GWAS data

PINBPA 1.1.9

:: DESCRIPTION

PINBPA (Protein interaction network-based pathway analysis) for genome-wide association studies (GWAS) has been developed as a Cytoscape app, to enable analysis of GWAS data in a network fashion.

::DEVELOPER

PINBPA team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 PINBPA

:: MORE INFORMATION

Citation

PINBPA: Cytoscape app for network analysis of GWAS data.
Wang L, Matsushita T, Madireddy L, Mousavi P, Baranzini S.
Bioinformatics. 2014 Sep 25. pii: btu644

NetBox 1.0 – Perform Network Analysis on Human Interaction Networks

NetBox 1.0

:: DESCRIPTION

NetBox is a Java-based software tool for performing network analysis on human interaction networks. It is pre-loaded with a Human Interaction Network (HIN) derived from four literature curated data sources, including the Human Protein Reference Database (HPRD), Reactome, NCI-Nature Pathway Interaction (PID) Database, and the MSKCC Cancer Cell Map.

::DEVELOPER

Computational Biology Center @ Memorial Sloan Kettering Cancer Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 NetBox

:: MORE INFORMATION

Citation

Cerami E, Demir E, Schultz N, Taylor BS, Sander C (2010)
Automated Network Analysis Identifies Core Pathways in Glioblastoma.
PLoS ONE 5(2): e8918.

Cytoscape 3.8.2 – Platform for Complex-Network Analysis & Visualization

Cytoscape 3.8.2

:: DESCRIPTION

Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.

Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization.

::DEVELOPER

Cytoscape Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

Cytoscape

:: MORE INFORMATION

Citation:

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T.
Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Genome Research 2003 Nov; 13(11):2498-504

PINTA – Gene Prioritization by Network Analysis

PINTA

:: DESCRIPTION

PINTA is a gene prioritization tool that identifies the most promising candidates within a region when only sparse information about the phenotype is available by replacing this knowledge by experimental data on differential gene expression between affected and healthy individuals. Considering the problem from the perspective of a gene/protein network, it assesses the relevance of a candidate gene by considering the level of differential expression in its network neighborhood under the assumption that strong candidates tend to be surrounded by differentially expressed neighbors.

::DEVELOPER

Bioinformatics Research Group, Belgium

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W334-8. doi: 10.1093/nar/gkr289. Epub 2011 May 20.
PINTA: a web server for network-based gene prioritization from expression data.
Nitsch D, Tranchevent LC, Gon?alves JP, Vogt JK, Madeira SC, Moreau Y.