VANTED 2.6.5 – Visualization and Analysis of Networks containing Experimental Data

VANTED 2.6.5

:: DESCRIPTION

VANTED (Visualisation and Analysis of Networks containing Experimental Data) is an open source software that offers the possibility to load and edit graphs, which may represent biological pathways or functional hierarchies. It allows to integrate different *omics data into the functional context and provides a variety of functions for data mapping and processing, statistical analysis, and visualisation. With the VANTED Add-on interface it is easily possible to extend the functionality of the software.

::DEVELOPER

Life Science Informatics – Prof. Dr. Falk Schreiber

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux/  MacOSX
  • Java

:: DOWNLOAD

 VANTED

:: MORE INFORMATION

Citation

Klukas and Schreiber (2010)
Integration of -omics data and networks for biomedical research with VANTED.
Journal of Integrative Biology, 7(2)

Björn H. Junker, Christian Klukas and Falk Schreiber (2006)
VANTED: A system for advanced data analysis and visualization in the context of biological networks.
BMC Bioinformatics, 7:109

SalmoNet – An Integrated multi-layered Network of Salmonella

SalmoNet

:: DESCRIPTION

SalmoNet is an unique resource which combines manual curation, high-throughput data and computational predictions to provide an integrated network for Salmonella at the transcriptional regulatory, metabolic and protein-protein interaction levels.

::DEVELOPER

the Earlham Institute.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

SalmoNet, an integrated network of ten Salmonella enterica strains reveals common and distinct pathways to host adaptation
Métris A., Sudhakar P., Fazekas D., Demeter A., Ari E., Branchu P, Kingsley R.A., Baranyi J., Korcsmáros T.
NPJ Syst Biol Appl. 2017 Oct 18;3:31. doi: 10.1038/s41540-017-0034-z. eCollection 2017.

GWAB – Web Server for Network-based Boosting of Human Genome-wide Association data

GWAB

:: DESCRIPTION

GWAB (genome-wide Association Boosting) is a web server for the network-based boosting of human GWAS data.

::DEVELOPER

Network Biomedicine Laboratory at Yonsei University, Korea

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2017 Jul 3;45(W1):W154-W161. doi: 10.1093/nar/gkx284.
GWAB: a web server for the network-based boosting of human genome-wide association data.
Shim JE, Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom UM, Marcotte EM, Lee I.

NGSEA – Network-augmented Gene Set Enrichment analysis tool

NGSEA

:: DESCRIPTION

NGSEA (network-based GSEA) measures the enrichment score of functional gene sets using the expression difference of not only individual genes but also their neighbors in the functional network.

::DEVELOPER

Network Biomedicine Laboratory at Yonsei University, Korea

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Mol Cells. 2019 Aug 31;42(8):579-588. doi: 10.14348/molcells.2019.0065.
NGSEA: Network-Based Gene Set Enrichment Analysis for Interpreting Gene Expression Phenotypes with Functional Gene Sets.
Han H, Lee S, Lee I

HumanNet v2 – Human Gene Networks for Disease Research

HumanNet v2

:: DESCRIPTION

HumanNet is a human functional gene network by integrating diverse types of omics data using Bayesian statistics framework and demonstrated its ability to retrieve disease genes.

::DEVELOPER

Network Biomedicine Laboratory at Yonsei University, Korea

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

HumanNet v2: human gene networks for disease research.
Hwang S, Kim CY, Yang S, Kim E, Hart T, Marcotte EM, Lee I.
Nucleic Acids Res. 2019 Jan 8;47(D1):D573-D580. doi: 10.1093/nar/gky1126.

RIDDLE – Network-assisted Gene Set Analysis

RIDDLE

:: DESCRIPTION

RIDDLE (Reflective diffusion and local extension)is a network-based method for characterizing gene sets. It asks if an input query set is significantly “close” to a known pathway or disease set in the human functional network.

::DEVELOPER

Network Biomedicine Laboratory at Yonsei University, Korea and the Marcotte Lab at University of Texas at Austin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Genome Biol. 2012 Dec 26;13(12):R125. doi: 10.1186/gb-2012-13-12-r125.
RIDDLE: reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network.
Wang PI, Hwang S, Kincaid RP, Sullivan CS, Lee I, Marcotte EM.

FNV 1.0 – Light-weight Flash-based Network and Pathway Viewer

FNV 1.0

:: DESCRIPTION

FNV (Flashed-based Network Viewer) is for the visualization of small to moderately sized biological networks and pathways. FVN can also be used to embed pathways inside PDF files for the communication of pathways in soft publication materials

::DEVELOPER

Ma’ayan Laboratory

:: SCREENSHOTS

FNV

:: REQUIREMENTS

  • Windows/Linux
  • Flash Player 

:: DOWNLOAD

 FNV

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Apr 15;27(8):1181-2. doi: 10.1093/bioinformatics/btr098. Epub 2011 Feb 23.
FNV: light-weight flash-based network and pathway viewer.
Dannenfelser R, Lachmann A, Szenk M, Ma’ayan A.

CIPHER – Correlating Protein Interaction Network and Phenotype Network to predict Disease Genes

CIPHER

:: DESCRIPTION

CIPHER, which stands for Correlating interactome and phenome networks to predict disease genes, is a computational framework we proposed to prioritize human disease genes. It was one of the first studies to explore interactome-phenome wide gene-disease relationships, and generated the first comprehensive genetic landscape of human disease,connecting 5080 human disease phenotypes with 14433 human genes.

::DEVELOPER

Wu Lab @ Columbia

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • MatLab

:: DOWNLOAD

NO

 :: MORE INFORMATION

Citation:

Mol Syst Biol. 2008;4:189. doi: 10.1038/msb.2008.27. Epub 2008 May 6.
Network-based global inference of human disease genes.
Wu X1, Jiang R, Zhang MQ, Li S.

GeneStitch 1.2.1 – Network Matching Algorithm to Gene Assembly

GeneStitch 1.2.1

:: DESCRIPTION

GeneStitch is a tool to assemble genes using network matching algorithm. Given an already-assembled dataset, it is capable of assembling contigs together to form more complete genes with the help of a reference gene set. Currently the assembly software that GeneStitch support is SOAPdenovo.

::DEVELOPER

Yuzhen Ye lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  GeneStitch

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Sep 15;28(18):i363-i369. doi: 10.1093/bioinformatics/bts388.
Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics.
Wu YW, Rho M, Doak TG, Ye Y.

CytoscapeRPC 1.8 – Create, Query and Modify Cytoscape Networks

CytoscapeRPC 1.8

:: DESCRIPTION

CytoscapeRPC is a Cytoscape plug-in which allows users to create, query and modify Cytoscape networks. This means that you can automate your Cytoscape tasks from any programming language which supports XML-RPC

::DEVELOPER

The Delft Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CytoscapeRPC

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Sep 1;27(17):2451-2. Epub 2011 Jun 27.
CytoscapeRPC: a plugin to create, modify and query Cytoscape networks from scripting languages.
Bot JJ, Reinders MJ.