Tag: Pathway

Pathview 1.24.0 – R package for Pathway based Data Integration and Visualization

Pathview 1.24.0

:: DESCRIPTION

Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs.

::DEVELOPER

Weijun Luo <luo_weijun at yahoo dot com>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 Pathview

:: MORE INFORMATION

Citation

Pathview: an R/Bioconductor package for pathway-based data integration and visualization.
Luo W, Brouwer C.
Bioinformatics. 2013 Jul 15;29(14):1830-1. doi: 10.1093/bioinformatics/btt285.

CluePedia 1.0.5 – Provide Insights into Pathways by integrating Experimental and in silico Information

CluePedia 1.0.5

:: DESCRIPTION

CluePedia provides a holistic view on a pathway or process by investigating experimental and in silico data from different perspectives: gene interrelations revealed by correlation weights, miRNAs regulatory aspects, protein – protein interactions as well as the functional context, in conjunction with ClueGO. This review is helpful for defining new hypothesis and strategies that allow one more step in understanding complex processes.

::DEVELOPER

Integrative Cancer Immunology Laboratory

:: SCREENSHOTS

CluePedia

:: REQUIREMENTS

:: DOWNLOAD

 CluePedia

:: MORE INFORMATION

Citation

Bindea G, Galon J and Mlecnik B.
CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data.
Bioinformatics. 2013 Mar 1;29(5):661-3.

ClueGO 2.0.5 – Cytoscape Plugin to Decipher Gene Ontology and Pathway Annotation Networks

ClueGO 2.0.5

:: DESCRIPTION

ClueGO is a Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network and it can be used in combination with GOlorize. The identifiers can be uploaded from a text file or interactively from a network of Cytoscape. The type of identifiers supported can be easely extended by the user. ClueGO performs single cluster analysis and comparison of clusters. From the ontology sources used, the terms are selected by different filter criteria. The related terms which share similar associated genes can be fused to reduce redundancy. The ClueGO network is created with kappa statistics and reflects the relationships between the terms based on the similarity of their associated genes. On the network, the node colour can be switched between functional groups and clusters distribution. ClueGO charts are underlying the specificity and the common aspects of the biological role.

::DEVELOPER

Integrative Cancer Immunology Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 ClueGO

:: MORE INFORMATION

Citation

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks.
Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Pagès F, Trajanoski Z, Galon J.
Bioinformatics. 2009 Apr 15;25(8):1091-3. Epub 2009 Feb 23.

InCroMAP 1.5 – Integrated Analysis of Cross-platform MicroArray and Pathway data

InCroMAP 1.5

:: DESCRIPTION

InCroMAP is a powerful tool for pathway-based analysis or visualization of heterogeneous cross-platform microarray datasets (mRNA, miRNA, DNA methylation and protein).

::DEVELOPER

InCroMAP TEam

:: SCREENSHOTS

InCroMAP

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 InCroMAP

:: MORE INFORMATION

Citation:

InCroMAP: integrated analysis of cross-platform microarray and pathway data.
Wrzodek C, Eichner J, Büchel F, Zell A.
Bioinformatics. 2013 Jan 16.

Pathway Projector – Zoomable Pathway Browser using KEGG Atlas

Pathway Projector

:: DESCRIPTION

The Pathway Projector was implemented according to the aforementioned requirements, including the availability of a large-scale comprehensive pathway map, pathways from a wide variety of organisms, and searching and mapping capabilities.

::DEVELOPER

PathwayProjector team

:: SCREENSHOTS

Pathwayprojector

:: REQUIREMENTS

  • Web Browser 
:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API.
Kono N, Arakawa K, Ogawa R, Kido N, Oshita K, Ikegami K, Tamaki S, Tomita M.
PLoS One. 2009 Nov 11;4(11):e7710. doi: 10.1371/journal.pone.0007710.

NetPathID – Network-based Analysis Identifies common Pathways

NetPathID

:: DESCRIPTION

NetPathID is a network-based method to integrate copy number alteration data with human protein-protein interaction networks and pathway databases to identify pathways that are disrupted by copy number alterations from 2172 patients across 16 different types of cancer.

::DEVELOPER

Rui Kuang 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows / MacOsX
  • Matlab

:: DOWNLOAD

 NetPathID

:: MORE INFORMATION

ACIB PGDB Toolbox 1.0 – Create, Maintain and Query Pathway/Genome Databases

ACIB PGDB Toolbox 1.0

:: DESCRIPTION

ACIB PGDB Toolbox is a plug-in for Pathway Tools, an integrated systems biology software to create, maintain and query Pathway/Genome Databases. Fully integrated into the graphical user interface (GUI) and menu of Pathway Tools, this plug-in provides functions to create multiple sequence alignments, systematically annotate insertion sequence (IS) elements and analyze their activity by cross-species comparison tools. Microarray probes can be automatically mapped to target genes, and expression data obtained with these arrays can be transformed into input formats needed to visualize them in the various -omics viewers of Pathway Tools

::DEVELOPER

Genomics & Bioinformatics Graz, Graz University of Technology

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

  ACIB PGDB Toolbox

:: MORE INFORMATION

Citation

Krempl PM, Mairhofer J, Striedner G, Thallinger GG.
A Sequence Comparison and Gene Expression Data Integration Add-on for the Pathway Tools Software.
Bioinformatics. 2012 Sep 1;28(17):2283-4.

PathwayLab 1.3 – Pathway Analysis tool

PathwayLab 1.3

:: DESCRIPTION

PathwayLab is an in silico pathway analysis tool, enabling pharmaceutical R&D to reach their target decisions faster and with higher accuracy.

::DEVELOPER

InNetics AB

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • MS Visio 2003 or later.

:: DOWNLOAD

 PathwayLab

:: MORE INFORMATION

Citation

Drug Discov Today. 2010 May;15(9-10):365-70. Epub 2010 Mar 6.
Biochemical modeling with Systems Biology Graphical Notation.
Jansson A, Jirstrand M.

PMAP II – Resolve pathway mapping problem with Operon and Regulon information

PMAP II

:: DESCRIPTION

P-MAP is an software for resolving pathway mapping problem with Operon and Regulon information.

PMAP Online Version

::DEVELOPER

the Computational Systems Biology Laboratory at the University of Georgia 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PMAP

:: MORE INFORMATION

Citation

F. Mao, Z. Su, V. Olman, P. Dam, Z. Liu, Ying Xu,
“Mapping of orthologous genes in the context of biological pathways: an application of integer programming“,
Proc Natl Acad Sci USA, 103 (1): 129-134, 2006.

Linear Pathway Simulator – Control Parameters of the Pathway & Study the Response

Linear Pathway Simulator

:: DESCRIPTION

Linear Pathway Simulator is a simple interactive linear pathway simulation. Sliders allow a user to control all the parameters of the pathway and can study the response of the pathway time course of steady state.at steady state the flux and concentration control coefficients are also computed.

::DEVELOPER

Herbert M Sauro

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Linear Pathway Simulator

:: MORE INFORMATION