ICSNPathway 1.1 – Identify Candidate Causal SNPs and Pathways from Genome-wide Association Study

ICSNPathway 1.1

:: DESCRIPTION

ICSNPathway is a web server developed to discover candidate causal SNPs and corresponding candidate causal pathways from genome-wide association study (GWAS).

::DEVELOPER

Bioinformatics Lab, Institute of Psychology, Chinese Academy of Sciences

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • Java

:: DOWNLOAD

  ICSNPathway

:: MORE INFORMATION

Citation

K. Zhang, S. Chang, et al. (2011).
ICSNPathway: identify candidate causal SNPs and pathways from genome-wide association study by one analytical framework.”
Nucleic Acids Res. 39(suppl 2): W437-W443.

GWAS Pathway Identifier 1.0.0 – Pathway- and Protein-Interaction-Based Identification of Disease Specific SNP Sets in GWAS

GWAS Pathway Identifier 1.0.0

:: DESCRIPTION

GWAS Pathway Identifier combines GWAS(Genome-Wide Accociation Studies) and pathway data as well as known and predicted protein-interaction data to identify disease specific SNP sets.

::DEVELOPER

the Interfaculty Institute for Biomedical Informatics (IBMI)

:: SCREENSHOTS

gwaspi

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 GWAS Pathway Identifier

:: MORE INFORMATION

ContextTRAP – Pathway based analysis of Gene Expression data

ContextTRAP

:: DESCRIPTION

ContextTRAP is novel approach for prioritizing pathways by utilizing both results from pathway analysis tools and the literature information.

::DEVELOPER

Bio & Health Informatics Lab , Seoul National University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Lee J, Jo K, Lee S, Kang J, Kim S.
Prioritizing biological pathways by recognizing context in time-series gene expression data.
BMC Bioinformatics. 2016 Dec 23;17(Suppl 17):477. doi: 10.1186/s12859-016-1335-8. PMID: 28155707; PMCID: PMC5259824.

Pathway Processor 2.0 – Pathway-based analysis of High-throughput data

Pathway Processor 2.0

:: DESCRIPTION

Pathway Processor is a web application designed to analyze high-throughput datasets, including but not limited to microarray and next-generation sequencing, using a pathway centric logic.

::DEVELOPER

Computational Biology Center @ FEM

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Pathway Processor 2.0: a web resource for pathway-based analysis of high-throughput data.
Beltrame L, Bianco L, Fontana P, Cavalieri D.
Bioinformatics. 2013 Jul 15;29(14):1825-6. doi: 10.1093/bioinformatics/btt292.

IPATHCONS 1.0.6 – Insect Pathway Construction tool

IPATHCONS 1.0.6

:: DESCRIPTION

iPathCons is a tool for knowledge-based construction of pathways from the transcriptomes or the official gene sets of genomes.

::DEVELOPER

Li Lab: Insect Genomic and Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 IPATHCONS

:: MORE INFORMATION

Citation

iPathCons and iPathDB: an improved insect pathway construction tool and the database.
Zhang Z, Yin C, Liu Y, Jie W, Lei W, Li F.
Database (Oxford). 2014 Nov 11;2014. pii: bau105. doi: 10.1093/database/bau105.

PiiL – Pathway Interactive data Visualization tool

PiiL

:: DESCRIPTION

PiiL is an open-source and biologist-friendly tool. You can easily PiiL your data; i.e. load your DNA methylation and/or gene expression data over any of the KEGG pathways and let PiiL color it for you, in order to identify or discover genes with differential methylation / expression patterns. DNA methylation data can be from Illumina’s methylation arrays or RRBS. PiiL provides a set of analytical features facilitating quick assessment of specific patterns, and selecting subsets of CpG sites and examine their impact on expression of the host gene.

::DEVELOPER

Grabherr Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

PiiL

:: MORE INFORMATION

Citation

Moghadam BT, Zamani N, Komorowski J, Grabherr M.
PiiL: visualization of DNA methylation and gene expression data in gene pathways.
BMC Genomics. 2017 Aug 2;18(1):571. doi: 10.1186/s12864-017-3950-9. PMID: 28768481; PMCID: PMC5541427.

Path 1.1.0 / Path2 0.8 – Pathway-based / Ontology , Genetic Association Analysis

Path 1.1.0 / Path2 0.8

:: DESCRIPTION

Path is designed to help researchers interface bioinformatic information from several online resources with data from genetic association studies. Path is a valuable tool for investigating gene-gene interactions in large genetic association studies. In addition, Path can be used to help store and visualize data from genetic association studies. Path is compatible with LINKAGE pre-makeped data files that are accompanied by standard QTDT data files.

Path2 is designed to conduct pathway-based analyses of Genome-wide association studies (GWASs). Path2 aims to better understand the complex nature of genetic susceptibility to complex diseases by applying pathway-based models using bioinformatics techniques.

::DEVELOPER

Genapha

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/windows with cygwin/MacOsX
  • Java
  • Perl

:: DOWNLOAD

 Path , Path2

:: MORE INFORMATION

Citation

Zamer, Tripp, Ellis, Daley (2009),
Path: a tool to facilitate pathway-based genetic association analysis“,
Bioinformatics, 25(18):2444-2446.

ARTP 2.0.9.45 – Gene and Pathway p-values computed using the Adaptive Rank Truncated Product

ARTP 2.0.9.45

:: DESCRIPTION

ARTP (Adaptive Rank Truncated Product) is an R package for analyzing pre-defined genetic pathway based on a genetic association study.

::DEVELOPER

 DCEG

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R package

:: DOWNLOAD

 ARTP

:: MORE INFORMATION

Citation

Cancer Res. 2010 Jun 1;70(11):4453-9. doi: 10.1158/0008-5472.CAN-09-4502. Epub 2010 May 11.
Pathway analysis of breast cancer genome-wide association study highlights three pathways and one canonical signaling cascade.
Menashe I, Maeder D, Garcia-Closas M, Figueroa JD, Bhattacharjee S, Rotunno M, Kraft P, Hunter DJ, Chanock SJ, Rosenberg PS, Chatterjee N.

Pathprint 2.0 – Pathway Fingerprinting for Analysis of Gene Expression Arrays

Pathprint 2.0

:: DESCRIPTION

Pathprint integrates pathway curation, profiling methods, and public repositories, to represent any expression profile as a ternary score (-1, 0, +1) in a standardized pathway panel.

::DEVELOPER

Hide Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • R

:: DOWNLOAD

  Pathprint

:: MORE INFORMATION

Citation

Genome Med. 2013 Jul 26;5(7):68. doi: 10.1186/gm472. eCollection 2013.
Pathprinting: An integrative approach to understand the functional basis of disease.
Altschuler GM, Hofmann O, Kalatskaya I, Payne R, Ho Sui SJ, Saxena U, Krivtsov AV, Armstrong SA, Cai T, Stein L, Hide WA

PathWhiz 1.0 – Pathway Drawing Web Server

PathWhiz 1.0

:: DESCRIPTION

PathWhiz is a web server designed for the creation of colourful, visually pleasing, and biologically accurate pathway diagrams that are machine-readable and interactive.

::DEVELOPER

the Wishart Research Group, University of Alberta

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Pathways with PathWhiz.
Pon A, Jewison T, Su Y, Liang Y, Knox C, Maciejewski A, Wilson M, Wishart DS.
Nucleic Acids Res. 2015 May 1. pii: gkv399

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