Tag: Signaling Pathway

SPIA 2.44.0 – Signaling Pathway Impact Analysis

SPIA 2.44.0

:: DESCRIPTION

SPIA is a standard Bioconductor style R package designed to perform pathway analysis using over representation evidence and pathway topology information.

::DEVELOPER

the Bioinformatics and Computational Biology Unit of the Perinatology Research Branch (NICHD)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • R package
  • Bioconductor

:: DOWNLOAD

 SPIA

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Jan 1;25(1):75-82. doi: 10.1093/bioinformatics/btn577. Epub 2008 Nov 5.
A novel signaling pathway impact analysis.
Tarca AL, Draghici S, Khatri P, Hassan SS, Mittal P, Kim JS, Kim CJ, Kusanovic JP, Romero R.

PATHiWAYS – web-based Signaling Pathway visualization system

PATHiWAYS

:: DESCRIPTION

PATHiWAYS is a web tool for the interpretation of the consequences of the combined changes in expression levels of genes in the context of signaling pathways. Specifically, this tool allows the user to identify the stimulus-response subpathways that are significantly activated or deactivated in the typical case/control experiment. PATHiWAYS identifies all the stimulus-response subpathways of KEGG signaling pathways, calculates the probability of activation of each one, based on the individual gene expression values and identifies those with a significant differential activity between the two conditions compared.

::DEVELOPER

the Computational Biology Unit, at Computational Medicine Institute at CIPF in Valencia, Spain.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W213-7. doi: 10.1093/nar/gkt451. Epub 2013 Jun 8.
Inferring the functional effect of gene expression changes in signaling pathways.
Sebastián-León P1, Carbonell J, Salavert F, Sanchez R, Medina I, Dopazo J.

GeneNT 1.4.1 – Relevance or Dependency network and Signaling Pathway Discovery

GeneNT 1.4.1

:: DESCRIPTION

GeneNT is a R package to estimate co-expression gene networks

::DEVELOPER

Dongxiao Zhu, Ph.D

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/MacOsX/ Linux
  • R package

:: DOWNLOAD

 GeneNT

:: MORE INFORMATION

Citation:

Network constrained clustering for gene microarray data.
Zhu D, Hero AO, Cheng H, Khanna R, Swaroop A.
Bioinformatics. 2005 Nov 1;21(21):4014-20.

SPIKE – Database of highly curated human Signaling Pathways

SPIKE

:: DESCRIPTION

SPIKE (Signaling Pathways Integrated Knowledge Engine) is a database of highly curated human signaling pathways with an associated interactive software tool.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

SPIKE: a database of highly curated human signaling pathways.
Paz A, Brownstein Z, Ber Y, Bialik S, David E, Sagir D, Ulitsky I, Elkon R, Kimchi A, Avraham KB, Shiloh Y, Shamir R.
Nucleic Acids Res. 2011 Jan;39(Database issue):D793-9. doi: 10.1093/nar/gkq1167.