SPIA pipeline

SPIA specifications

Information


Unique identifier OMICS_10400
Name SPIA
Alternative name Signaling Pathway Impact Analysis
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data DE genes with values
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 2.22.0
Stability Stable
Requirements graphics, KEGGgraph
Maintained Yes

Versioning


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Documentation


Maintainer


  • person_outline Sorin Draghici <>

Additional information


An other algorithm of SPIA, SPIA-GPF (Signaling Pathway Impact Analysis - Global Perturbation Factor) has also been created : https://www.ncbi.nlm.nih.gov/pubmed/27193997

Publication for Signaling Pathway Impact Analysis

SPIA IN pipelines

 (9)
2017
PMCID: 5487013
PMID: 28654683
DOI: 10.1371/journal.pone.0179613

[…] factor binding sites. the gene ontology libraries in enrichr are based on the gene ontology database [28]., to identify signaling pathways affected during the mesoderm differentiation of hescs, signaling pathway impact analysis (spia) was carried out using the filtered dataset (1,108 genes). spia is implemented in the r package spia and can identify kegg pathways that are significantly […]

2017
PMCID: 5487013
PMID: 28654683
DOI: 10.1371/journal.pone.0179613

[…] biologically relevant processes and their various levels of abstraction, compared to long lists of partially redundant terms and their p-values., the results from pathway perturbation analysis with spia were visualized as a relative pathway perturbation plot. the y-axis of this plot (spia ta) represents the sum of all pathway fold changes at each time point compared to day 0. the sum […]

2017
PMCID: 5487013
PMID: 28654683
DOI: 10.1371/journal.pone.0179613

[…] lists of partially redundant terms and their p-values., the results from pathway perturbation analysis with spia were visualized as a relative pathway perturbation plot. the y-axis of this plot (spia ta) represents the sum of all pathway fold changes at each time point compared to day 0. the sum is calculated following propagation of the fold change signal throughout the pathway based […]

2017
PMCID: 5487013
PMID: 28654683
DOI: 10.1371/journal.pone.0179613

[…] following propagation of the fold change signal throughout the pathway based on its topology, and can be interpreted as a measure of relative pathway activity. it is based on this measure that spia infers if the pathway is either activated (ta > 0) or inhibited (ta < 0). to clarify the causes for pathway perturbation, the wnt signaling pathway was further visualized using a pathway […]

2016
PMCID: 5054603
PMID: 27774052
DOI: 10.3389/fncel.2016.00230

[…] pathways, the data matrix of log2 transformed and rma-normalized microarray data were analyzed using a public web server graphite web (sales et al., 2013). of the available analytical methods, signaling pathway impact analysis (spia) was used. over the classical probabilistic components, the spia also applies statistical systems biology approaches: it takes into consideration (1) […]

SPIA institution(s)
Department of Computer Science, Wayne State University, Detroit, MI, USA; Perinatology Research Branch-NIH/NICHD, Detroit, MI, USA
SPIA funding source(s)
The Intramural Research Program of the Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH/DHHS (in part); NSF DBI 0234806, CCF 0438970, 1R01HG003491, 1U01CA117478, 1R21CA100740, 1R01 NS045207, 5R21EB000990, 2P30 CA022453

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