SPIA specifications


Unique identifier OMICS_10400
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


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  • 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

SPIA article

SPIA citations

PMCID: 5487013

[…] 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 […]

PMCID: 4654831

[…] stored at −80 °c. total rna was subsequently isolated with the paxgene blood rna kit (qiagen). the synthesis of cdna was performed using the ovation® rna amplification system v2 including the ribo-spia® amplification process according to the instructions of the manufacturer (nugen technologies inc., san carlos, ca). the amplification process was performed in 3 stages: (1) a 1st-strand cdna […]

PMCID: 4453519

[…] fisher exact test with data fit to a negative binomial distribution of the deseq package was used to identify the differentially expressed genes. differentially expressed genes were output to spia (30) to evaluate pathway activation., cell culture supernatants of hct-8 cells in transwell incubations with bl21, w3110, and medium alone were harvested and subsequently assayed with the human […]

PMCID: 3137220

[…] tissues. the reference definition of the tlr3 pathway was retrieved from reactome (http://www.reactome.org) as a gene list., the bcml file was then converted to gene list and to a format usable by spia, the r implementation of impact analysis (tarca et al., 2009)., the hypergeometric test was carried out on the gene lists using r. spia was performed with a modified package (to support custom […]

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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