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Protocols

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 2.32.0
Stability Stable
Requirements
graphics, R(>=2.14.0), graph, Rgraphviz, KEGGgraph, hgu133plus2.db
Maintained Yes

Versioning


No version available

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 citations

 (46)
call_split

CD1d dependent immune suppression mediated by regulatory B cells through modulations of iNKT cells

2018
Nat Commun
PMCID: 5814456
PMID: 29449556
DOI: 10.1038/s41467-018-02911-y
call_split See protocol

[…] edgeR algorithm under default settings. Genes with false-discovery rate (FDR) values <0.05 were considered to be differentially expressed. Significantly overrepresented pathways were identified using signaling pathway impact analysis (SPIA). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways database was used as a reference, while full mouse genome was used as a background for enrichment. […]

library_books

The epigenetic modifier Fam208a is required to maintain epiblast cell fitness

2017
Sci Rep
PMCID: 5570896
PMID: 28839193
DOI: 10.1038/s41598-017-09490-w

[…] sor of transgene variegation, we included heterozygous samples in our analysis in an attempt to identify any dosage-dependant changes in transcript abundance.Using signalling pathway impact analysis (SPIA) against the KEGG database, we saw significant enrichment of the p53 signalling pathway (mmu04115, p = 0.0023) (Fig. ). This enrichment is readily apparent in a related 24 member gene set defined […]

library_books

A data analysis framework for biomedical big data: Application on mesoderm differentiation of human pluripotent stem cells

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

[…] of 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 is calculat […]

library_books

Exposure of Induced Pluripotent Stem Cell‐Derived Vascular Endothelial and Smooth Muscle Cells in Coculture to Hemodynamics Induces Primary Vascular Cell‐Like Phenotypes

2017
Stem Cells Transl Med
PMCID: 5689791
PMID: 28628273
DOI: 10.1002/sctm.17-0004

[…] ansformed), raw null hypothesis testing p values, and Benjamini‐Hochberg adjusted false discovery rates (FDR) were used as input for downstream pathway analyses with ingenuity pathway analysis (IPA), signaling pathway impact analysis (SPIA), top gene ontology (topGO), and gene set enrichment analysis (GSEA) pathway enrichment algorithms, which included known pathway gene lists from KEGG, Reactome, […]

library_books

Identifying biologically relevant putative mechanisms in a given phenotype comparison

2017
PLoS One
PMCID: 5423614
PMID: 28486531
DOI: 10.1371/journal.pone.0176950

[…] e list generated with the proposed method ranked the KEGG pathways with the KO gene similarly or higher than the gene list of the classical approach when combined with the methods including ORA [, ], SPIA [], and LEGO []. We applied the three methods ORA, SPIA, and LEGO, to show that the comparison with the classical approach is not favoring a particular pathway analysis method. We also show that […]

library_books

Detecting Disease Specific Pathway Substructures through an Integrated Systems Biology Approach

2017
Noncoding RNA
PMCID: 5831934
PMID: 29657291
DOI: 10.3390/ncrna3020020

[…] ch a statistic is then combined for each element in a pathway, and a p-value is computed by means of exponential distribution.The analysis presented by Draghici et al. [] has been further improved by Signaling Pathway Impact Analysis (SPIA) [], which attenuates the dominant effect caused by the change in expression within PF computation, while reducing the high rate of false positives when the inp […]

Citations

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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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