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SPIA

Performs pathway analysis using Signaling Pathway Impact Analysis (formerly known as Pathway-Express). Uses Entrez Gene ID's, use Korvasieni to convert.

NOTE: Currently replaces comma separated multiple ID's for one gene with only the first one of those ID's.

Version 1.1
Bundle microarray
Categories Pathway
Authors Viljami Aittomaki (viljami.aittomaki@helsinki.fi)
Issue tracker View/Report issues
Requires R ; SPIA (R-bioconductor)
Source files component.xml SPIA.r
Usage Example with default values

Inputs

Name Type Mandatory Description
deg LogMatrix Mandatory An expression matrix containing log2 fold changes for differentially expressed genes (DEG's). Gene ID's must be Entrez Gene ID's! Lines containing 'NA' are removed.
reference IDList Mandatory An IDList containing the Entrez ID's in the reference set. If the data was obtained from a microarray experiment, this list will contain all genes present on the specific array used for the experiment. This vector must contain all names of the DEG's in the deg input.

Outputs

Name Type Description
pathways CSV A CSV containing the ranked pathways and various statistics for them. Has the following columns: 'Name' is the name of the pathway; 'ID' is the KEGG internal ID for the pathway (eg. hsa04612 ; 'pSize' is the number of genes in the pathway; 'NDE' is the number of DEG's in the pathway; 'tA' is the observed total perturbation accumulation in the pathway; 'pNDE' is the probability to observe at least 'NDE' genes on the pathway; 'pPERT' is the probability to observe a total perturbation accumulation more extreme than 'tA' only by chance; 'pG' is the p-value obtained by combining 'pNDE' and 'pPERT'; 'pGFdr' and 'pGFWER' are the False Discovery Rate and Bonferroni adjusted global p-values respectively; and 'Status' gives the direction in which the pathway is perturbed ('Activated' or 'Inhibited'); 'KEGGurl' is the link to the corresponding KEGG pathway diagram to which up and down regulated genes are colored in red and blue respectively.
pathwayGenes Array<LogMatrix> An array containing one LogMatrix for each pathway in 'pathways'. Each matrix has the genes in the pathway and fold changes for the genes. The fold changes are the ones in input 'deg' (or zero for genes in pathway but not in 'deg'). The array key for each matrix is the KEGG ID of the pathway (e.g. hsa00001).

Parameters

Name Type Default Description
foldChangeColumn string "" Name of the column in deg that has wanted input fold-change values. If an empty string defaults to the second column in deg (first numerical column).
keggPath string "extdata" Path where organismSPIA.RData is located. The default parameter uses the outdated KEGG pathways included with SPIA. Check SPIA documentation for creating your own updated SPIA.RData.
nboot int 2000 Number of bootstrap samples used in computing pPERT. Should be larger than 100. A recommended value is 2000.
organism string "hsa" KEGG organism code corresponding to input genes (e.g., hsa=homo sapiens).
verbose boolean false If true, report progress (number of pathways already analyzed reported to stdout).

Test cases

Test case Parameters IN
deg
IN
reference
OUT
pathways
OUT
pathwayGenes
case1-vessels properties deg reference pathways pathwayGenes

foldChangeColumn=foldChange,
verbose=true

case2-failureReference properties deg reference (expecting failure) (expecting failure)

nboot=1000,
foldChangeColumn=foldChange,
verbose=true,

case3-noDegs properties deg reference pathways pathwayGenes

case4-NAs properties deg reference (missing) (missing)


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