Differentially expressed Genes in a pathway on Insulin Signaling in case of Diabetes Mellitus

DifExInsullinSIgnalling.R

library(SPARQL)
library(ggplot2)
wpSparql <- "http://sparql.wikipathways.org"
ebiSparql <- "https://www.ebi.ac.uk/rdf/services/atlas/sparql"
efoPathwaysQuery <- "PREFIX identifiers: <http://identifiers.org/ensembl/>
PREFIX atlas: <http://rdf.ebi.ac.uk/resource/atlas/>
PREFIX atlasterms: <http://rdf.ebi.ac.uk/terms/atlas/>
PREFIX efo: <http://www.ebi.ac.uk/efo/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX dcterms: <http://purl.org/dc/terms/>

SELECT DISTINCT ?pwIdentifier ?pwTitle ?dbxref ?experiment ?experimentPage ?experimentDescription ?difExpAnalysis ?expressionValue ?pvalue ?tstatistic WHERE {

SERVICE <https://www.ebi.ac.uk/rdf/services/atlas/sparql> {
VALUES ?efoValues {efo:EFO_0000400 efo:EFO_0001359 efo:EFO_0001360 }
VALUES ?pwIdentifier {<http://identifiers.org/wikipathways/WP481> }

?experiment dcterms:description ?experimentDescription .
?experiment foaf:page ?experimentPage .
?experiment atlasterms:hasAnalysis ?difExpAnalysis .
?difExpAnalysis atlasterms:hasExpressionValue ?value .
?factor rdf:type ?efoValues . 
?value atlasterms:hasFactorValue ?factor . 
?value atlasterms:isMeasurementOf ?probe . 
?value atlasterms:pValue ?pvalue . 
?value atlasterms:tStatistic ?tstatistic .
?value rdfs:label ?expressionValue . 
?probe atlasterms:dbXref ?dbxref .
}
?pwElement dcterms:isPartOf ?pathway .
?pathway dc:title ?pwTitle .		 
?pathway dc:identifier ?pwIdentifier .
?pwElement wp:bdbEntrezGene ?dbxref .
}
"

tempResults <- SPARQL(wpSparql, efoPathwaysQuery)
tempResults$results$ensembl = gsub("\"", "", gsub(">","", gsub("<http://identifiers.org/ncbigene/", "", tempResults$results$dbxref)))
papertable <- as.matrix(tempResults$results)
View(papertable)
write.csv(papertable, "/tmp/WP481.csv")