linc2go: Linc2GO GeneSetCollection
In tpq/miSciTools: Miscellaneous Science Tools for Bioinformatic Analysis

Description Usage Format Details Source Examples

These data expose the Linc2GO database as a GeneSetCollection object to use in conjunction with the Category and GOstats packages for gene set enrichment analysis. The gene ontology terms in this database stem from an application of the competing endogenous RNA (ceRNA) hypothesis which speculates that lncRNAs regulate expression, at least in part, by competing with mRNAs for microRNA binding sites. Since microRNAs bind mRNA transcriptS to silence their expression, a microRNA-lncRNA complex could free up that mRNA for expression. Therefore, the curators integrate microRNA-mRNA and microRNA-lncRNA binding patterns to predict potential lncRNA-mRNA collaborations. Based on the gene ontology of the mRNA transcript pairs, the curators can make an educated guess about the gene ontology of the lncRNA.

1	data(linc2go)

A GeneSetCollection object from the GSEABase package.

This database uses the lincRNA ID archived by the Human lincRNA Catalog. Conveniently, these represent the same terms used by UCSC in the TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts TxDb object.

http://www.bioinfo.tsinghua.edu.cn/~liuke/Linc2GO/

## Not run: 
library(miSciTools)
data(linc2go)
show(linc2go)
universe <- unique(unlist(geneIds(linc2go))) # Pull out all features
genes <- geneIds(linc2go)[[2]] # Pull out all GO:0000003 terms
params <-
  Category::GSEAGOHyperGParams(name = "ExampleGSEA",
                               geneSetCollection = linc2go,
                               geneIds = genes,
                               universeGeneIds = universe,
                               ontology = "BP",
                               pvalueCutoff = 0.05,
                               conditional = FALSE,
                               testDirection = "over")
Over <- GOstats::hyperGTest(params)
head(summary(Over))

## End(Not run)