CummeRbund is a R package for analyzing cufflink results. By default, it uses XLOC values as the identifiers for each gene. All the gene information is stored in CuffGene instances, including the short name (if available). To get short gene names instead of XLOC values, the following R code is helpful.
>diffGenes <- getGenes(cuff_data, sig_gene_data$gene_id)
>head( featureNames(diffGenes), n=3)
1 XLOC_000186 GRHL3
2 XLOC_000302 NDUFS5
3 XLOC_000374 UQCRH
> head(featureNames(diffGenes)$gene_short_name, n=3)
 GRHL3 NDUFS5 UQCRH
*** Levels …..
There is some recommended method for newer version of CummeRbund as discussed here, but the idea is similar (use featureNames on CuffGeneSet instance).