Genome Annotations? RepeatMasker class/family? Regulation?

Question

[Susmita Mandal]

Hi everybody,

I want to plot my genes of interest coinciding with the enrichment sites from another paper. But the other paper has not provided a particular table of those sites but an excel sheet giving genome annotations of regulation, repeat masker classes and family with the fold enrichment and p value of those sites. So how to make sense of all of that? Below are few lines of the tsv file

Feature Fold enrichment  P-value
GenomeAnnotations.Genes.RefSeqGenes 2.13    1.72E-07
GenomeAnnotations.Genes.RefSeqGenes_nonrandom   2.13    1.72E-07
GenomeAnnotations.Genes.RefSeqNMGenes_nonrandom 2.10    3.71E-07
GenomeAnnotations.Genes.RefSeqTSS   2.13    1.18E-06
GenomeAnnotations.Regulation.Kagey2010_mES_CTCF 1.80    7.14E-06
GenomeAnnotations.Genes.RefSeqExons 1.66    7.37E-06
GenomeAnnotations.Genes.RefSeqIntrons   1.57    4.73E-05
GenomeAnnotations.Regulation.Kagey2010_mES_Smc3 1.80    1.56E-04
GenomeAnnotations.Regulation.Kagey2010_MEF_CTCF 2.17    4.14E-04
GenomeAnnotations.RepeatMasker.name_L1Md_F2 0.68    8.79E-04
GenomeAnnotations.Regulation.wgEncodeLicrTfbs_MEF_Ctcf_Peaks    1.62    1.37E-03
GenomeAnnotations.RepeatMasker.class_Simple_repeat  1.16    1.59E-03

So if anybody knows what are these and how to do what I want? Please let me know.

Susmita