CAGE defined TSS All files are tab-delimited text files with a header on the first line. Missing data is denoted by 'NULL' (e.g. where no TSS can be mapped to a gene). humanTss.txt ============ All human CAGE defined TSS from the macrophage derived libraries (both mapping to probeset and non-probeset defined genes). tssID Unique TSS identifier chrom Chromosome refPos Chromosomal coordinate strand Chromosome strand totalTpmCount Tag count (Tags per million averaged over macrophage libraries) maxTpmCount Maximum tag count (Tags per million) seen in any macrophage library. mouseTss.txt ============ All mouse CAGE defined TSS from the macrophage derived libraries (both mapping to probeset and non-probeset defined genes). tssID Unique TSS identifier chrom Chromosome refPos Chromosomal coordinate strand Chromosome strand totalTpmCount Tag count (Tags per million averaged over macrophage libraries) maxTpmCount Maximum tag count (Tags per million) seen in any macrophage library. humanProbesetToTssMapping.txt ============================= TSS mapped to human genes with custom microarray probesets. ensID tssID Unique TSS identifier refPos Chromosomal coordinate chrom Chromosome strand Chromosome strand closest_transcript Annotated transcript with 5' end closest to TSS refPos closest_dist Distance between TSS refPos and 5' end of closest annotated transcript transcripts Annotated transcripts that link CAGE defined TSS to probeset tag_num Tag count (Tags per million averaged over macrophage libraries) humanProbesetToTssMapping.txt ============================= TSS mapped to human genes with custom microarray probesets. ensID tssID Unique TSS identifier refPos Chromosomal coordinate chrom Chromosome strand Chromosome strand closest_transcript Annotated transcript with 5' end closest to TSS refPos closest_dist Distance between TSS refPos and 5' end of closest annotated transcript transcripts Annotated transcripts that link CAGE defined TSS to probeset tag_num Tag count (Tags per million averaged over macrophage libraries) TSS_orthology_projection/projectedOrthology.txt ====================== File contains orthology and probeset mapping "rescue" data for macrophage transcription start sites (TSS) between human and mouse. The table is a tab-delimited file with the first line as a header. Only contains lines TSS for which human:mouse orthologues can be defined. humanTssID Human TSS identifier. mouseTssID Mouse TSS identifier. humanDist Distance (nt) between annotated human transcript 5' end and TSS. mouseDist Distance (nt) between annotated mouse transcript 5' end and TSS. humanEnsID Human gene Ensembl identifier mouseEnsID Mouse gene Ensembl identifier humanDirectProbesetMap 1 for direct mapping of TSS to human probeset, 0 for orthologous mapping. mouseDirectProbesetMap 1 for direct mapping of TSS to mouse probeset, 0 for orthologous mapping.