Figure 2.

Identification of transcription start regions (TSRs) using a combination of EnsEMBL annotations and CAGE data. To improve our alignments, we determine putative alternative TSSs for the human and mouse genes. For each gene, the entire repertoire of transcripts from both EnsEMBL core genes and EST genes are retrieved. The TSSs for all transcripts are recorded, followed by a clustering step such that TSSs within 500 bp of one another are merged to form a transcriptional start region (TSR). For each TSR containing a transcript annotated as ‘known’ or ‘novel’, we accept the TSR as is. For TSRs based solely on EST gene transcripts, we require a minimum of 5 CAGE tags as evidence for transcription initiation.