Overview of Help-Pages

Tissue Profiles

Introduction

• Since ElDorado 04-2021:
  A transcriptional start region (TSR) is defined as a genomic region for which experimental evidence for transcriptional initiation is available. TSRs are directly based on CAGE peaks from the FANTOM5 project. Those CAGE peaks were derived from primary cell, cell line and tissue samples. The "Tissue Profiles" table shows the total number of available tissue specific CAGE tags for transcripts and TSRs. Furthermore, the tissues the CAGE tags have been derived from are listed. For each tissue, the number of CAGE tags is given in parentheses.

  Note: The total number of CAGE tags for TSRs shown in the "Tissue Profiles" table may differ from the number shown in GenomeBrowser, because there the CAGE tags derived from primary cell and cell line samples are also counted, not just the CAGE tags from the tissue samples.

• Before ElDorado 04-2021:
  A transcriptional start region (TSR) is defined as a genomic region for which experimental evidence for transcriptional initiation is available. Information about transcription initiation was derived from individual full-length cDNAs and from CAGE tags. Both data sources make use of the oligo-capping method. The 5' ends of full-length transcripts and CAGE tags are taken as experimentally verified transcription start sites (TSS). TSSs separated by less than 40bp are grouped in a TSR.

  For most of the CAGE tags the tissue the cDNA libraries where derived from are known. The transcriptional activity therefore can be assigned to specific tissues. The "Tissue Profiles" table shows the total number of available CAGE tags for transcripts and TSRs. Furthermore, the tissues the CAGE tags have been derived from are listed. For each tissue, the number of CAGE tags is given in parentheses.

Example

The example below shows the tissue information for two transcripts and two TSRs on human chromosome 20.

For the current ElDorado release tissue specific TSRs based on CAGE tags are available for human and mouse.