Transcriptional Start Region / Tissue Profile

[Introduction] [Graphical Overview] [Table Output] [Statistics]

Introduction

A transcriptional start region (TSR) is defined as a genomic region for which experimental evidence for transcriptional initiation is available. Information about transcription initiation is 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. Information about the relative distribution of the TSS in the transcriptional start region and the tissue association is displayed in a graphics and a table view.

Graphical Overview

The graphical overview shows the relative distribution of the TSS by a separate curve for each of the tissues tags are available for in the TSR. The positions on the x-axis are relative to the TSR (5'- 3' direction). Above the curves the corresponding ElDorado annotation is indicated. Exons, promoters, and PromoterInspector predictions are shown by their respective color code. In addition the 5' end of a transcript is indicated by a small vertical bar. The color of the bar (gold, silver, bronze) indicates the quality of the corresponding transcript.
In the example (Commd2) there are four different gold transcripts starting from overlapping first exons but using different TSS. The use of different TSS for Commd2 is supported by a large number of CAGE tags from a variety of tissues concentrated in 4 peaks correlated with the annotated transcripts.

Note that for TSRs of less than 3 basepairs in length, no graphical profile is displayed.

graphical overview

Table Output

The detailed numbers for the TSS in the transcriptional start region are given in the table below the graphical overview. The table contains a column for each position in the TSR at least one TSS is available for. The position number is given in the last line.
The numbers for each tissue are given in a separate line. The number behind the tissue name in the first column indicates how many TSS are available in the TSR for the tissue. The second last line shows the sum of all tissues.
The check boxes in front of each line can be used to select the tissues shown in the graphical overview. The graphic is updated by pressing the button 'Refresh Graphics' between graphical overview and table output. By default all tissues are selected. The sum ('ALL') is deselected.
There are two different numbers given in the table. The upper number shows how many tags are available at a position for a specific tissue. The second number (in parentheses) indicates how many tags would have been expected for this position. This calculation is based on the number of TSS available for this position (from all tissues) and the overall number of TSS available for a specific tissue.
In the example 54 TSS are annotated for position 25. With 7,777,171 TSS available for the mouse genome and 1,159,452 from embryo one would expect 8 TSS for this position and tissue which is exactly the number of TSS observed. If the two numbers differ this indicates an over/underrepresentation of TSS in the respective tissue.
The maximum values for each tissue are highlighted in red.

table view

Statistics

For the current release (ElDorado 11-2007) tissue specific TSS based on CAGE tags are only available for human and mouse.

human		mouse
tissue	count	tissue	count
adipose	647,823	adipose	268,084
adrenal gland	316,245	amnion	1,036
blood	74,730	brain	156,130
bone marrow	365,447	cerebellum	235,099
brain	491,526	cerebral cortex	20,847
cecum	445,358	diencephalon	47,915
cerebellum	93,908	embryo	1,159,452
cerebrum	646,865	eye	2,216
colon	355,840	heart	35,671
embryo	345,335	hippocampus	3,181
epididymis	7,008	liver	2,279,202
frontal lobe	49,123	lung	1,242,530
heart	109,527	macrophage	1,336,478
kidney	133,919	mammary gland	6,920
large intestine	506,697	medulla oblongata	4,780
liver	1,926,768	muscle	43,270
lung	433,672	placenta	931
mammary gland	89,946	prostate gland	60,604
muscle	88,172	somatosensory cortex	199,102
occipital lobe	122,244	striatal primordia	49,415
pancreas	123,899	testis	120,053
parietal lobe	29,011	undefined tissue type	378,713
prostate gland	11,220	visual cortex	221,500
rectum	76,683	all	7,777,171
renal artery	13,630
skin	13
small intestine	138,255
spleen	115,867
stomach	1,011
testis	184,072
thymus	84,757
undefined tissue type	1,450,915
ureter	10,621
urinary bladder	12,061
all	9,472,161