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 02-2010) tissue specific TSS based on CAGE tags are only available for human and mouse.

human		mouse
tissue	count	tissue	count
adipose	946,078	adipose	261,796
adrenal gland	334,351	amnion	2,222
blood	80,583	brain	179,688
bone marrow	394,970	cerebellum	222,179
brain	523,733	cerebral cortex	22,500
cecum	476,685	diencephalon	50,725
cerebellum	108,704	embryo	1,087,570
cerebrum	924,909	eye	3,690
colon	372,100	heart	31,791
embryo	366,646	hippocampus	2,986
epididymis	9,972	liver	2,165,308
frontal lobe	52,347	lung	1,178,409
heart	118,039	macrophage	1,231,785
kidney	152,200	mammary gland	16,795
large intestine	616,778	medulla oblongata	7,268
liver	2,177,168	muscle	38,946
lung	476,036	placenta	2,108
mammary gland	113,932	prostate gland	52,685
muscle	91,112	somatosensory cortex	180,056
occipital lobe	121,279	striatal primordia	63,087
pancreas	178,644	testis	125,988
parietal lobe	32,109	undefined tissue type	390,340
prostate gland	18,000	visual cortex	200,889
rectum	88,798	all	7,518,811
renal artery	27,255
skin	23
small intestine	154,685
spleen	112,430
stomach	2,792
testis	209,648
thymus	9,9858
undefined tissue type	1,860,705
ureter	24,781
urinary bladder	22,507
all	11,289,857