Genomatix-Logo
Overview of Help-Pages

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