Description
This track shows 5' cap analysis gene expression (CAGE) tags and clusters in
RNA extracts
from different
sub-cellular localizations
in multiple
cell lines.
A CAGE cluster is a region of overlapping tags with
an assigned value that represents the expression level.
The data in this track were produced as part of the ENCODE
Transcriptome Project.
Display Conventions and Configuration
This track is a multi-view composite track that contains multiple data types
(views). For each view, there are multiple subtracks that
display individually on the browser. Instructions for configuring multi-view
tracks are
here.
To show only selected subtracks, uncheck the boxes next to the tracks that
you wish to hide.
This track contains the following views:
- TSS HMM
- Transcriptional Start Sites based on Hidden Markov Modeling for pooled replicates where two replicates exist.
- Expression levels are shown in reads per kilobase of exon per million reads mapped (RPKM).
- The IDR value is the irreproducible discovery rate. This is a measurement that measures
expression variances between genomic replicates in large scale experiments.
- Plus and Minus Signals
- These views display signals representing the amount of overlapping CAGE reads (clusters) mapped on the forward and reverse genomic strands.
- Alignments
- The Alignments view shows reads mapped to the genome and indicates where
bases may mismatch. Every mapped read is displayed, i.e. uncollapsed.
The alignment file follows the standard SAM format of Bowtie output. The custom tag XP can be
ignored. See the
Bowtie Manual
for more information about the SAM Bowtie output (including other tags) and the
SAM Format Specification
for more information on the SAM/BAM file format.
Where mapping quality is not available for this track, a score of 255 is used in accordance with
the SAM Format Specification. Also, where the sequence quality scores are not available,
all scores are displayed as 40.
Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks.
Replicate numbering in the track display page is done by rank. The first replicate available may be replicate number three.
Color differences in subtracks may be set as a visual cue to
distinguish between the different cell types or between annotations
on the plus and minus strand.
Downloadable Files
- TSS GencV7
- For some samples, there are download files in a modified gtf format with Transcriptional Start
Sites based on GENCODE V7. A complete description of the TSS files is located in the
supplemental materials directory.
Methods
Cells were grown according to the approved
ENCODE cell culture protocols.
RNA molecules longer than 200 nt were isolated
from each subcellular compartment and then
were fractionated into polyA+ and polyA- fractions as described in
these
protocols.
The CAGE tags were sequenced from the 5' ends of cap-trapped cDNAs produced
using RIKEN CAGE technology
(Kodzius et al. 2006; Valen et al. 2009).
To create the tag, a linker was attached to the 5'
end of polyA+ or polyA- reverse-transcribed cDNAs which were selected by cap
trapping (Carninci et al. 1996). The first 27 bp of
the cDNA were cleaved using class II restriction enzymes. A linker was then
attached to the 3' end of the cDNA.
After PCR amplification, the tags were sequenced using Illumina's Genome analyzer or HiSeq. The read lengths for each sample
are specified in the metadata.
Tags were mapped to the human genome (hg19) using the program Delve (T. Lassmann manuscript in preparation).
Delve is a new probabilistic aligner focused on giving the best possible alignment of reads to a genome rather
than focusing on speed. It calculates the mapping accuracy (probability of each alignment being true or not)
for each alignment. There is no set limit on the number of errors allowed and therefore the mapping rate is
commonly 100%. However, for analysis it is recommended to discard alignments with low mapping qualities.
Exceptions to the above protocol are the polyA- RNA samples from K562 cytosol, K562 nucleus, and prostate whole cell
which were sequenced using ABI SOLiD technology. These reads were mapped using Bowtie with its default parameters.
Clusters were defined as regions of overlapping CAGE reads. The expression level was computed as the number
of reads making up the cluster, divided by the total number of reads sequenced, times 1 million.
Release Notes
This is Release 4 (July 2012) of Riken CAGE. Three missing Transcription Start Sites determined by Hidden Markov Models
(TssHmm) tables have been added (H1-hesc Nucleus, H1-hesc Cytosol and NHEK Nucleus polyA+ samples).
As with previous releases, the orignal data from the hg18 version of this track is still included and can be noted in the metadata as having a bioRepId that starts with gen0. This older data may be missing some information and does not have replicates. If there are new data available for an older sample, only the newer data is displayed. The older data is still availble for downloads.
Credits
These data were generated and analyzed by Timo Lassmann, Phil Kapranov,
Hazuki Takahashi, Yoshihide Hayashizaki, Carrie Davis, Tom Gingeras, and Piero Carninci.
Contact:
Piero Carninci at
RIKEN Omics Science Center
References
Carninci P, Kvam C, Kitamura A, Ohsumi T, Okazaki Y, Itoh M, Kamiya M,
Shibata K, Sasaki N, Izawa M, et al.
High-efficiency full-length cDNA cloning by biotinylated CAP trapper.
Genomics. 1996 November 1; 37(3):327-336.
Kodzius R, Kojima M, Nishiyori H, Nakamura M, Fukuda S, Tagami M, Sasaki D,
Imamura K, Kai C, Harbers M, et al.
CAGE: cap analysis of gene expression.
Nat Methods. 2006 March 1; 3(3):211-222.
Valen E, Pascarella G, Chalk A, Maeda N, Kojima M, Kawazu C, Murata M, Nishiyori
H, Lazarevic D, Motti D, et al.
Genome-wide detection and analysis of hippocampus core promoters using
DeepCAGE.
Genome Res. 2009 February; 19(2):255-265.
Data Release Policy
Data users may freely use ENCODE data, but may not, without prior
consent, submit publications that use an unpublished ENCODE dataset until
nine months following the release of the dataset. This date is listed in
the Restricted Until column, above. The full data release policy
for ENCODE is available
here.