Track Descriptions & Citations

Tracks Built into this Server

Centromere
No additional information available.

A01. Transcripts
Transcripts (DDBJ/EMBL/GenBank mRNAs, RefSeq, and EnsEMBL transcripts). Their genomic coordinates are derived from the RTPS pipeline (See PMID:12466851 and PMID:15533708).

A02. miRNA
Genomic coordindates of miRNAs based on miRbase 10.0.

A03. snoRNA
See UCSC description.

A04. TU
Transcriptional Unit (TU), clusters of transcripts, which is derived from the RTPS pipeline. See PMID:12466851 and PMID:15533708

B04. Fantom3/Fantom4 TC
Tag Cluster. Only single mapped tags are shown. See PubmedID:19374775
Grey color indicates that the CAGE tag is not single mapped, but multi mapped. Fat arrows in red tones are clickable.
The levels of red are displayed according to the mean-normalized value of the expression for the cluster: black or dark red means low expression and bright red means high expression. The table that opens up at a mouse click on the feature displays informations on all the tissues and the libraries (with the corresponding samples) that are in a cluster.
The 'Intensity' column shows a heatmap where the color is obtained varying the RGB code red channel values.
The values for red channel are the integer of the actual TPM values. If the value of the TPM is over 255 it is set to this value. The resulting color is bright red.

A08. LiftOver TC from hg17
Fantom3 tag clusters (hg17 assembly). See PubmedID:16645617 and PubmedID:16141072
A one-step liftover - see UCSC liftOver for details- has been done.The original genome is hg17 (May 2004) and the new genome is hg18 (July 2007).
The parameters used in the liftover are:
  1. Minimum ratio of bases that must remap 0.95
  2. Minimum chain size in target 0
  3. Minimum hit size in query 0
  4. Allow multiple output regions NO
  5. Min ratio of alignment blocks/exons that must map 1

The clusters are represented in a old-fashioned, Fantom3-style way where:
  1. Red tinged color, such as "RED" and "PINK", indicates that its representative tag is a CAGE tag.
  2. Strong color, such as "RED" and "BLACK", indicates that it contains 2 or more CAGE tags
  3. Large arrow indicate over 10 CAGE tags.

Statistics
Number of tag clusters deleted from hg17 to hg18 : 10 (0.0015%)
Number of tag clusters partially deleted from hg17 to hg18 : 3 (0.00059%)
Number of tag clusters split from hg17 to hg18 : 4 (0.0006%)

A05. EST
See UCSC description.

A06. tRNA
tRNAs extracted from NCBI.

A07. Entrez Gene / transcript boundary
Transcripts associated with EntrezGene. See here

B01. Promoter (CAGE level2) Apr 2008
Promoters of THP1 PMA timecourse (CAGE). See PubmedID:19377474 and PubmedID:19624849
CAGE tags are mapped on the genome, aggregated into individual TSS position (level1), the TSS positions are aggregated into promoters (level2), and the promoters are aggreated into promoter regions (level3). See our paper for the details. This track shows the promoters (level2) as clickable arrows, showing the tag counts and TPMs along the time course as bar plot. The arrow is colored accroding to the log10(the mean of the normalized TPMs), simply:
 Score > 2 (TPM > 100)
 Score > 1 (TPM > 10)
 Score > 0.4 (TPM > 2.5)
 Score > 0 (TPM > 0)
 Score <=0 (TPM <= 0)

B02. Promoter region (CAGE level3) Apr 2008
This track shows the promoter regions (level3). See "CAGE promoter" description for further details.

B03. Illumina all experiments
Illumina v2 all experiments (Biological replicates PMA and siRNA series1-4 KD). See PubmedID:19377474
The feature in the display panel are clickable. On click, a histogram is shown. x-axis shows the expression level in TPM, while the y-axis shows each condition, such as each time points or a knock down of a transcription factor. The bars are colored according to the experiment type. A grey bar means that the detection score for that time point, TF or miRNA is below 0.99.

B05. TF qRT-PCR PMA 1st & 2nd
Copy number of transcription factors by qRT-PCR at PMA Full Time Course.
See PubmedID:19374774
Score value intensity by Copy number. The color code is:
 Copy number > 300
 Copy number > 100
 Copy number > 30
 Copy number > 10
 Copy number <=10

B06. shortRNA Cluster
Fantom4 shortRNA clusters. The color coding for the clusters is similar to the one used for CAGE clusters.Those clusters are clickable.
Clusters in grey have zero expression over all the time points.
See PubmedID:20051555

F11. ShortRNA libraries s06s08
Fantom4 shortRNA mapping. Multi and single mappers are shown. The color coding is as follows:
Red for single mappers.
lightgrey for multimappers.

C11_F. CAGE level1 RIKEN1 0h Forward
Individual TSS positions defined by the 5'-end of the CAGE tags. TPM values for each TSS are shown using a histogram. See "CAGE promoter" description for further details. For each time point (0h, 1h,4h,12h,24h,96h), for both strands separately (forward and reverse) and for each RIKEN replicate (1,3,6) one histogram is shown.

C11_R. CAGE level1 RIKEN1 0h Reverse
No additional information available.

C12_F. CAGE level1 RIKEN1 1h Forward
No additional information available.

C12_R. CAGE level1 RIKEN1 1h Reverse
No additional information available.

C13_F. CAGE level1 RIKEN1 4h Forward
No additional information available.

C13_R. CAGE level1 RIKEN1 4h Reverse
No additional information available.

C14_F. CAGE level1 RIKEN1 12h Forward
No additional information available.

C14_R. CAGE level1 RIKEN1 12h Reverse
No additional information available.

C15_F. CAGE level1 RIKEN1 24h Forward
No additional information available.

C15_R. CAGE level1 RIKEN1 24h Reverse
No additional information available.

C16_F. CAGE level1 RIKEN1 96h Forward
No additional information available.

C16_R. CAGE level1 RIKEN1 96h Reverse
No additional information available.

C21_F. CAGE level1 RIKEN3 0h Forward
No additional information available.

C21_R. CAGE level1 RIKEN3 0h Reverse
No additional information available.

C22_F. CAGE level1 RIKEN3 1h Forward
No additional information available.

C22_R. CAGE level1 RIKEN3 1h Reverse
No additional information available.

C23_F. CAGE level1 RIKEN3 4h Forward
No additional information available.

C23_R. CAGE level1 RIKEN3 4h Reverse
No additional information available.

C24_F. CAGE level1 RIKEN3 12h Forward
No additional information available.

C24_R. CAGE level1 RIKEN3 12h Reverse
No additional information available.

C25_F. CAGE level1 RIKEN3 24h Forward
No additional information available.

C25_R. CAGE level1 RIKEN3 24h Reverse
No additional information available.

C26_F. CAGE level1 RIKEN3 96h Forward
No additional information available.

C26_R. CAGE level1 RIKEN3 96h Reverse
No additional information available.

C31_F. CAGE level1 RIKEN6 0h Forward
No additional information available.

C31_R. CAGE level1 RIKEN6 0h Reverse
No additional information available.

C32_F. CAGE level1 RIKEN6 1h Forward
No additional information available.

C32_R. CAGE level1 RIKEN6 1h Reverse
No additional information available.

C33_F. CAGE level1 RIKEN6 4h Forward
No additional information available.

C33_R. CAGE level1 RIKEN6 4h Reverse
No additional information available.

C34_F. CAGE level1 RIKEN6 12h Forward
No additional information available.

C34_R. CAGE level1 RIKEN6 12h Reverse
No additional information available.

C35_F. CAGE level1 RIKEN6 24h Forward
No additional information available.

C35_R. CAGE level1 RIKEN6 24h Reverse
No additional information available.

C36_F. CAGE level1 RIKEN6 96h Forward
No additional information available.

C36_R. CAGE level1 RIKEN6 96h Reverse
No additional information available.

D01. H3K9 by Whole Tiling Array PMA0h (1st)
ChIP/chip experiments for the H3K9 Acetylation with the whole genome tiling array. The experiments were conducted before and after PMA differentiation (0h and 96hr). See PubmedID:19377474

D02. H3K9 by Whole Tiling Array PMA96h (1st)
No additional information available.

D04. H3K9 by Whole Tiling Array PMA0h (2nd)
No additional information available.

D05. H3K9 by Whole Tiling Array PMA96h (2nd)
No additional information available.

D07. PU.1 Promoter Array PMA0h (1st)
ChIP/chip experiments for PU.1 with the promoter tiling array. The experiments were conducted before and after PMA differentiation (0h and 96hr). See PubmedID:19377474

D08. PU.1 Promoter Array PMA96h (1st)
No additional information available.

D10. PU.1 Promoter Array PMA0h (2nd)
No additional information available.

D11. PU.1 Promoter Array PMA96h (2nd)
No additional information available.

D13. SP1 Promoter Array PMA0h (1st)
ChIP/chip experiments for SP1 with the promoter tiling array. The experiments were conducted before and after PMA differentiation (0h and 96hr). See PubmedID:19377474

D14. SP1 Promoter Array PMA96h (1st)
No additional information available.

D16. SP1 Promoter Array PMA0h (2nd)
No additional information available.

D17. SP1 Promoter Array PMA96h (2nd)
No additional information available.

D19. Pol II by Whole Tiling Array PMA0h (1st)
ChIP/chip experiments for Polymerase II with the whole genome tiling array. The experiments were conducted before and after PMA differentiation (0h and 96hr). See PubmedID:19377474

D20. Pol II by Whole Tiling Array PMA96h (1st)
No additional information available.

D21. EGR1 promoter array PMA1h (1st)
Pilot analysis of promoter array for EGR1 at PMA 1h (1st). See PubmedID:19374776

D22. EGR1 promoter array PMA1h (2nd)
Pilot analysis of promoter array for EGR1 at PMA 1h (2nd)

Z5. Array CGH for THP1
See PubmedID:19635138.

Z1. Gene prediction
Predicted transcripts by genscan, geneid, twinscan. See UCSC description for genscan and geneid.

Z2. Conserved Region (axtNet v.s Mm8)
No additional information available.

Z3. DNA/GC Content
No additional information available.

Z4. TFBS MotEvo cage
See PubmedID:19377474 and PubmedID:19624849

CpG Island
See UCSC description.

Gap
See UCSC description.

Simple Repeat
Repeat region detected by Tandem repeats finder(TRF). See UCSC description.

Repeat Masker
See UCSC description.

Promoter Array Probe
Pilot analysis of promoter array for PU.1 (SPI1)

Whole Tiling Array Probe ( H3K9 )
Pilot analysis of whole tiling array for H3K9

Whole Tiling Array Probe ( Pol II )
Pilot analysis of whole tiling array for Pol II

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