FILTERS:
pvalue:1.0
Region for Stat1 Peak: Stat1_PK_37
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This page describes one search region that corresponds to a peak generated by chromatin immunoprecipication and massively parallel Solexa sequencing.

Page Contents

Overview
Genomic Context
Image of Motifs and Modules
Motifs Found in this Region
Search region overview
Search region location chr16:10,830,136-10,830,736 (+) (601 bp)
Assembly Human, Ensembl v35 (NCBI 35)
Region ID Stat1_PK_37
Modules
(Co-occurring motif patterns)		 277 annotation-based module(s)
No 'de novo' modules exist in this database.

Genomic Context: Human genome assembly from Aug 2004. (UCSC hg17, NCBI 35, Ensembl v35)

The image shown below was created to provide context for this search region by showing a 100000 bp span of the genome, centered on this search region.

UCSC Genome Browser Image    
  • The first track shows the location of the search region in red.
  • The next two (or four) green tracks show the extent of the ChIP-seq data reported in this image, and the height of the ChIP-seq peaks located within that extent.
  • The last track shows known gene locations in this 100000 bp span of the genome.

This is a ChIP-seq-based search region and thus gene locations were not a factor in selecting the location of this region. However, the identity of any genes that overlap with, or are closest to, this search region are still of interest, and are described in the table below.

Gene near this search region
Ensembl ID ENSG00000182597
transcripts:
1) ENST00000329364
Gene description MHC class II transactivator type I (Fragment). [Source:Uniprot/SPTREMBL;Acc:O46786]
Gene type protein_coding
Transcript location(s) 1) chr16: 10,867,648-10,867,929 (+) (282 bp)
Distance from the region's midpoint to each transcript's TSS and TTS: 1) to TSS: -37,210, to TTS: -37,491
Gene near this search region
Ensembl ID ENSG00000181404
transcripts:
1) ENST00000327824
Gene type protein_coding
Transcript location(s) 1) chr16: 4,092-8,073 (-) (3,982 bp)
Distance from the region's midpoint to each transcript's TSS and TTS: 1) to TSS: -10,822,363, to TTS: -10,826,344
The distance from a cisred search region to a gene, is measured from the center of the search region to either the transcription termination site (TTS) or the transcription start site (TSS), whichever is closer.
A distance is negative if the TTS/TTS is downstream of the search region's center, relative to the gene's strand.
A distance is positive if the TTS/TTS is upstream of the search region's center, relative to the gene's strand.

A transcript's location is always reported relative to the positive strand.

Image of Motifs and Modules

The image shown below illustrates the location of the motifs and modules within this search region.
However, the number of modules in a region may exceed the genome browser's track limit. Thus, for each type of module (pattern), the text in the yellow box below indicates whether or not any modules of that type exist, and if so, whether or not all the modules of that type are displayed. (If it indicates that only the top 20 modules are displayed, this ranking is based on the number of instances of each module.)

User-specified filter settings do not affect the features displayed in the UCSC genome browser view.

About the patterns shown in this image:
Note: This search region contains more patterns than are displayed in this UCSC genome browser image.
There are no 'de novo' patterns to show.
Only the top 20 ranked (TRANSFAC) annotation-based patterns are shown.
There are no (JASPAR) annotation-based patterns to show.

UCSC Genome Browser Image
Click on the image to view this region at UCSC.
     This image uses the Human genome assembly from Aug 2004. (UCSC hg17, NCBI 35, Ensembl v35) and contains a number of custom tracks followed by several UCSC tracks. The custom tracks show:
  • The long red and gray bar at the top shows the nominal 'search region' within which comparative genomics discovery methods were applied. Motif predictions were not made in coding exons and most types of repeats. In this database, the locations of masks applied to the search region are shown in gray.
  • The numbered brown blocks are 'atomic' motifs, i.e. conserved DNA sequence motifs that were identified by discovery methods and post-processing operations. Motifs are shaded to indicate the discovery p-value; a darker motif was more significant at the discovery stage.
  • Following the motif discovery stage, motifs were filtered by membership in co-occurring patterns, and patterns were ranked by genome-scale properties. Motifs instances that occur in highly-ranked putative regulatory modules may be more reliable predictions of functional genomic elements.
  • The connected sets of blue boxes are co-occurring patterns, i.e. putative regulatory modules. Modules are shaded to indicate the number of times that a pattern is found in the target genome; a darker module is associated with more search regions. An pattern is called either 'de novo' or annotation-based, depending on the type of groups that appear in the pattern. (see next point)
  • Before patterns (i.e. modules) can be identified from atomic motifs, groups of similar motifs must be found; modules are then identified as co-occurring 'group labels' that satisfy certain criteria. Such groups can be identified a) by annotating atomic motifs with known binding site resources from TRANSFAC, JASPAR or ORegAnno; or b) by 'de novo' clustering. Currently we show both types of patterns, but we consider annotation-based groups and patterns to be more reliable than 'de novo' groups and patterns. Work to improve genome-scale 'de novo' grouping is ongoing.

Motifs Found in this Region
The contents of the table below can be modified by changing your filter settings.
Currently, this table only contains motifs which:
+ have a discovery p-value < 1.0
+ were found using any of these algorithms: MotifSampler, Consensus.oops, Consensus.omops, Consensus.zmops, MEME.tcm, MEME.oops, MEME.zoops

Showing 21 out of 21 atomic motifs.

Group(s)
crtHsap#(name) [p-value]		 Motif
craHsap#		 Discovery
p-value		 Location Width (+)motif (-)motif
1 annotated group(s):
 200143 (Pax-5) [4.41E-05] 		4462 2.70E-02 chr16:10,830,149-10,830,159 11  Seq Logo
AGCmCAGGCCC 		Seq Logo
GGGCCTGkGCT
2 annotated group(s):
 200806 (CTF) [9.68E-05]
 200257 (RREB-1) [3.58E-04] 		4463 9.54E-01 chr16:10,830,175-10,830,182 8  Seq Logo
TCCCGTAA 		Seq Logo
TTACGGGA
0 annotated groups 4464 8.91E-01 chr16:10,830,200-10,830,209 10  Seq Logo
CwmCATGGAG 		Seq Logo
CTCCATGksG
4 annotated group(s):
 200938 (E2F-1) [1.15E-04]
 200803 (DP-1) [4.15E-04]
 200803 (DP-1) [4.77E-04]
... 		4465 1.26E-01 chr16:10,830,228-10,830,238 11  Seq Logo
GGCnGGGAGCC 		Seq Logo
GGCTCCCnGCC
0 annotated groups 4466 5.58E-01 chr16:10,830,345-10,830,356 12  Seq Logo
CTCTTGCArGAG 		Seq Logo
CTCyTGCAAGAG
1 annotated group(s):
 200056 (NF-1) [4.28E-04] 		4467 8.47E-01 chr16:10,830,394-10,830,404 11  Seq Logo
CTGnGAGsCAG 		Seq Logo
CTGwCTCnCAG
16 annotated group(s):
 201051 (ISRE_d) [4.49E-05]
 201051 (ISRE_d) [4.49E-05]
 200024 (E2F) [3.79E-04]
... 		4468 4.85E-02 chr16:10,830,418-10,830,437 20  Seq Logo
ACCAyTTACGGGAAATGCnC 		Seq Logo
GnGCATTTCCCGTAArTGGT
2 annotated group(s):
 200261 (Olf-1) [4.23E-04]
 200113 (CREB) [6.04E-04] 		4469 8.53E-01 chr16:10,830,436-10,830,448 13  Seq Logo
TCCrCTGAGGAGA 		Seq Logo
TCTCCTCAGyGGA
4 annotated group(s):
 200261 (Olf-1) [4.23E-04]
 201051 (ISRE_d) [7.63E-04]
 201051 (ISRE_d) [7.63E-04]
... 		4470 1.00E-08 chr16:10,830,446-10,830,451 6  Seq Logo
AGAAAG 		Seq Logo
CTTTCT
6 annotated group(s):
 10066 (PPARgamma) [1.21E-04]
 10040 (HFH-1) [5.95E-04]
 200472 (FOXO4) [6.39E-04]
... 		4471 6.33E-01 chr16:10,830,460-10,830,466 7  Seq Logo
GTTGTTT 		Seq Logo
AAACAAC
13 annotated group(s):
 200792 (Smad1) [2.33E-05]
 200806 (CTF) [3.23E-05]
 200638 (HNF-4) [1.07E-04]
... 		4473 7.16E-01 chr16:10,830,463-10,830,498 36  Seq Logo
kkTTwGCCCAGCCCTGG... 		Seq Logo
wAyCCAGTCTGGAyAGG...
3 annotated group(s):
 200056 (NF-1) [3.01E-04]
 200761 (DeltaNp63alpha) [4.78E-04]
 200005 (AP-4) [6.88E-04] 		4472 2.19E-01 chr16:10,830,472-10,830,482 11  Seq Logo
AGCCCwGGsCC 		Seq Logo
GGwCCsGGGCT
8 annotated group(s):
 200964 (CAR) [7.73E-05]
 200056 (NF-1) [1.51E-04]
 200032 (c-Ets-1) [4.87E-04]
... 		4474 1.28E-01 chr16:10,830,497-10,830,508 12  Seq Logo
TCAGGAAGCCTk 		Seq Logo
mAGGCTTCCTGA
4 annotated group(s):
 200242 (PPAR-alpha) [2.50E-05]
 200056 (NF-1) [1.51E-04]
 200057 (COMP1) [7.56E-04]
... 		4475 6.73E-01 chr16:10,830,508-10,830,518 11  Seq Logo
AGCCCwGksCC 		Seq Logo
GGwmCsGGGCT
2 annotated group(s):
 200056 (NF-1) [4.59E-04]
 201028 (NRSF) [9.07E-04] 		4476 3.74E-01 chr16:10,830,533-10,830,545 13  Seq Logo
AGGCTCAGTTCCT 		Seq Logo
AGGAACTGAGCCT
0 annotated groups 4477 6.25E-01 chr16:10,830,584-10,830,596 13  Seq Logo
GGGAGTCACTGCC 		Seq Logo
GGCAGTGACTCCC
3 annotated group(s):
 200531 (NERF-1a) [7.23E-04]
 200658 (PU.1) [7.49E-04]
 200999 (AIRE) [9.91E-04] 		4478 9.54E-01 chr16:10,830,607-10,830,614 8  Seq Logo
CTTCCTGw 		Seq Logo
sCAGGAAG
2 annotated group(s):
 200135 (POU2F1) [3.49E-04]
 200999 (AIRE) [9.91E-04] 		4479 8.72E-01 chr16:10,830,614-10,830,623 10  Seq Logo
TGTAyCCArA 		Seq Logo
TyTGGrTACA
4 annotated group(s):
 200987 (FOXP1a) [1.27E-04]
 10041 (HFH-2) [3.21E-04]
 200130 (FOXD3) [4.10E-04]
... 		4481 6.04E-01 chr16:10,830,626-10,830,639 14  Seq Logo
AACAACAACAAAAA 		Seq Logo
TTTTTGTTGTTGTT
7 annotated group(s):
 200987 (FOXP1a) [1.27E-04]
 10041 (HFH-2) [3.21E-04]
 200130 (FOXD3) [4.10E-04]
... 		4480 4.17E-01 chr16:10,830,629-10,830,634 6  Seq Logo
AACAAC 		Seq Logo
GTTGTT
1 annotated group(s):
 200005 (AP-4) [2.30E-04] 		4482 3.40E-01 chr16:10,830,643-10,830,654 12  Seq Logo
AAACAGCAGTTT 		Seq Logo
AAACTGCTGTTT

Questions or comments: cisred@bcgsc.ca