Region for Stat1 Peak: Stat1_PK_2

This page describes one search region that corresponds to a peak generated by chromatin immunoprecipication and massively parallel Solexa sequencing.

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.

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.

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.

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.

Showing 29 out of 29 atomic motifs.

Group(s) crtHsap#(name) [p-value]	Motif craHsap#	Discovery p-value	Location	Width	(+)motif	(-)motif
1 annotated group(s): 200641 (HSF) [4.64E-04]	2683	1.00E-08	chr17:37,794,035-37,794,046	12	AAACCGCTGAAT	ATTCAGCGGTTT
2 annotated group(s): 200456 (FAC1) [3.94E-04] 200510 (Lhx3a) [4.61E-04]	2684	1.32E-04	chr17:37,794,040-37,794,052	13	GCTGAATTACAGC	GCTGTAATTCAGC
0 annotated groups	2685	7.85E-04	chr17:37,794,048-37,794,056	9	ACAGCCCCT	AGGGGCTGT
0 annotated groups	2686	7.33E-01	chr17:37,794,081-37,794,093	13	CCCGGnsGGAGGG	CCCTCCwnCCGGG
6 annotated group(s): 200465 (POU6F1_(c2)) [8.88E-05] 200744 (POU1F1) [1.06E-04] 200097 (Pax-6) [1.91E-04] ...	2687	1.42E-02	chr17:37,794,102-37,794,114	13	ATGCATAATTCAT	ATGAATTATGCAT
0 annotated groups	2688	6.47E-01	chr17:37,794,115-37,794,127	13	GwrCkGsCwGyTC	GArCsGwCmGysC
8 annotated group(s): 200333 (ZF5) [3.57E-05] 200433 (Nkx5-1) [9.74E-05] 200235 (AhR) [1.86E-04] ...	2689	9.01E-01	chr17:37,794,151-37,794,156	6	TGCGTG	CACGCA
3 annotated group(s): 200056 (NF-1) [2.75E-04] 10067 (Pax-2) [4.49E-04] 200775 (CBF(2)) [7.38E-04]	2690	5.77E-03	chr17:37,794,180-37,794,191	12	CACTGrCCAATG	CATTGGyCAGTG
2 annotated group(s): 200085 (ZID) [7.86E-04] 200806 (CTF) [9.65E-04]	2691	6.51E-01	chr17:37,794,212-37,794,222	11	kGGCGrAGCCm	kGGCTyCGCCm
1 annotated group(s): 200808 (Pax-1) [4.35E-04]	2692	7.06E-04	chr17:37,794,244-37,794,259	16	GTGCTGGCTGTTCCGA	TCGGAACAGCCAGCAC
3 annotated group(s): 200706 (TFII-I) [1.24E-04] 200964 (CAR) [2.44E-04] 201001 (DEAF-1) [3.06E-04]	2693	7.28E-03	chr17:37,794,275-37,794,280	6	CCCTCC	GGAGGG
0 annotated groups	2694	2.82E-02	chr17:37,794,281-37,794,293	13	sCCrsnGGGAGGG	CCCTCCCnwyGGw
0 annotated groups	2695	4.59E-01	chr17:37,794,299-37,794,311	13	CCsAGGnCyTGGG	CCCArGnCCTwGG
3 annotated group(s): 200706 (TFII-I) [1.24E-04] 200649 (MAZ) [6.43E-04] 200008 (Sp1) [9.21E-04]	2696	1.00E-08	chr17:37,794,318-37,794,335	18	AGCCCGGGGGGAGGGAGG	CCTCCCTCCCCCCGGGCT
5 annotated group(s): 200113 (CREB) [6.23E-05] 10048 (Hen-1) [1.25E-04] 200005 (AP-4) [3.17E-04] ...	2697	1.00E-08	chr17:37,794,359-37,794,380	22	GAAAACTCAGCTGAGTT...	CCAGGAACTCAGCTGAG...
0 annotated groups	2698	1.00E-08	chr17:37,794,375-37,794,385	11	TCCTGGCAGTG	CACTGCCAGGA
15 annotated group(s): 200691 (ATF-1) [4.44E-06] 200113 (CREB) [8.88E-06] 200513 (ATF3) [9.60E-06] ...	2699	1.00E-08	chr17:37,794,384-37,794,398	15	TGCGTGACGTCAAGr	yCTTGACGTCACGCA
2 annotated group(s): 200133 (POU3F1) [1.55E-05] 200489 (Nkx6-2) [6.86E-04]	2700	1.00E-08	chr17:37,794,398-37,794,411	14	rCACTTTAAATGCC	GGCATTTAAAGTGy
3 annotated group(s): 200693 (E12) [2.31E-04] 200651 (NF-muE1) [3.71E-04] 200242 (PPAR-alpha) [6.47E-04]	2701	1.00E-08	chr17:37,794,447-37,794,457	11	CCCGGCCCTTG	CAAGGGCCGGG
1 annotated group(s): 200242 (PPAR-alpha) [6.47E-04]	2702	7.37E-04	chr17:37,794,454-37,794,465	12	CTTGGCACCACG	CGTGGTGCCAAG
15 annotated group(s): 10059 (Myc-Max) [2.66E-05] 10058 (Max) [8.86E-05] 200985 (Stra13) [1.34E-04] ...	2703	2.58E-01	chr17:37,794,459-37,794,470	12	CACCACGTGGkG	CmCCACGTGGTG
1 annotated group(s): 200999 (AIRE) [9.64E-04]	2704	2.07E-03	chr17:37,794,480-37,794,488	9	AGAGCCTCT	AGAGGCTCT
7 annotated group(s): 10004 (ARNT) [3.15E-04] 200261 (Olf-1) [4.11E-04] 10059 (Myc-Max) [6.13E-04] ...	2705	3.94E-03	chr17:37,794,489-37,794,500	12	TACCACGTGGGA	TCCCACGTGGTA
0 annotated groups	2706	4.92E-03	chr17:37,794,500-37,794,511	12	AmTCAGCyAGTT	AACTrGCTGAkT
0 annotated groups	2707	6.50E-03	chr17:37,794,522-37,794,534	13	CAGGTrTCkCCAG	CTGGmGAyACCTG
1 annotated group(s): 200261 (Olf-1) [4.08E-04]	2708	4.84E-01	chr17:37,794,542-37,794,549	8	GGGGACCC	GGGTCCCC
0 annotated groups	2709	3.73E-01	chr17:37,794,547-37,794,559	13	CCCAACTCCTGAr	yTCAGGAGTTGGG
3 annotated group(s): 201001 (DEAF-1) [6.05E-04] 10066 (PPARgamma) [6.36E-04] 200113 (CREB) [9.07E-04]	2710	5.67E-01	chr17:37,794,588-37,794,600	13	TGGGTGACTCCnG	CnGGAGTCACCCA
2 annotated group(s): 200631 (FXR) [3.31E-04] 200453 (IRF-7A) [4.44E-04]	2711	1.31E-03	chr17:37,794,608-37,794,619	12	GAACTTCAGTTT	AAACTGAAGTTC