Region for Stat1 Peak: Stat1_PK_21

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 36 out of 36 atomic motifs.

Group(s) crtHsap#(name) [p-value]	Motif craHsap#	Discovery p-value	Location	Width	(+)motif	(-)motif
3 annotated group(s): 200454 (MRF-2) [1.25E-04] 200097 (Pax-6) [2.97E-04] 200395 (HOXA3) [4.86E-04]	2968	4.43E-01	chr19:10,242,517-10,242,529	13	CAAGCTTAGCCTG	CAGGCTAAGCTTG
0 annotated groups	2969	9.79E-01	chr19:10,242,556-10,242,568	13	GGGnGCAGCyCCC	GGGrGCTGCnCCC
1 annotated group(s): 201045 (AP-2alphaA) [4.13E-04]	2970	1.77E-01	chr19:10,242,564-10,242,572	9	nyyCCGGGG	CCCCGGrrn
0 annotated groups	2971	8.16E-01	chr19:10,242,574-10,242,583	10	CATsGCCCTG	CAGGGCwATG
9 annotated group(s): 200054 (NF-kappaB) [4.50E-06] 200052 (RelA) [7.09E-05] 10107 (p65) [7.09E-05] ...	2972	4.02E-01	chr19:10,242,605-10,242,625	21	AryTyGGAAATTCCGrA...	wAGCTyCGGAATTTCCr...
0 annotated groups	2973	2.50E-01	chr19:10,242,656-10,242,666	11	GsCCnGGGCrC	GyGCCCnGGwC
4 annotated group(s): 200007 (Elk-1) [1.25E-04] 10028 (Elk-1) [1.33E-04] 10076 (SAP-1) [2.65E-04] ...	2974	4.80E-01	chr19:10,242,669-10,242,687	19	TCTCAGTCCGGAAATrmCn	nGkyATTTCCGGACTGAGA
6 annotated group(s): 200056 (NF-1) [1.85E-04] 200805 (LEF-1) [2.22E-04] 10076 (SAP-1) [2.65E-04] ...	2975	4.94E-02	chr19:10,242,692-10,242,713	22	CmyTyGTTCCGGAGGGG...	GCCTTCCCCTCCGGAAC...
20 annotated group(s): 200777 (STAT1) [8.93E-06] 201048 (GAS) [9.77E-05] 201048 (GAS) [9.77E-05] ...	2976	6.80E-04	chr19:10,242,707-10,242,731	25	GGAAGGCGCGAGGTTTC...	CTTTCCCGGAAACCTCG...
0 annotated groups	2977	1.10E-02	chr19:10,242,731-10,242,742	12	GCAGCACCGCCC	GGGCGGTGCTGC
0 annotated groups	2978	1.26E-01	chr19:10,242,732-10,242,739	8	CAGCACCG	CGGTGCTG
0 annotated groups	2979	5.52E-04	chr19:10,242,732-10,242,741	10	CAGCACCGCC	GGCGGTGCTG
0 annotated groups	2991	1.42E-01	chr19:10,242,732-10,242,744	13	CAGCACCGCCCCy	rGGGGCGGTGCTG
2 annotated group(s): 200008 (Sp1) [4.47E-05] 200800 (AP-2) [7.02E-04]	2980	1.00E-08	chr19:10,242,733-10,242,744	12	AGCACCGCCCCT	AGGGGCGGTGCT
2 annotated group(s): 200008 (Sp1) [4.47E-05] 200800 (AP-2) [7.02E-04]	2981	1.26E-01	chr19:10,242,733-10,242,740	8	AGCACCGC	GCGGTGCT
2 annotated group(s): 200008 (Sp1) [4.47E-05] 200800 (AP-2) [7.02E-04]	2982	1.08E-02	chr19:10,242,733-10,242,742	10	AGCACCGCCC	GGGCGGTGCT
2 annotated group(s): 200008 (Sp1) [4.47E-05] 200800 (AP-2) [7.02E-04]	2983	1.26E-01	chr19:10,242,734-10,242,741	8	GCACCGCC	GGCGGTGC
2 annotated group(s): 200008 (Sp1) [4.47E-05] 200800 (AP-2) [7.02E-04]	2984	1.08E-02	chr19:10,242,734-10,242,743	10	GCACCGCCCC	GGGGCGGTGC
4 annotated group(s): 200008 (Sp1) [4.47E-05] 200693 (E12) [4.38E-04] 10065 (PPARgamma-RXRal) [6.22E-04] ...	2985	1.26E-01	chr19:10,242,735-10,242,742	8	CACCGCCC	GGGCGGTG
4 annotated group(s): 200008 (Sp1) [4.47E-05] 200693 (E12) [4.38E-04] 10065 (PPARgamma-RXRal) [6.22E-04] ...	2986	1.09E-02	chr19:10,242,735-10,242,744	10	CACCGCCCCT	AGGGGCGGTG
3 annotated group(s): 200693 (E12) [4.38E-04] 10065 (PPARgamma-RXRal) [6.22E-04] 200800 (AP-2) [7.02E-04]	2987	4.96E-01	chr19:10,242,736-10,242,747	12	ACCGCCCCTyGG	CCrAGGGGCGGT
4 annotated group(s): 200411 (HNF-4alpha1) [3.89E-04] 200693 (E12) [4.38E-04] 10065 (PPARgamma-RXRal) [6.22E-04] ...	2988	5.32E-01	chr19:10,242,737-10,242,746	10	CCGCCCCTyG	CrAGGGGCGG
4 annotated group(s): 200411 (HNF-4alpha1) [3.89E-04] 200693 (E12) [4.38E-04] 10065 (PPARgamma-RXRal) [6.22E-04] ...	2989	1.08E-02	chr19:10,242,737-10,242,748	12	CCGCCCCyyGGC	GCCrrGGGGCGG
4 annotated group(s): 200411 (HNF-4alpha1) [3.89E-04] 200693 (E12) [4.38E-04] 10065 (PPARgamma-RXRal) [6.22E-04] ...	2990	5.32E-01	chr19:10,242,738-10,242,747	10	CGCCCCTyGG	CCrAGGGGCG
3 annotated group(s): 200411 (HNF-4alpha1) [3.89E-04] 200693 (E12) [4.38E-04] 10065 (PPARgamma-RXRal) [6.22E-04]	2992	5.06E-01	chr19:10,242,738-10,242,749	12	CGCCCCTyGGCC	GGCCrAGGGGCG
4 annotated group(s): 200411 (HNF-4alpha1) [3.89E-04] 200693 (E12) [4.38E-04] 10065 (PPARgamma-RXRal) [6.22E-04] ...	2993	4.98E-01	chr19:10,242,740-10,242,751	12	CCCCTyGGCCCC	GGGGCCrAGGGG
3 annotated group(s): 200150 (Brachyury) [1.59E-04] 10065 (PPARgamma-RXRal) [6.22E-04] 200938 (E2F-1) [9.63E-04]	2994	9.19E-01	chr19:10,242,743-10,242,754	12	CTnGGCCCCCmG	CkGGGGGCCnAG
4 annotated group(s): 200150 (Brachyury) [1.59E-04] 200395 (HOXA3) [2.91E-04] 200693 (E12) [5.64E-04] ...	2995	9.16E-01	chr19:10,242,747-10,242,759	13	GCCCCCAGGksGC	GCwmCCTGGGGGC
1 annotated group(s): 200095 (CUTL1) [6.50E-04]	2996	7.74E-01	chr19:10,242,766-10,242,773	8	TATAAArG	CyTTTATA
1 annotated group(s): 200538 (HTF) [6.05E-04]	2997	5.95E-01	chr19:10,242,788-10,242,804	17	TCGACGCTGAGCTCCTC	GAGGAGCTCAGCGTCGA
0 annotated groups	2998	8.51E-01	chr19:10,242,824-10,242,834	11	CnsAGCCTCrs	wyGAGGCTwnG
9 annotated group(s): 200051 (NF-kappaB1) [2.30E-04] 200059 (YY1) [4.69E-04] 200052 (RelA) [4.87E-04] ...	2999	2.37E-02	chr19:10,242,915-10,242,928	14	GGGGrTkGCCGTCs	wGACGGCmAyCCCC
5 annotated group(s): 200647 (LXR-alpha) [2.95E-04] 200457 (STAT5A) [6.43E-04] 200056 (NF-1) [7.79E-04] ...	3000	5.02E-01	chr19:10,242,922-10,242,933	12	GCCGwsGGGCsr	ywGCCCwsCGGC
2 annotated group(s): 200641 (HSF) [2.68E-05] 201001 (DEAF-1) [6.43E-05]	3001	5.61E-02	chr19:10,242,945-10,242,952	8	yyCCGGGA	TCCCGGrr
1 annotated group(s): 201001 (DEAF-1) [6.43E-05]	3002	3.55E-01	chr19:10,242,949-10,242,961	13	GGGAGGACCrsCy	rGwyGGTCCTCCC
2 annotated group(s): 200098 (Pax-2) [2.14E-04] 200143 (Pax-5) [3.89E-04]	3003	2.97E-01	chr19:10,242,968-10,242,978	11	TCAGGwCwTGm	kCAsGsCCTGA