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ENCODE: H3K4me3 ChIP-Seq of primary human cells

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CREMA is a free online tool that recognizes most important transcription factors that change the chromatin state across different samples.

Results for NKX6-3

Z-value: 0.45

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Transcription factors associated with NKX6-3

Gene Symbol	Gene ID	Gene Info
NKX6-3 Ensembl NCBI GeneCards UniProt	ENSG00000165066.11	NKX6-3

Correlations of motif activity and signal intensity at CREs associated with the motif's TFs:

This plot shows correlation between observed signal intensity of a CRE associated with the transcription factor across all samples and activity of the motif.

For each TF, only the top 5 correlated CREs are shown.

CRE	Gene	Distance	Association probability	Pearson corr. coef.	P-value	Plot
NKX6-3	chr8_41511279_41511901	2735	0.179446	-0.69	4.2e-02	Click!
NKX6-3	chr8_41503949_41504289	759	0.542759	-0.68	4.4e-02	Click!
NKX6-3	chr8_41510934_41511242	2233	0.206680	-0.56	1.2e-01	Click!

Activity of the NKX6-3 motif across conditions

Conditions sorted by the z-value of the NKX6-3 motif activity

Move your cursor over a bar to see sample name and corresponding Z-value.

Top target CREs of the motif:

Cis Regulatory Element (CRE)	Target Score	Top associated gene	Gene Info	Distance of CRE to TSS	CRE/Gene association probability
chrX_114829080_114829277	0.33	PLS3	plastin 3	1313	0.48
chr7_129933276_129933885	0.26	CPA4	carboxypeptidase A4	461	0.76
chrX_13906420_13906604	0.18	GPM6B	glycoprotein M6B	664	0.81
chr19_58488964_58489115	0.18	C19orf18	chromosome 19 open reading frame 18	3137	0.15
chr5_147285141_147285292	0.18	C5orf46	chromosome 5 open reading frame 46	849	0.57
chr18_60385543_60385694	0.17	PHLPP1	PH domain and leucine rich repeat protein phosphatase 1	2935	0.28
chr10_33798417_33798757	0.17	NRP1	neuropilin 1	173397	0.03
chr7_98970111_98970529	0.16	ARPC1B	actin related protein 2/3 complex, subunit 1B, 41kDa	1552	0.28
chr5_120114861_120115414	0.16	ENSG00000222609	.	68602	0.14
chr5_1883178_1883404	0.15	IRX4	iroquois homeobox 4	411	0.66
chr11_22724799_22724998	0.15	ENSG00000222427	.	15001	0.2
chr6_21227526_21227677	0.15	ENSG00000252046	.	233802	0.02
chr5_97850230_97850381	0.14	ENSG00000223053	.	124630	0.06
chr3_128207705_128209147	0.14	RP11-475N22.4		326	0.79
chrX_83589461_83589612	0.14	ENSG00000221494	.	108700	0.07
chr19_6087775_6088269	0.14	CTC-232P5.3		20058	0.13
chr4_90850866_90851017	0.14	MMRN1	multimerin 1	27807	0.23
chr2_110872434_110873339	0.14	MALL	mal, T-cell differentiation protein-like	713	0.63
chr13_24146066_24146217	0.13	TNFRSF19	tumor necrosis factor receptor superfamily, member 19	1338	0.59
chr3_69796924_69797075	0.13	MITF	microphthalmia-associated transcription factor	8377	0.25
chr5_97850046_97850197	0.13	ENSG00000223053	.	124814	0.06
chr14_101867418_101867569	0.13	ENSG00000258498	.	159266	0.02
chr16_64450080_64450292	0.13	CDH11	cadherin 11, type 2, OB-cadherin (osteoblast)	643395	0.0
chr1_82670427_82670613	0.13	LPHN2	latrophilin 2	224947	0.02
chr2_158039761_158039912	0.13	GALNT5	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 5 (GalNAc-T5)	74274	0.11
chr20_45754385_45754678	0.13	ENSG00000264901	.	41078	0.18
chr6_148831295_148831530	0.12	ENSG00000223322	.	13964	0.3
chr3_54897831_54897982	0.12	CACNA2D3-AS1	CACNA2D3 antisense RNA 1	37376	0.21
chr3_10315639_10315790	0.12	TATDN2	TatD DNase domain containing 2	3110	0.16
chr13_79182716_79183828	0.12	POU4F1	POU class 4 homeobox 1	5599	0.19
chr14_73778052_73778238	0.11	NUMB	numb homolog (Drosophila)	12062	0.17
chr7_4046197_4046504	0.11	SDK1	sidekick cell adhesion molecule 1	55798	0.18
chr9_67293693_67293844	0.11	RP11-236F9.2		8470	0.29
chr19_19823801_19824098	0.11	ZNF14	zinc finger protein 14	19957	0.13
chr8_93114852_93115389	0.11	RUNX1T1	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)	334	0.94
chr7_94025506_94025990	0.11	COL1A2	collagen, type I, alpha 2	1875	0.46
chr10_60401833_60402026	0.10	BICC1	bicaudal C homolog 1 (Drosophila)	129029	0.06
chr14_52123850_52124001	0.10	FRMD6	FERM domain containing 6	5227	0.22
chr6_85823864_85824548	0.10	NT5E	5'-nucleotidase, ecto (CD73)	335603	0.01
chr12_15304261_15304412	0.10	RERG	RAS-like, estrogen-regulated, growth inhibitor	13239	0.23
chr1_198238845_198238996	0.10	NEK7	NIMA-related kinase 7	48991	0.19
chr7_17720120_17720505	0.10	SNX13	sorting nexin 13	259779	0.02
chr5_140989194_140989345	0.10	AC008781.7		8712	0.11
chr2_101731109_101731260	0.10	ENSG00000265860	.	21153	0.19
chr9_20041214_20041376	0.10	ENSG00000266224	.	211544	0.02
chr5_92922789_92922940	0.10	ENSG00000237187	.	1510	0.41
chr13_45242490_45242715	0.10	ENSG00000238932	.	39793	0.2
chr10_101689203_101689354	0.10	DNMBP	dynamin binding protein	1475	0.38
chr9_132796775_132796926	0.10	FNBP1	formin binding protein 1	8591	0.2
chr2_230138192_230138530	0.10	PID1	phosphotyrosine interaction domain containing 1	2360	0.4
chr6_130180797_130180948	0.10	TMEM244	transmembrane protein 244	1544	0.54
chr2_38828054_38829790	0.10	AC011247.3		182	0.89
chr12_54473950_54474101	0.10	RP11-834C11.7		47	0.95
chr3_133020367_133020518	0.10	RP11-402L6.1		44410	0.17
chr8_41200524_41200675	0.10	SFRP1	secreted frizzled-related protein 1	33583	0.15
chr5_71643973_71644124	0.09	PTCD2	pentatricopeptide repeat domain 2	27823	0.16
chr18_52804048_52804199	0.09	ENSG00000252437	.	9753	0.29
chr16_4424352_4424847	0.09	VASN	vasorin	2750	0.17
chrX_9269682_9269833	0.09	TBL1X	transducin (beta)-like 1X-linked	161578	0.04
chr3_89163237_89163857	0.09	EPHA3	EPH receptor A3	6721	0.35
chr12_78336292_78336638	0.09	NAV3	neuron navigator 3	23591	0.28
chr15_56204998_56205389	0.09	NEDD4	neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase	2659	0.34
chr5_10551768_10551919	0.09	ANKRD33B	ankyrin repeat domain 33B	12737	0.19
chr5_76134459_76134610	0.09	ENSG00000264391	.	1514	0.35
chr7_92224542_92224693	0.09	FAM133B	family with sequence similarity 133, member B	4909	0.24
chrX_95690881_95691032	0.09	ENSG00000223260	.	25175	0.28
chr6_45536778_45536929	0.09	ENSG00000252738	.	76988	0.11
chr7_92254665_92254816	0.09	FAM133B	family with sequence similarity 133, member B	35032	0.17
chr2_19172713_19172864	0.09	ENSG00000266738	.	375402	0.01
chr6_42284093_42284281	0.09	ENSG00000221252	.	95947	0.06
chr15_73345145_73345907	0.09	NEO1	neogenin 1	575	0.85
chr18_46620789_46620940	0.09	DYM	dymeclin	2999	0.26
chr13_97906946_97907208	0.09	MBNL2	muscleblind-like splicing regulator 2	21381	0.26
chr18_20407102_20407268	0.08	RBBP8	retinoblastoma binding protein 8	28961	0.16
chr10_15368154_15368305	0.08	FAM171A1	family with sequence similarity 171, member A1	44829	0.17
chr17_69531749_69531900	0.08	ENSG00000222563	.	224515	0.02
chr4_53507903_53508112	0.08	USP46	ubiquitin specific peptidase 46	14750	0.2
chr18_42313149_42313495	0.08	SETBP1	SET binding protein 1	36193	0.24
chr9_93557702_93558119	0.08	SYK	spleen tyrosine kinase	6159	0.34
chr12_11850521_11850672	0.08	ETV6	ets variant 6	47808	0.17
chr7_13985407_13985644	0.08	ETV1	ets variant 1	40541	0.2
chr1_51171312_51171463	0.08	ENSG00000252825	.	44581	0.17
chr15_96893541_96893692	0.08	AC087477.1	Uncharacterized protein	10871	0.16
chr1_65005729_65006114	0.08	ENSG00000264470	.	39609	0.19
chr14_77543003_77543154	0.08	CIPC	CLOCK-interacting pacemaker	21362	0.15
chr9_12882212_12882363	0.08	ENSG00000222658	.	3033	0.35
chr4_140808579_140808865	0.08	MAML3	mastermind-like 3 (Drosophila)	2484	0.4
chr18_28779723_28779874	0.08	DSC1	desmocollin 1	36979	0.15
chr13_80658291_80658484	0.08	SPRY2	sprouty homolog 2 (Drosophila)	255407	0.02
chr5_133861629_133862874	0.08	JADE2	jade family PHD finger 2	76	0.97
chr21_36286009_36286160	0.08	RUNX1	runt-related transcription factor 1	23997	0.27
chr13_77897361_77897512	0.08	MYCBP2	MYC binding protein 2, E3 ubiquitin protein ligase	3378	0.37
chr12_64580629_64580780	0.08	ENSG00000212298	.	17869	0.15
chr9_89952337_89952906	0.08	ENSG00000212421	.	77256	0.11
chr5_152602934_152603085	0.08	GRIA1	glutamate receptor, ionotropic, AMPA 1	267097	0.02
chr15_48436377_48436744	0.08	MYEF2	myelin expression factor 2	4963	0.17
chr6_27060216_27060434	0.08	ENSG00000222800	.	17434	0.13
chrX_107685038_107685189	0.08	COL4A5	collagen, type IV, alpha 5	2001	0.34
chr14_93720610_93720761	0.08	UBR7	ubiquitin protein ligase E3 component n-recognin 7 (putative)	35658	0.11
chr7_115967399_115967904	0.08	AC073130.3		299	0.91
chr6_159514146_159514297	0.08	TAGAP	T-cell activation RhoGTPase activating protein	48037	0.13
chr4_177930341_177930492	0.08	ENSG00000222859	.	172180	0.03
chr3_37363190_37363371	0.07	ENSG00000222208	.	19860	0.18
chr14_88851403_88852544	0.07	SPATA7	spermatogenesis associated 7	15	0.98
chrX_133523066_133523217	0.07	ENSG00000251962	.	14271	0.17
chr4_141866142_141866293	0.07	RNF150	ring finger protein 150	51973	0.17
chr8_116675050_116675578	0.07	TRPS1	trichorhinophalangeal syndrome I	1409	0.6
chr1_215183894_215184045	0.07	KCNK2	potassium channel, subfamily K, member 2	4771	0.37
chr10_69831641_69832005	0.07	HERC4	HECT and RLD domain containing E3 ubiquitin protein ligase 4	2071	0.33
chr2_38295840_38295991	0.07	RMDN2-AS1	RMDN2 antisense RNA 1	1731	0.34
chr15_93362136_93362546	0.07	FAM174B	family with sequence similarity 174, member B	9313	0.17
chr15_50427680_50427831	0.07	ATP8B4	ATPase, class I, type 8B, member 4	16336	0.2
chr6_83094369_83094520	0.07	TPBG	trophoblast glycoprotein	20483	0.28
chr13_36058740_36058891	0.07	NBEA	neurobeachin	7929	0.2
chr10_63812743_63812894	0.07	ARID5B	AT rich interactive domain 5B (MRF1-like)	3848	0.32
chr12_26164349_26164500	0.07	RASSF8	Ras association (RalGDS/AF-6) domain family (N-terminal) member 8	245	0.95
chr6_6005898_6006049	0.07	NRN1	neuritin 1	1227	0.56
chr11_111849006_111849202	0.07	DIXDC1	DIX domain containing 1	1071	0.39
chr7_104854367_104854518	0.07	SRPK2	SRSF protein kinase 2	55020	0.13
chr10_111217087_111217238	0.07	ENSG00000200217	.	217765	0.02
chr2_25978953_25979253	0.07	ASXL2	additional sex combs like 2 (Drosophila)	24075	0.18
chr3_87036535_87037613	0.07	VGLL3	vestigial like 3 (Drosophila)	2778	0.42
chr4_170081571_170081722	0.07	RP11-327O17.2		41299	0.18
chr11_128600565_128600716	0.07	FLI1	Fli-1 proto-oncogene, ETS transcription factor	34045	0.15
chr7_48210671_48210822	0.07	ABCA13	ATP-binding cassette, sub-family A (ABC1), member 13	311	0.94
chr7_85112676_85112827	0.07	SEMA3D	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	296580	0.01
chr6_125684129_125684280	0.07	RP11-735G4.1		11266	0.27
chr9_100743461_100743673	0.07	ANP32B	acidic (leucine-rich) nuclear phosphoprotein 32 family, member B	2076	0.25
chr7_70201396_70202343	0.07	AUTS2	autism susceptibility candidate 2	7744	0.34
chr10_33670460_33670611	0.07	NRP1	neuropilin 1	45345	0.19
chr12_67041467_67041618	0.07	GRIP1	glutamate receptor interacting protein 1	413	0.92
chr10_34189936_34190141	0.07	ENSG00000199200	.	300964	0.01
chr10_74600201_74600352	0.07	OIT3	oncoprotein induced transcript 3	53063	0.12
chr6_9139698_9139849	0.07	SLC35B3	solute carrier family 35 (adenosine 3'-phospho 5'-phosphosulfate transporter), member B3	703979	0.0
chr14_20895899_20896050	0.07	KLHL33	kelch-like family member 33	7827	0.08
chr8_90742457_90742611	0.07	RIPK2	receptor-interacting serine-threonine kinase 2	27441	0.25
chr7_87720149_87720440	0.07	ADAM22	ADAM metallopeptidase domain 22	72052	0.11
chr3_30553614_30553765	0.07	TGFBR2	transforming growth factor, beta receptor II (70/80kDa)	94305	0.09
chr4_15685369_15685921	0.07	FAM200B	family with sequence similarity 200, member B	2216	0.26
chr17_73348111_73348291	0.07	RP11-16C1.3		7715	0.11
chr10_24754741_24755189	0.07	KIAA1217	KIAA1217	495	0.84
chr6_143026333_143026484	0.07	RP1-67K17.3		43172	0.2
chr15_82414957_82415108	0.07	RP11-597K23.2	Uncharacterized protein	34000	0.16
chr10_103442163_103442336	0.07	FBXW4	F-box and WD repeat domain containing 4	12767	0.18
chr4_139143471_139143622	0.07	SLC7A11	solute carrier family 7 (anionic amino acid transporter light chain, xc- system), member 11	19957	0.26
chr5_140420029_140420180	0.07	PCDHB1	protocadherin beta 1	10875	0.12
chr4_14728626_14728777	0.07	ENSG00000202449	.	36367	0.24
chr2_191517520_191517671	0.07	NAB1	NGFI-A binding protein 1 (EGR1 binding protein 1)	856	0.66
chr20_17538596_17539086	0.07	BFSP1	beaded filament structural protein 1, filensin	642	0.72
chr4_81118792_81119547	0.07	PRDM8	PR domain containing 8	511	0.82
chr20_657176_657327	0.07	SCRT2	scratch family zinc finger 2	428	0.66
chr2_189361179_189361330	0.07	GULP1	GULP, engulfment adaptor PTB domain containing 1	73511	0.13
chr1_79297788_79297939	0.06	ELTD1	EGF, latrophilin and seven transmembrane domain containing 1	85707	0.1
chr4_134070427_134071051	0.06	PCDH10	protocadherin 10	269	0.96
chr4_112244997_112245242	0.06	ENSG00000200963	.	7449	0.34
chr4_135119262_135119413	0.06	PABPC4L	poly(A) binding protein, cytoplasmic 4-like	3566	0.39
chr15_77575085_77575236	0.06	PEAK1	pseudopodium-enriched atypical kinase 1	27266	0.24
chr3_44045083_44045345	0.06	ENSG00000252980	.	67365	0.13
chr12_109122720_109122871	0.06	CORO1C	coronin, actin binding protein, 1C	1532	0.34
chr11_36253008_36253159	0.06	COMMD9	COMM domain containing 9	57891	0.13
chr1_8138513_8138990	0.06	ERRFI1	ERBB receptor feedback inhibitor 1	52383	0.13
chr7_95107815_95108198	0.06	ASB4	ankyrin repeat and SOCS box containing 4	7207	0.2
chr5_106805601_106805833	0.06	EFNA5	ephrin-A5	200611	0.03
chr12_12551242_12551393	0.06	LOH12CR1	loss of heterozygosity, 12, chromosomal region 1	40965	0.13
chr20_50384318_50384901	0.06	ATP9A	ATPase, class II, type 9A	258	0.94
chr3_49424014_49424165	0.06	RHOA-IT1	RHOA intronic transcript 1 (non-protein coding)	19650	0.09
chr14_56711281_56711464	0.06	PELI2	pellino E3 ubiquitin protein ligase family member 2	125545	0.06
chr4_119950142_119950384	0.06	SYNPO2	synaptopodin 2	5637	0.3
chr5_103680813_103681290	0.06	ENSG00000239808	.	84524	0.11
chr5_30944702_30944853	0.06	CDH6	cadherin 6, type 2, K-cadherin (fetal kidney)	249080	0.02
chr10_104102183_104102477	0.06	NFKB2	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)	51537	0.08
chr8_48282315_48282609	0.06	SPIDR	scaffolding protein involved in DNA repair	70501	0.12
chr21_28640922_28641073	0.06	ADAMTS5	ADAM metallopeptidase with thrombospondin type 1 motif, 5	302165	0.01
chr4_177824622_177824937	0.06	VEGFC	vascular endothelial growth factor C	110898	0.07
chr7_27141205_27141470	0.06	HOXA2	homeobox A2	1093	0.25
chr12_86222890_86223044	0.06	RASSF9	Ras association (RalGDS/AF-6) domain family (N-terminal) member 9	7381	0.28
chr6_56595678_56595829	0.06	DST	dystonin	54924	0.16
chr1_8537218_8537608	0.06	ENSG00000221083	.	34565	0.16
chrX_12908437_12908588	0.06	TLR8	toll-like receptor 8	16227	0.17
chr11_103677106_103677422	0.06	ENSG00000264200	.	43370	0.2
chr12_32635785_32635936	0.06	FGD4	FYVE, RhoGEF and PH domain containing 4	3046	0.28
chr6_111922654_111922805	0.06	C6orf3		1651	0.34
chr15_51367983_51368134	0.06	RP11-394B5.2		6275	0.24
chr8_29388025_29388176	0.06	RP4-676L2.1		177413	0.03
chr2_141580056_141580207	0.06	ENSG00000201892	.	169981	0.04
chr6_19691587_19692480	0.06	ENSG00000200957	.	49273	0.18
chr12_72670200_72670351	0.06	ENSG00000236333	.	1588	0.43
chr21_39807445_39807798	0.06	ERG	v-ets avian erythroblastosis virus E26 oncogene homolog	62724	0.14
chr1_164665790_164665949	0.06	RP11-477H21.2		16547	0.21
chr12_109118598_109118801	0.06	CORO1C	coronin, actin binding protein, 1C	5628	0.17
chr2_46933523_46933944	0.06	SOCS5	suppressor of cytokine signaling 5	7407	0.22
chr4_119130339_119130490	0.06	ENSG00000269893	.	69931	0.13
chr1_100317573_100317724	0.06	AGL	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	578	0.74
chr12_10902988_10903139	0.06	YBX3	Y box binding protein 3	27152	0.13
chr11_126517104_126517255	0.06	RP11-115C10.1		5568	0.3
chr3_18024994_18025145	0.06	TBC1D5	TBC1 domain family, member 5	240925	0.02
chr17_20388317_20388497	0.06	LGALS9B	lectin, galactoside-binding, soluble, 9B	17559	0.13
chr1_8166685_8166836	0.06	ERRFI1	ERBB receptor feedback inhibitor 1	80392	0.08
chr21_38367175_38367326	0.06	HLCS	holocarboxylase synthetase (biotin-(proprionyl-CoA-carboxylase (ATP-hydrolysing)) ligase)	4714	0.17
chr11_60686819_60686970	0.06	TMEM109	transmembrane protein 109	256	0.81

Histogram of CRE-TSS distances for CREs targeted by :

Rank distribution of CRE target scores:

Distribution of target CREs across different genomic regions:

Network of associatons between targets according to the STRING database.

First level regulatory network of NKX6-3

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View png image

Gene Ontology Analysis

Gene overrepresentation in biological process category:

Total log-likelihood	Term	Description
0.1	GO:0007221	positive regulation of transcription of Notch receptor target(GO:0007221)
0.0	GO:0045425	positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process(GO:0045425)
0.0	GO:0035385	Roundabout signaling pathway(GO:0035385) regulation of negative chemotaxis(GO:0050923)
0.0	GO:0045627	positive regulation of T-helper 1 cell differentiation(GO:0045627)
0.1	GO:0070208	protein heterotrimerization(GO:0070208)
0.0	GO:0030948	negative regulation of vascular endothelial growth factor receptor signaling pathway(GO:0030948)

Gene overrepresentation in molecular function category:

Total log-likelihood	Term	Description
0.1	GO:0003953	NAD+ nucleosidase activity(GO:0003953)
0.0	GO:0005010	insulin-like growth factor-activated receptor activity(GO:0005010)
0.0	GO:0051371	muscle alpha-actinin binding(GO:0051371)