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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 HOXC11

Z-value: 0.22

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Transcription factors associated with HOXC11

Gene Symbol	Gene ID	Gene Info
HOXC11 Ensembl NCBI GeneCards UniProt	ENSG00000123388.4	HOXC11

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
HOXC11	chr12_54366652_54366803	183	0.827388	0.31	4.1e-01	Click!
HOXC11	chr12_54367124_54367311	305	0.691051	0.31	4.2e-01	Click!
HOXC11	chr12_54366891_54367088	77	0.901702	0.20	6.0e-01	Click!
HOXC11	chr12_54367495_54368083	877	0.242171	-0.19	6.2e-01	Click!

Activity of the HOXC11 motif across conditions

Conditions sorted by the z-value of the HOXC11 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
chr3_183893852_183894003	0.11	AP2M1	adaptor-related protein complex 2, mu 1 subunit	639	0.55
chr7_121514140_121514423	0.09	PTPRZ1	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	866	0.74
chr2_213977055_213977206	0.09	IKZF2	IKAROS family zinc finger 2 (Helios)	36223	0.21
chr7_27138540_27138742	0.09	HOTAIRM1	HOXA transcript antisense RNA, myeloid-specific 1	183	0.86
chr2_151385576_151386025	0.09	RND3	Rho family GTPase 3	9725	0.33
chr2_184180506_184180887	0.08	NUP35	nucleoporin 35kDa	191523	0.03
chr6_128529501_128529738	0.08	PTPRK	protein tyrosine phosphatase, receptor type, K	113707	0.07
chr1_170631765_170631991	0.07	PRRX1	paired related homeobox 1	397	0.91
chr10_89686715_89686866	0.07	RP11-380G5.2		48341	0.12
chr12_56308297_56308448	0.07	WIBG	within bgcn homolog (Drosophila)	12524	0.09
chr19_4059827_4060036	0.07	CTD-2622I13.3		2816	0.16
chr4_163496269_163496420	0.06	FSTL5	follistatin-like 5	411157	0.01
chr3_116755274_116755493	0.06	ENSG00000200372	.	71309	0.12
chr10_104253427_104253578	0.06	ACTR1A	ARP1 actin-related protein 1 homolog A, centractin alpha (yeast)	8933	0.1
chr4_39570973_39571124	0.06	UGDH	UDP-glucose 6-dehydrogenase	41117	0.11
chr8_83181283_83181434	0.06	SNX16	sorting nexin 16	426257	0.01
chr8_42063953_42065062	0.06	PLAT	plasminogen activator, tissue	576	0.71
chr13_107382919_107383070	0.06	ARGLU1	arginine and glutamate rich 1	162482	0.04
chr14_81453709_81453897	0.06	CEP128	centrosomal protein 128kDa	27955	0.21
chr11_22380798_22380949	0.06	CTD-2140G10.4		2967	0.27
chr3_29327656_29328192	0.06	RBMS3-AS3	RBMS3 antisense RNA 3	4293	0.26
chr8_91782901_91783052	0.05	NECAB1	N-terminal EF-hand calcium binding protein 1	20802	0.19
chr9_81871537_81871846	0.05	TLE4	transducin-like enhancer of split 4 (E(sp1) homolog, Drosophila)	314997	0.01
chr17_32078540_32078804	0.05	ENSG00000221699	.	122805	0.05
chr10_120966033_120966362	0.05	GRK5	G protein-coupled receptor kinase 5	904	0.45
chrX_31284117_31284268	0.05	DMD	dystrophin	782	0.77
chr9_133814218_133814626	0.05	FIBCD1	fibrinogen C domain containing 1	33	0.97
chr1_178310607_178310919	0.05	RASAL2	RAS protein activator like 2	157	0.97
chr1_216897072_216897310	0.05	ESRRG	estrogen-related receptor gamma	396	0.93
chr5_67483384_67483535	0.05	RP11-404L6.2	Uncharacterized protein	2245	0.34
chr11_94671451_94671602	0.05	RP11-856F16.2		12840	0.19
chr13_32859694_32859925	0.05	FRY	furry homolog (Drosophila)	2179	0.28
chr6_108486676_108487297	0.04	OSTM1	osteopetrosis associated transmembrane protein 1	58	0.78
chr20_52517333_52517726	0.04	AC005220.3		39170	0.2
chr20_11882046_11882285	0.04	BTBD3	BTB (POZ) domain containing 3	9024	0.24
chr3_168890820_168890971	0.04	MECOM	MDS1 and EVI1 complex locus	25373	0.27
chr10_24756981_24757214	0.04	KIAA1217	KIAA1217	1637	0.45
chr5_58412336_58412487	0.04	RP11-266N13.2		76823	0.11
chr12_93515628_93515779	0.04	RP11-511B23.2		17164	0.2
chr5_145319076_145319227	0.04	SH3RF2	SH3 domain containing ring finger 2	1711	0.46
chr12_11325045_11325196	0.04	RP11-785H5.2		1168	0.4
chr8_8745358_8745509	0.04	MFHAS1	malignant fibrous histiocytoma amplified sequence 1	5722	0.22
chr9_20511940_20512213	0.04	ENSG00000264941	.	9736	0.23
chr14_85707273_85707789	0.04	ENSG00000252529	.	30745	0.26
chr17_79315981_79316442	0.04	TMEM105	transmembrane protein 105	11737	0.13
chr12_96184496_96184659	0.04	NTN4	netrin 4	35	0.97
chr10_83723729_83723880	0.04	NRG3	neuregulin 3	86087	0.1
chr4_36534650_36534801	0.04	RP11-431M7.2		140693	0.05
chr5_112822732_112823004	0.04	MCC	mutated in colorectal cancers	1659	0.35
chr15_93428286_93428633	0.04	CHD2	chromodomain helicase DNA binding protein 2	1933	0.32
chr2_198572573_198572724	0.04	MARS2	methionyl-tRNA synthetase 2, mitochondrial	2561	0.27
chr15_25637624_25637775	0.04	UBE3A	ubiquitin protein ligase E3A	12954	0.11
chr3_15823018_15823169	0.04	ANKRD28	ankyrin repeat domain 28	14935	0.19
chr1_70768783_70768934	0.04	ANKRD13C	ankyrin repeat domain 13C	51547	0.11
chr2_222287657_222287808	0.04	EPHA4	EPH receptor A4	79548	0.11
chr4_153269690_153269947	0.04	FBXW7	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	140	0.97
chr11_79150724_79151047	0.04	TENM4	teneurin transmembrane protein 4	810	0.68
chr17_62971851_62972399	0.04	AMZ2P1	archaelysin family metallopeptidase 2 pseudogene 1	2490	0.23
chr10_22899285_22899436	0.04	PIP4K2A	phosphatidylinositol-5-phosphate 4-kinase, type II, alpha	18718	0.27
chr8_49321315_49321611	0.04	ENSG00000252710	.	100873	0.08
chr9_12859535_12860149	0.04	ENSG00000222658	.	25478	0.2
chr4_26240703_26241213	0.04	RBPJ	recombination signal binding protein for immunoglobulin kappa J region	33271	0.24
chr3_49538097_49538499	0.04	DAG1	dystroglycan 1 (dystrophin-associated glycoprotein 1)	30546	0.11
chr12_86228304_86228474	0.04	RASSF9	Ras association (RalGDS/AF-6) domain family (N-terminal) member 9	1959	0.44
chr15_48739773_48739924	0.04	DUT	deoxyuridine triphosphatase	115245	0.05
chr6_113966553_113966868	0.04	ENSG00000266650	.	42593	0.17
chr1_115711115_115711431	0.04	TSPAN2	tetraspanin 2	79152	0.1
chr11_77072652_77072803	0.04	PAK1	p21 protein (Cdc42/Rac)-activated kinase 1	12395	0.24
chr6_153911669_153911820	0.04	ENSG00000199246	.	90838	0.09
chr3_151743926_151744077	0.04	RP11-454C18.2		98038	0.08
chr5_57751342_57751690	0.04	PLK2	polo-like kinase 2	4571	0.26
chr13_43649218_43649369	0.04	DNAJC15	DnaJ (Hsp40) homolog, subfamily C, member 15	51954	0.17
chr14_77998583_77998734	0.04	ENSG00000240233	.	15554	0.15
chr13_80511227_80511398	0.03	SPRY2	sprouty homolog 2 (Drosophila)	402482	0.01
chr2_166477820_166478090	0.03	CSRNP3	cysteine-serine-rich nuclear protein 3	47336	0.18
chr9_101891255_101891406	0.03	TGFBR1	transforming growth factor, beta receptor 1	1114	0.52
chr9_12775321_12775833	0.03	LURAP1L	leucine rich adaptor protein 1-like	557	0.78
chr1_224690897_224691172	0.03	WDR26	WD repeat domain 26	66299	0.1
chr6_167539321_167539472	0.03	CCR6	chemokine (C-C motif) receptor 6	3137	0.25
chr9_100173959_100174113	0.03	TDRD7	tudor domain containing 7	196	0.95
chr6_53928552_53928746	0.03	MLIP-AS1	MLIP antisense RNA 1	15875	0.2
chr2_121716938_121717089	0.03	ENSG00000221321	.	75636	0.11
chr17_55131735_55131912	0.03	AKAP1	A kinase (PRKA) anchor protein 1	30630	0.13
chrX_15965760_15965911	0.03	ENSG00000200566	.	31409	0.2
chr3_104994911_104995062	0.03	ALCAM	activated leukocyte cell adhesion molecule	90767	0.1
chr1_83031111_83031295	0.03	LPHN2	latrophilin 2	585630	0.0
chr10_4174092_4174250	0.03	KLF6	Kruppel-like factor 6	346698	0.01
chr10_33620428_33620906	0.03	NRP1	neuropilin 1	2643	0.37
chr6_56598112_56598263	0.03	DST	dystonin	52490	0.16
chr5_143300598_143300749	0.03	HMHB1	histocompatibility (minor) HB-1	108947	0.07
chr14_89507425_89507846	0.03	FOXN3	forkhead box N3	139453	0.05
chr10_62174410_62174561	0.03	ANK3	ankyrin 3, node of Ranvier (ankyrin G)	24997	0.28
chr12_95606332_95606483	0.03	FGD6	FYVE, RhoGEF and PH domain containing 6	4748	0.2
chr5_180676019_180676390	0.03	GNB2L1	guanine nucleotide binding protein (G protein), beta polypeptide 2-like 1	1108	0.22
chr22_25507961_25508112	0.03	CTA-221G9.11		623	0.77
chr11_111381371_111381522	0.03	BTG4	B-cell translocation gene 4	1618	0.2
chr6_3501213_3501364	0.03	SLC22A23	solute carrier family 22, member 23	44032	0.18
chr8_97583871_97584022	0.03	SDC2	syndecan 2	8631	0.28
chr2_213976639_213976790	0.03	IKZF2	IKAROS family zinc finger 2 (Helios)	36639	0.21
chr2_134432207_134432889	0.03	ENSG00000200708	.	78886	0.11
chr5_32164159_32164310	0.03	GOLPH3	golgi phosphoprotein 3 (coat-protein)	10222	0.19
chr16_81577563_81578015	0.03	CMIP	c-Maf inducing protein	48835	0.17
chr5_110846365_110846666	0.03	STARD4-AS1	STARD4 antisense RNA 1	1409	0.37
chr19_4717454_4717717	0.03	DPP9	dipeptidyl-peptidase 9	315	0.83
chr22_36291410_36291691	0.03	RBFOX2	RNA binding protein, fox-1 homolog (C. elegans) 2	43395	0.19
chr4_139160727_139161292	0.03	SLC7A11	solute carrier family 7 (anionic amino acid transporter light chain, xc- system), member 11	2494	0.42
chr15_69367071_69367289	0.03	RP11-809H16.4		31275	0.17
chr5_124748322_124748473	0.03	ENSG00000222107	.	61573	0.16
chr15_26273691_26273918	0.03	ENSG00000212604	.	19583	0.26
chr6_111947186_111947610	0.03	TRAF3IP2	TRAF3 interacting protein 2	19917	0.16
chr12_123210436_123210665	0.03	HCAR1	hydroxycarboxylic acid receptor 1	4579	0.15
chr10_131323764_131323955	0.03	AL355531.2	Uncharacterized protein	14334	0.23
chr18_7958694_7958932	0.03	PTPRM	protein tyrosine phosphatase, receptor type, M	11861	0.23
chrX_151140998_151141149	0.03	GABRE	gamma-aminobutyric acid (GABA) A receptor, epsilon	2070	0.24
chr15_38361508_38361698	0.03	TMCO5A	transmembrane and coiled-coil domains 5A	134145	0.05
chr12_80329810_80330005	0.03	PPP1R12A	protein phosphatase 1, regulatory subunit 12A	667	0.6
chr1_115820493_115820644	0.03	RP4-663N10.1		5087	0.3
chr3_37031282_37031460	0.03	EPM2AIP1	EPM2A (laforin) interacting protein 1	3424	0.2
chr16_68299633_68299784	0.03	SLC7A6	solute carrier family 7 (amino acid transporter light chain, y+L system), member 6	289	0.77
chr1_94789725_94789884	0.03	ARHGAP29	Rho GTPase activating protein 29	86615	0.08
chr1_172327726_172327959	0.03	ENSG00000206684	.	7838	0.18
chr4_40059743_40060131	0.03	N4BP2	NEDD4 binding protein 2	1381	0.41
chr11_89113858_89114276	0.03	NOX4	NADPH oxidase 4	109833	0.07
chr16_80181289_80181449	0.03	DYNLRB2	dynein, light chain, roadblock-type 2	393262	0.01
chr17_55372937_55373088	0.03	MSI2	musashi RNA-binding protein 2	966	0.68
chr4_85420275_85420452	0.03	NKX6-1	NK6 homeobox 1	760	0.77
chr16_73089798_73090050	0.03	ZFHX3	zinc finger homeobox 3	3673	0.28
chr1_218524044_218525060	0.03	TGFB2	transforming growth factor, beta 2	4975	0.24
chr18_20612011_20612377	0.03	ENSG00000223023	.	7635	0.17
chr11_82904254_82904445	0.03	ANKRD42	ankyrin repeat domain 42	432	0.8
chr8_103664786_103665058	0.03	KLF10	Kruppel-like factor 10	1681	0.44
chr21_16429371_16429522	0.03	NRIP1	nuclear receptor interacting protein 1	7680	0.28
chr14_23448905_23449056	0.03	AJUBA	ajuba LIM protein	1815	0.14
chr4_169752801_169753072	0.03	PALLD	palladin, cytoskeletal associated protein	220	0.9
chr2_27861313_27861464	0.03	ENSG00000206731	.	3648	0.13
chrX_78666635_78666786	0.03	ITM2A	integral membrane protein 2A	43661	0.22
chr16_48641989_48642140	0.03	N4BP1	NEDD4 binding protein 1	2056	0.33
chr6_125401116_125401267	0.03	RNF217	ring finger protein 217	31833	0.2
chr18_19753166_19753317	0.03	GATA6	GATA binding protein 6	2347	0.21
chr2_85196569_85196904	0.03	KCMF1	potassium channel modulatory factor 1	1480	0.46
chr2_235167151_235167323	0.03	SPP2	secreted phosphoprotein 2, 24kDa	207806	0.02
chr3_114225259_114225410	0.03	ZBTB20	zinc finger and BTB domain containing 20	51670	0.16
chr1_159931930_159932191	0.03	SLAMF9	SLAM family member 9	8016	0.12
chr5_53386895_53387046	0.03	ENSG00000265421	.	15557	0.24
chr3_191048468_191048928	0.03	UTS2B	urotensin 2B	373	0.85
chr10_116634887_116635113	0.03	FAM160B1	family with sequence similarity 160, member B1	14450	0.25
chr17_814224_814439	0.03	RP11-676J12.7	Uncharacterized protein	1459	0.38
chr6_17914331_17914482	0.03	KIF13A	kinesin family member 13A	73288	0.11
chr22_24114508_24114741	0.03	MMP11	matrix metallopeptidase 11 (stromelysin 3)	382	0.71
chr17_4135715_4135866	0.03	ANKFY1	ankyrin repeat and FYVE domain containing 1	31352	0.12
chr1_241271770_241271921	0.03	ENSG00000265831	.	23727	0.23
chr13_21654404_21654812	0.03	LATS2	large tumor suppressor kinase 2	18922	0.14
chr3_81724848_81724999	0.03	GBE1	glucan (1,4-alpha-), branching enzyme 1	67857	0.14
chr3_64149261_64149412	0.03	PRICKLE2-AS3	PRICKLE2 antisense RNA 3	23884	0.16
chr4_114367456_114367607	0.03	ENSG00000206820	.	26052	0.18
chr8_34689780_34689931	0.03	ENSG00000265560	.	137869	0.05
chr13_20844899_20845050	0.03	GJB6	gap junction protein, beta 6, 30kDa	38440	0.17
chr11_11472823_11472974	0.03	CSNK2A3	casein kinase 2, alpha 3 polypeptide	97994	0.07
chr11_89955284_89955841	0.03	CHORDC1	cysteine and histidine-rich domain (CHORD) containing 1	665	0.79
chr18_55889348_55889572	0.03	NEDD4L	neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase	657	0.77
chr6_17413520_17413671	0.03	CAP2	CAP, adenylate cyclase-associated protein, 2 (yeast)	19652	0.26
chr5_60728941_60729092	0.03	ZSWIM6	zinc finger, SWIM-type containing 6	100916	0.08
chr7_141628433_141628584	0.03	OR9A4	olfactory receptor, family 9, subfamily A, member 4	9891	0.12
chr15_99788624_99789059	0.03	TTC23	tetratricopeptide repeat domain 23	895	0.51
chr16_80603632_80603783	0.03	RP11-525K10.3		6675	0.18
chr2_166802065_166802216	0.03	TTC21B	tetratricopeptide repeat domain 21B	8213	0.19
chr6_21417907_21418058	0.03	SOX4	SRY (sex determining region Y)-box 4	175990	0.04
chrX_119596476_119596627	0.03	LAMP2	lysosomal-associated membrane protein 2	6296	0.25
chr8_94859053_94859497	0.03	TMEM67	transmembrane protein 67	61778	0.09
chr20_6764834_6765429	0.03	BMP2	bone morphogenetic protein 2	16820	0.28
chr13_44389557_44389806	0.03	ENOX1	ecto-NOX disulfide-thiol exchanger 1	28637	0.21
chr13_30002091_30002575	0.03	MTUS2	microtubule associated tumor suppressor candidate 2	431	0.89
chr3_39448821_39449415	0.03	ENSG00000206760	.	762	0.4
chr7_25896786_25897110	0.03	ENSG00000199085	.	92658	0.09
chr17_57699008_57699159	0.03	CLTC	clathrin, heavy chain (Hc)	1790	0.37
chr6_54564223_54564374	0.02	ENSG00000251946	.	86887	0.1
chr4_83787091_83787242	0.02	SEC31A	SEC31 homolog A (S. cerevisiae)	918	0.55
chr13_99629621_99629906	0.02	DOCK9	dedicator of cytokinesis 9	481	0.85
chr5_114868008_114868159	0.02	FEM1C	fem-1 homolog c (C. elegans)	12508	0.22
chr19_45995836_45996758	0.02	RTN2	reticulon 2	228	0.87
chr4_14728626_14728777	0.02	ENSG00000202449	.	36367	0.24
chrX_73068432_73068583	0.02	RP13-216E22.5		120813	0.06
chr14_45367367_45367627	0.02	C14orf28	chromosome 14 open reading frame 28	959	0.41
chr11_27486888_27487039	0.02	RP11-159H22.2		6313	0.18
chr3_160700419_160700570	0.02	B3GALNT1	beta-1,3-N-acetylgalactosaminyltransferase 1 (globoside blood group)	118461	0.06
chr15_71054590_71054766	0.02	UACA	uveal autoantigen with coiled-coil domains and ankyrin repeats	1091	0.55
chr9_132175724_132175951	0.02	ENSG00000242281	.	43097	0.14
chr16_20922292_20922443	0.02	LYRM1	LYR motif containing 1	9941	0.16
chr11_94441338_94441489	0.02	AMOTL1	angiomotin like 1	1816	0.4
chr17_62648329_62648480	0.02	SMURF2	SMAD specific E3 ubiquitin protein ligase 2	9626	0.22
chr8_10268256_10268407	0.02	RP11-981G7.1		22851	0.2
chr10_8315388_8315539	0.02	GATA3	GATA binding protein 3	218694	0.02
chr16_50400842_50400993	0.02	RP11-21B23.1		1574	0.3
chr7_17977598_17977749	0.02	SNX13	sorting nexin 13	2418	0.38
chr3_120168336_120168615	0.02	FSTL1	follistatin-like 1	1363	0.54
chr1_23476622_23476773	0.02	ENSG00000206935	.	12500	0.13
chr5_128796123_128796371	0.02	ADAMTS19-AS1	ADAMTS19 antisense RNA 1	135	0.71
chr18_21418407_21418558	0.02	LAMA3	laminin, alpha 3	4565	0.28
chr14_96681269_96681420	0.02	RP11-404P21.5		4147	0.14
chr12_64480628_64481033	0.02	RP11-196H14.2		10568	0.2

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 HOXC11

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Gene Ontology Analysis

Gene overrepresentation in biological process category:

Log-likelihood per target	Total log-likelihood	Term	Description
0.0	0.0	GO:0035426	extracellular matrix-cell signaling(GO:0035426)

Gene overrepresentation in molecular function category:

Total log-likelihood	Term	Description
0.0	GO:0008061	chitin binding(GO:0008061)
0.0	GO:0050682	AF-2 domain binding(GO:0050682)
0.0	GO:0002162	dystroglycan binding(GO:0002162)
0.1	GO:0008330	protein tyrosine/threonine phosphatase activity(GO:0008330)
0.0	GO:0051371	muscle alpha-actinin binding(GO:0051371)