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ENCODE: H3K4me1 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: 0.40

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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_54367610_54367772	779	0.289126	0.49	1.9e-01	Click!
HOXC11	chr12_54366324_54366475	511	0.503307	0.25	5.2e-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
chr18_7958757_7958908	0.11	PTPRM	protein tyrosine phosphatase, receptor type, M	11880	0.23
chr5_16493939_16494090	0.10	FAM134B	family with sequence similarity 134, member B	15093	0.21
chr1_82265506_82265657	0.09	LPHN2	latrophilin 2	501	0.89
chr1_170631689_170631840	0.09	PRRX1	paired related homeobox 1	511	0.87
chr5_80263913_80264064	0.09	CTC-459I6.1		7262	0.24
chr1_158913144_158913295	0.09	PYHIN1	pyrin and HIN domain family, member 1	11861	0.21
chr3_73595877_73596028	0.08	PDZRN3	PDZ domain containing ring finger 3	14817	0.24
chr10_112506565_112506716	0.08	ENSG00000252036	.	9574	0.18
chr6_45632042_45632279	0.08	ENSG00000252738	.	18319	0.29
chr6_35362532_35362683	0.07	PPARD	peroxisome proliferator-activated receptor delta	52205	0.1
chr12_52673287_52673438	0.07	RP11-845M18.7		422	0.69
chr2_69894789_69894940	0.07	ENSG00000238708	.	373	0.88
chr5_64493902_64494516	0.07	ENSG00000207439	.	75013	0.12
chr13_99961636_99961787	0.07	GPR183	G protein-coupled receptor 183	2052	0.34
chr20_42474741_42474892	0.07	ENSG00000206801	.	49633	0.14
chr4_39531124_39531275	0.07	UGDH	UDP-glucose 6-dehydrogenase	1268	0.35
chr3_73072628_73072858	0.07	ENSG00000238959	.	4216	0.2
chr2_88920682_88920833	0.07	EIF2AK3	eukaryotic translation initiation factor 2-alpha kinase 3	3690	0.2
chr1_83031153_83031304	0.07	LPHN2	latrophilin 2	585655	0.0
chr6_64516560_64517136	0.07	RP11-59D5__B.2		119	0.98
chr2_192182945_192183393	0.07	MYO1B	myosin IB	41558	0.17
chr2_175766480_175766631	0.07	CHN1	chimerin 1	54076	0.13
chr6_163849459_163849641	0.07	QKI	QKI, KH domain containing, RNA binding	5310	0.35
chr2_197056759_197056910	0.07	STK17B	serine/threonine kinase 17b	15607	0.18
chr9_5465910_5466061	0.07	CD274	CD274 molecule	15460	0.19
chr18_56353868_56354019	0.07	RP11-126O1.4		9097	0.15
chr7_114871692_114871916	0.07	ENSG00000199764	.	23754	0.28
chr16_27252390_27252716	0.07	NSMCE1	non-SMC element 1 homolog (S. cerevisiae)	8154	0.17
chr20_19973253_19973404	0.07	NAA20	N(alpha)-acetyltransferase 20, NatB catalytic subunit	24432	0.19
chr1_94792467_94792618	0.07	ARHGAP29	Rho GTPase activating protein 29	89353	0.08
chr20_5755973_5756124	0.07	C20orf196	chromosome 20 open reading frame 196	24949	0.22
chr4_38685842_38686144	0.06	RP11-617D20.1		19489	0.15
chr3_115719451_115719602	0.06	ENSG00000243359	.	162811	0.04
chr3_142919123_142919274	0.06	ENSG00000211483	.	34708	0.19
chr16_1666082_1666233	0.06	CRAMP1L	Crm, cramped-like (Drosophila)	1516	0.23
chr7_150440672_150440823	0.06	GIMAP5	GTPase, IMAP family member 5	6311	0.17
chr3_172033208_172033359	0.06	AC092964.1	Uncharacterized protein	935	0.62
chr2_239693558_239693739	0.06	TWIST2	twist family bHLH transcription factor 2	63025	0.13
chr15_60085307_60085458	0.06	BNIP2	BCL2/adenovirus E1B 19kDa interacting protein 2	103649	0.06
chr2_64750645_64750930	0.06	AFTPH	aftiphilin	678	0.74
chr17_55723600_55723751	0.06	ENSG00000242889	.	28206	0.16
chr8_141125038_141125212	0.06	C8orf17	chromosome 8 open reading frame 17	181709	0.03
chr6_128529618_128529908	0.06	PTPRK	protein tyrosine phosphatase, receptor type, K	113563	0.07
chr2_73334235_73334398	0.06	RAB11FIP5	RAB11 family interacting protein 5 (class I)	5830	0.18
chr5_139678742_139678893	0.06	PFDN1	prefoldin subunit 1	3851	0.19
chrX_39176359_39176510	0.06	ENSG00000207122	.	235896	0.02
chr17_61433493_61433644	0.06	AC037445.1		17154	0.15
chr6_18247333_18247484	0.06	DEK	DEK oncogene	2563	0.28
chr2_40507984_40508135	0.06	AC007377.1		19912	0.23
chr20_62169801_62169978	0.06	PTK6	protein tyrosine kinase 6	1166	0.3
chr12_66005489_66005640	0.06	HMGA2	high mobility group AT-hook 2	212347	0.02
chr16_69250892_69251043	0.06	RP11-70O5.2		23485	0.11
chr3_180648116_180648267	0.06	FXR1	fragile X mental retardation, autosomal homolog 1	14943	0.21
chr19_2215762_2215913	0.06	AC004490.1		273	0.8
chr22_21978223_21978374	0.06	YDJC	YdjC homolog (bacterial)	6027	0.1
chr5_38259654_38259805	0.06	EGFLAM	EGF-like, fibronectin type III and laminin G domains	1218	0.54
chr20_24387296_24387447	0.06	SYNDIG1	synapse differentiation inducing 1	62464	0.15
chr5_90476166_90476317	0.06	ENSG00000199643	.	90303	0.1
chr4_39570957_39571108	0.06	UGDH	UDP-glucose 6-dehydrogenase	41101	0.11
chr17_76531986_76532137	0.06	ENSG00000243426	.	2924	0.23
chr7_104631689_104631965	0.06	ENSG00000251911	.	20093	0.14
chr6_90854294_90854445	0.06	ENSG00000222078	.	143144	0.04
chr6_158283594_158283745	0.06	RP11-52J3.2		12573	0.17
chr17_62648244_62648405	0.06	SMURF2	SMAD specific E3 ubiquitin protein ligase 2	9706	0.22
chr6_140084162_140084413	0.06	CITED2	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	388530	0.01
chr2_144504368_144504519	0.06	RP11-434H14.1		5580	0.25
chr16_86817580_86817731	0.06	FOXL1	forkhead box L1	205540	0.02
chr3_43386050_43386201	0.06	RP11-188P20.3		3010	0.24
chr17_45959726_45959877	0.06	SP2	Sp2 transcription factor	13715	0.1
chr5_172425652_172425803	0.06	ATP6V0E1	ATPase, H+ transporting, lysosomal 9kDa, V0 subunit e1	14893	0.14
chr14_61125667_61125818	0.06	SIX1	SIX homeobox 1	765	0.7
chr9_108011375_108011526	0.06	SLC44A1	solute carrier family 44 (choline transporter), member 1	4547	0.34
chr5_172382388_172382600	0.06	RPL26L1	ribosomal protein L26-like 1	3238	0.19
chrX_19778013_19778164	0.05	SH3KBP1	SH3-domain kinase binding protein 1	12267	0.29
chr6_108486750_108487194	0.05	OSTM1	osteopetrosis associated transmembrane protein 1	72	0.78
chr3_66529878_66530029	0.05	LRIG1	leucine-rich repeats and immunoglobulin-like domains 1	21403	0.28
chr3_152808662_152808813	0.05	RP11-529G21.2		70827	0.11
chr12_8230719_8230959	0.05	NECAP1	NECAP endocytosis associated 1	3968	0.17
chr18_3252593_3253294	0.05	MYL12A	myosin, light chain 12A, regulatory, non-sarcomeric	670	0.64
chr16_18925014_18925165	0.05	SMG1	SMG1 phosphatidylinositol 3-kinase-related kinase	2054	0.25
chr9_20459022_20459173	0.05	ENSG00000222202	.	40778	0.14
chr5_124201652_124202095	0.05	ZNF608	zinc finger protein 608	117373	0.06
chr12_45227056_45227207	0.05	NELL2	NEL-like 2 (chicken)	42120	0.18
chr1_170562549_170562700	0.05	RP11-576I22.2		60836	0.12
chr17_37301012_37301163	0.05	PLXDC1	plexin domain containing 1	6815	0.14
chr1_162541630_162541823	0.05	UAP1	UDP-N-acteylglucosamine pyrophosphorylase 1	5899	0.17
chr17_73674018_73674169	0.05	RP11-474I11.8		1954	0.18
chr12_66548262_66548413	0.05	TMBIM4	transmembrane BAX inhibitor motif containing 4	14954	0.14
chr12_122592230_122592666	0.05	MLXIP	MLX interacting protein	19979	0.18
chr3_171812873_171813024	0.05	FNDC3B	fibronectin type III domain containing 3B	31816	0.22
chr16_53809610_53810340	0.05	FTO	fat mass and obesity associated	71881	0.11
chr12_123243849_123244000	0.05	DENR	density-regulated protein	6553	0.14
chr17_61857649_61857869	0.05	CCDC47	coiled-coil domain containing 47	4048	0.14
chr16_49686147_49686298	0.05	ZNF423	zinc finger protein 423	11459	0.24
chr7_140593399_140593550	0.05	ENSG00000271932	.	9602	0.22
chr3_30668319_30669005	0.05	TGFBR2	transforming growth factor, beta receptor II (70/80kDa)	20569	0.26
chr8_48648340_48648491	0.05	CEBPD	CCAAT/enhancer binding protein (C/EBP), delta	3233	0.24
chr1_198533037_198533238	0.05	ATP6V1G3	ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G3	23062	0.24
chr5_58187131_58187282	0.05	CTD-2176I21.2		27965	0.22
chr18_61442167_61442318	0.05	SERPINB7	serpin peptidase inhibitor, clade B (ovalbumin), member 7	402	0.88
chr14_72026196_72026347	0.05	SIPA1L1	signal-induced proliferation-associated 1 like 1	26727	0.25
chr5_176869820_176870094	0.05	PRR7-AS1	PRR7 antisense RNA 1	1521	0.22
chr3_73481941_73482092	0.05	PDZRN3	PDZ domain containing ring finger 3	1039	0.68
chr6_139492633_139492784	0.05	HECA	headcase homolog (Drosophila)	36459	0.17
chr12_110992885_110993169	0.05	PPTC7	PTC7 protein phosphatase homolog (S. cerevisiae)	28098	0.12
chr13_26636007_26636158	0.05	SHISA2	shisa family member 2	10913	0.27
chr6_106643256_106643407	0.05	ENSG00000244710	.	88255	0.07
chr11_116881940_116882091	0.05	ENSG00000264344	.	4230	0.2
chr3_28391593_28391746	0.05	ZCWPW2	zinc finger, CW type with PWWP domain 2	1029	0.41
chr2_25506534_25506685	0.05	DNMT3A	DNA (cytosine-5-)-methyltransferase 3 alpha	31429	0.17
chr11_121358351_121358610	0.05	RP11-730K11.1		34758	0.19
chr8_42052077_42052228	0.05	PLAT	plasminogen activator, tissue	907	0.54
chr13_99148708_99148963	0.05	STK24	serine/threonine kinase 24	22686	0.19
chr7_66397167_66397485	0.05	TMEM248	transmembrane protein 248	1715	0.35
chr7_28005907_28006058	0.05	JAZF1	JAZF zinc finger 1	25693	0.23
chr8_132857197_132857348	0.05	EFR3A	EFR3 homolog A (S. cerevisiae)	59063	0.16
chr5_70778847_70779136	0.05	BDP1	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	27549	0.21
chr14_55140117_55140268	0.05	SAMD4A	sterile alpha motif domain containing 4A	81359	0.1
chr12_67136436_67136587	0.05	GRIP1	glutamate receptor interacting protein 1	61249	0.16
chr10_116634856_116635150	0.05	FAM160B1	family with sequence similarity 160, member B1	14453	0.25
chr14_31663861_31664209	0.05	HECTD1	HECT domain containing E3 ubiquitin protein ligase 1	12654	0.17
chr7_139452923_139453350	0.05	HIPK2	homeodomain interacting protein kinase 2	24381	0.2
chr11_33769435_33769586	0.05	FBXO3	F-box protein 3	5435	0.16
chr5_39025357_39025508	0.05	RICTOR	RPTOR independent companion of MTOR, complex 2	49059	0.16
chr12_88728604_88728755	0.05	ENSG00000199245	.	95540	0.09
chr1_230784406_230784557	0.05	COG2	component of oligomeric golgi complex 2	5924	0.24
chr11_33295654_33295805	0.05	HIPK3	homeodomain interacting protein kinase 3	15852	0.21
chr4_169752514_169752665	0.05	PALLD	palladin, cytoskeletal associated protein	567	0.7
chr1_186271695_186271846	0.05	PRG4	proteoglycan 4	6359	0.19
chr8_24013639_24013790	0.05	ENSG00000207201	.	79043	0.11
chr8_48254486_48254637	0.05	SPIDR	scaffolding protein involved in DNA repair	81004	0.1
chrX_31284130_31284281	0.05	DMD	dystrophin	769	0.77
chr1_25771368_25771519	0.05	TMEM57	transmembrane protein 57	14032	0.15
chr7_7691133_7691284	0.05	RPA3	replication protein A3, 14kDa	10605	0.26
chr3_56501411_56501562	0.05	ERC2	ELKS/RAB6-interacting/CAST family member 2	905	0.72
chr5_179975750_179975903	0.05	CNOT6	CCR4-NOT transcription complex, subunit 6	19551	0.16
chrX_94314503_94314654	0.05	ENSG00000221187	.	3647	0.36
chr9_91151964_91152115	0.05	NXNL2	nucleoredoxin-like 2	2019	0.47
chr2_10121974_10122125	0.05	GRHL1	grainyhead-like 1 (Drosophila)	13385	0.16
chr15_39923761_39923912	0.05	FSIP1	fibrous sheath interacting protein 1	30709	0.17
chr2_230763302_230763453	0.05	ENSG00000222344	.	4315	0.18
chr9_21560365_21560626	0.04	MIR31HG	MIR31 host gene (non-protein coding)	827	0.62
chr1_92040002_92040153	0.04	CDC7	cell division cycle 7	73382	0.12
chr13_52390546_52391185	0.04	RP11-327P2.5		12432	0.19
chr8_107160982_107161133	0.04	ENSG00000251003	.	88305	0.1
chr2_38593562_38593713	0.04	ATL2	atlastin GTPase 2	9729	0.29
chr1_24022876_24023104	0.04	RPL11	ribosomal protein L11	3891	0.19
chr12_67355616_67355767	0.04	GRIP1	glutamate receptor interacting protein 1	157725	0.04
chr16_67538677_67538891	0.04	FAM65A	family with sequence similarity 65, member A	13537	0.09
chr18_73122194_73122345	0.04	RP11-321M21.3	HCG1996301; Uncharacterized protein	3302	0.31
chr6_157148026_157148177	0.04	RP11-230C9.3		46512	0.15
chr10_77879085_77879236	0.04	ENSG00000221232	.	7909	0.3
chr13_75018542_75018693	0.04	LINC00381	long intergenic non-protein coding RNA 381	25307	0.21
chr12_78412506_78412657	0.04	NAV3	neuron navigator 3	52525	0.17
chr2_26465301_26465452	0.04	HADHB	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), beta subunit	662	0.66
chr17_41739555_41740247	0.04	MEOX1	mesenchyme homeobox 1	579	0.74
chr10_89705727_89705964	0.04	ENSG00000200891	.	48607	0.13
chr1_113007964_113008322	0.04	WNT2B	wingless-type MMTV integration site family, member 2B	1020	0.58
chr17_60132149_60132300	0.04	MED13	mediator complex subunit 13	10419	0.17
chr17_77944274_77944425	0.04	TBC1D16	TBC1 domain family, member 16	18537	0.16
chr12_1875760_1875911	0.04	CACNA2D4	calcium channel, voltage-dependent, alpha 2/delta subunit 4	45051	0.13
chr13_25034322_25034473	0.04	TPTE2P6	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2 pseudogene 6	52102	0.12
chr9_137418567_137418718	0.04	COL5A1	collagen, type V, alpha 1	114978	0.05
chr5_98261626_98261777	0.04	CHD1	chromodomain helicase DNA binding protein 1	539	0.8
chr11_110167983_110168234	0.04	RDX	radixin	661	0.83
chr16_72281999_72282150	0.04	PMFBP1	polyamine modulated factor 1 binding protein 1	71297	0.1
chr2_118769373_118769761	0.04	CCDC93	coiled-coil domain containing 93	2142	0.23
chr17_70358516_70358667	0.04	SOX9	SRY (sex determining region Y)-box 9	241430	0.02
chr17_78762568_78762807	0.04	RP11-28G8.1		16745	0.23
chr14_89078082_89078377	0.04	ZC3H14	zinc finger CCCH-type containing 14	4601	0.21
chr16_21311524_21311721	0.04	CRYM	crystallin, mu	2750	0.29
chr13_27706090_27706241	0.04	USP12-AS1	USP12 antisense RNA 1	30827	0.15
chr13_114862694_114862923	0.04	RASA3-IT1	RASA3 intronic transcript 1 (non-protein coding)	11487	0.22
chr18_67232011_67232162	0.04	RP11-465I4.2		53844	0.17
chr21_43061018_43061225	0.04	ENSG00000252771	.	36278	0.17
chr1_225843948_225844099	0.04	ENAH	enabled homolog (Drosophila)	3179	0.27
chr19_11146514_11146699	0.04	SMARCA4	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	5117	0.16
chr1_31123601_31123752	0.04	MATN1-AS1	MATN1 antisense RNA 1	67675	0.1
chr11_95984153_95984304	0.04	ENSG00000266192	.	90374	0.08
chr14_90797503_90797880	0.04	NRDE2	NRDE-2, necessary for RNA interference, domain containing	588	0.77
chr8_714573_714724	0.04	ERICH1-AS1	ERICH1 antisense RNA 1	26906	0.18
chr2_87552860_87553169	0.04	IGKV3OR2-268	immunoglobulin kappa variable 3/OR2-268 (non-functional)	12620	0.29
chr5_51968673_51968824	0.04	ITGA1	integrin, alpha 1	114982	0.06
chr9_72878166_72878317	0.04	SMC5	structural maintenance of chromosomes 5	4304	0.21
chr8_98565933_98566084	0.04	MTDH	metadherin	90399	0.09
chr5_43554525_43554713	0.04	PAIP1	poly(A) binding protein interacting protein 1	1861	0.28
chr6_44598460_44598611	0.04	ENSG00000266619	.	195157	0.03
chr2_191513228_191513379	0.04	NAB1	NGFI-A binding protein 1 (EGR1 binding protein 1)	318	0.91
chr13_33199858_33200009	0.04	PDS5B	PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae)	39369	0.19
chr5_95534441_95534647	0.04	ENSG00000206997	.	11387	0.28
chr3_142754964_142755115	0.04	U2SURP	U2 snRNP-associated SURP domain containing	114	0.97
chr8_61446627_61446778	0.04	RAB2A	RAB2A, member RAS oncogene family	16962	0.2
chr1_107816447_107816598	0.04	NTNG1	netrin G1	125306	0.06
chr15_78715144_78715338	0.04	IREB2	iron-responsive element binding protein 2	14532	0.17
chr6_56598121_56598272	0.04	DST	dystonin	52481	0.16
chr8_94927918_94928069	0.04	ENSG00000264448	.	354	0.8
chr5_79447122_79447273	0.04	CTC-458I2.2		23013	0.19
chrX_72782730_72782881	0.04	CHIC1	cysteine-rich hydrophobic domain 1	231	0.96
chr12_127073806_127073957	0.04	ENSG00000239776	.	576791	0.0
chr3_153850737_153851019	0.04	ARHGEF26	Rho guanine nucleotide exchange factor (GEF) 26	11649	0.22

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:

Total log-likelihood	Term	Description
0.1	GO:0033152	immunoglobulin V(D)J recombination(GO:0033152)
0.0	GO:0051451	myoblast migration(GO:0051451)
0.0	GO:0046398	UDP-glucuronate metabolic process(GO:0046398)
0.0	GO:0060423	foregut regionalization(GO:0060423) lung field specification(GO:0060424) lung induction(GO:0060492)

Gene overrepresentation in molecular function category:

Log-likelihood per target	Total log-likelihood	Term	Description
0.0	0.1	GO:0051371	muscle alpha-actinin binding(GO:0051371)
0.0	0.0	GO:0002162	dystroglycan binding(GO:0002162)