Project

ENCODE: H3K4me3 ChIP-Seq of different mouse tissues during embryonic development

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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 Hoxb4

Z-value: 0.29

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Transcription factors associated with Hoxb4

Gene Symbol	Gene ID	Gene Info
Hoxb4 Ensembl NCBI MGI UniProt	ENSMUSG00000038692.7	Hoxb4

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
Hoxb4	chr11_96318060_96319501	513	0.505895	0.06	6.5e-01	Click!
Hoxb4	chr11_96319562_96320434	1731	0.139807	-0.01	9.2e-01	Click!

Activity of the Hoxb4 motif across conditions

Conditions sorted by the z-value of the Hoxb4 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
chr1_168426195_168428871	0.29	Pbx1	pre B cell leukemia homeobox 1	3971	0.3
chr11_117454277_117454520	0.27	Gm34418	predicted gene, 34418	28199	0.11
chr3_35332632_35333522	0.26	Gm25442	predicted gene, 25442	7463	0.26
chr1_190017944_190018756	0.26	Smyd2	SET and MYND domain containing 2	95987	0.07
chr10_102513522_102514467	0.25	Rassf9	Ras association (RalGDS/AF-6) domain family (N-terminal) member 9	1738	0.36
chr11_117600891_117601042	0.22	2900041M22Rik	RIKEN cDNA 2900041M22 gene	10281	0.19
chr5_35466165_35466783	0.21	Cpz	carboxypeptidase Z	59097	0.08
chr11_24740194_24740345	0.19	Gm10466	predicted gene 10466	9547	0.27
chr2_140668225_140669392	0.19	Flrt3	fibronectin leucine rich transmembrane protein 3	2592	0.43
chr3_30009457_30010152	0.19	Mecom	MDS1 and EVI1 complex locus	1635	0.36
chr1_72038129_72038714	0.18	4930556G22Rik	RIKEN cDNA 4930556G22 gene	310	0.88
chr11_96367227_96367378	0.18	Hoxb1	homeobox B1	1044	0.31
chr2_172934875_172936042	0.17	Bmp7	bone morphogenetic protein 7	4634	0.21
chr9_57803673_57803954	0.17	Arid3b	AT rich interactive domain 3B (BRIGHT-like)	7592	0.16
chr18_4137682_4137958	0.16	Lyzl1	lysozyme-like 1	28012	0.19
chr17_43360343_43362046	0.16	Adgrf5	adhesion G protein-coupled receptor F5	743	0.75
chr17_84082064_84082337	0.16	4933433H22Rik	RIKEN cDNA 4933433H22 gene	3540	0.19
chr13_15468099_15468909	0.16	Gli3	GLI-Kruppel family member GLI3	4524	0.2
chr11_85917986_85918561	0.16	Tbx4	T-box 4	21508	0.16
chr4_13242090_13242241	0.16	Gm26250	predicted gene, 26250	24885	0.26
chr1_38545635_38545840	0.15	Gm34727	predicted gene, 34727	58218	0.13
chr7_136342313_136342682	0.15	C230079O03Rik	RIKEN cDNA C230079O03 gene	6918	0.21
chr18_81091160_81091406	0.15	Gm50423	predicted gene, 50423	8219	0.2
chr3_37906898_37907049	0.15	Gm20755	predicted gene, 20755	8160	0.18
chr4_106977384_106977540	0.15	Ssbp3	single-stranded DNA binding protein 3	11036	0.19
chr7_27375253_27375939	0.14	Gm20479	predicted gene 20479	18177	0.1
chr2_76029030_76030067	0.13	Pde11a	phosphodiesterase 11A	23505	0.18
chr11_57616045_57616196	0.13	Galnt10	polypeptide N-acetylgalactosaminyltransferase 10	29322	0.13
chr13_23571443_23572971	0.13	H2bc8	H2B clustered histone 8	811	0.19
chr11_49246951_49247357	0.13	Mgat1	mannoside acetylglucosaminyltransferase 1	323	0.83
chr11_83877738_83877889	0.13	Hnf1b	HNF1 homeobox B	24853	0.13
chr17_24959159_24959310	0.12	Jpt2	Jupiter microtubule associated homolog 2	1402	0.28
chr10_60933986_60934521	0.12	Gm26947	predicted gene, 26947	2262	0.22
chr1_172218328_172218648	0.12	Casq1	calsequestrin 1	1227	0.28
chr10_77164464_77164999	0.12	Col18a1	collagen, type XVIII, alpha 1	1817	0.35
chr5_111893894_111894510	0.12	Gm42488	predicted gene 42488	50033	0.15
chr2_58000565_58000896	0.12	Galnt5	polypeptide N-acetylgalactosaminyltransferase 5	2846	0.28
chr3_109574671_109575218	0.12	Vav3	vav 3 oncogene	1037	0.69
chr17_47143536_47144571	0.11	Trerf1	transcriptional regulating factor 1	2837	0.31
chr2_72146177_72146373	0.11	Rapgef4os1	Rap guanine nucleotide exchange factor (GEF) 4, opposite strand 1	2521	0.29
chr16_21392882_21393033	0.11	Vps8	VPS8 CORVET complex subunit	30161	0.18
chr16_94714721_94714872	0.11	Gm41504	predicted gene, 41504	893	0.59
chr9_60518348_60518989	0.11	Thsd4	thrombospondin, type I, domain containing 4	3378	0.18
chr5_45534202_45534749	0.11	Fam184b	family with sequence similarity 184, member B	2067	0.2
chr16_72665443_72666078	0.11	Robo1	roundabout guidance receptor 1	2556	0.45
chr2_132562790_132562941	0.11	Gpcpd1	glycerophosphocholine phosphodiesterase 1	15268	0.16
chr17_32318505_32319028	0.11	Akap8	A kinase (PRKA) anchor protein 8	38	0.96
chr2_173789994_173790513	0.11	Vapb	vesicle-associated membrane protein, associated protein B and C	22053	0.16
chr7_98721638_98721789	0.10	Gm19656	predicted gene, 19656	7047	0.13
chr2_9906124_9906915	0.10	Gm13262	predicted gene 13262	341	0.81
chr4_9831058_9831848	0.10	Gdf6	growth differentiation factor 6	12919	0.23
chr10_122887302_122887925	0.10	Ppm1h	protein phosphatase 1H (PP2C domain containing)	7755	0.23
chr2_160537495_160537646	0.10	Gm14222	predicted gene 14222	45787	0.15
chr12_36826817_36826968	0.10	Mir5099	microRNA 5099	10687	0.24
chr2_106822583_106822852	0.10	Gm22813	predicted gene, 22813	13381	0.23
chr7_30908216_30909253	0.10	Mag	myelin-associated glycoprotein	5574	0.07
chr9_60562470_60563218	0.10	Gm17853	predicted gene, 17853	14649	0.13
chr11_108336593_108336967	0.10	Apoh	apolipoprotein H	6574	0.19
chr5_149353036_149353786	0.10	BC028471	cDNA sequence BC028471	14225	0.11
chr2_49272499_49272844	0.10	Mbd5	methyl-CpG binding domain protein 5	487	0.83
chr5_93097700_93097987	0.10	Septin11	septin 11	4272	0.14
chr6_107013042_107013673	0.10	Gm22418	predicted gene, 22418	11905	0.28
chr9_41272710_41272970	0.09	Gm48710	predicted gene, 48710	43958	0.11
chr7_89423254_89423405	0.09	AI314278	expressed sequence AI314278	2977	0.2
chr19_17489963_17490448	0.09	Rfk	riboflavin kinase	92768	0.08
chr18_54983558_54984280	0.09	Zfp608	zinc finger protein 608	6247	0.21
chr2_90892674_90892825	0.09	Gm32514	predicted gene, 32514	449	0.68
chr11_88313718_88313869	0.09	Ccdc182	coiled-coil domain containing 182	19735	0.14
chr1_12695048_12695280	0.09	Sulf1	sulfatase 1	2632	0.26
chr9_15308839_15309818	0.09	Taf1d	TATA-box binding protein associated factor, RNA polymerase I, D	572	0.37
chr14_79530531_79530770	0.09	Elf1	E74-like factor 1	14952	0.15
chr5_97935061_97936082	0.09	Antxr2	anthrax toxin receptor 2	60524	0.11
chr14_27044544_27045365	0.09	Il17rd	interleukin 17 receptor D	5698	0.22
chr10_8213906_8214393	0.09	Gm30906	predicted gene, 30906	38018	0.2
chr9_110676440_110676899	0.09	Gm35715	predicted gene, 35715	1715	0.22
chr2_157974620_157975884	0.09	Tti1	TELO2 interacting protein 1	31960	0.14
chr1_88668363_88668968	0.09	Gm29336	predicted gene 29336	12357	0.16
chr6_37645617_37646179	0.09	Ybx1-ps2	Y box protein 1, pseudogene 2	41297	0.18
chr5_128684296_128685182	0.09	Piwil1	piwi-like RNA-mediated gene silencing 1	17785	0.17
chr4_14103504_14103655	0.08	Gm24068	predicted gene, 24068	23639	0.22
chr2_74696421_74697223	0.08	Gm28793	predicted gene 28793	764	0.23
chr11_120710545_120710942	0.08	Cenpx	centromere protein X	1240	0.16
chr5_113279864_113280669	0.08	Sgsm1	small G protein signaling modulator 1	321	0.85
chr5_146282063_146282214	0.08	Cdk8	cyclin-dependent kinase 8	4038	0.19
chr1_118776754_118776905	0.08	Gm28467	predicted gene 28467	33307	0.18
chr2_139608706_139609326	0.08	Gm27385	predicted gene, 27385	20789	0.22
chr11_120228562_120229205	0.08	2900052L18Rik	RIKEN cDNA 2900052L18 gene	2702	0.14
chr4_32952734_32952939	0.08	Ankrd6	ankyrin repeat domain 6	1995	0.26
chr1_51697218_51698004	0.08	Gm28055	predicted gene 28055	289	0.93
chr5_101323183_101323902	0.08	Cycs-ps2	cytochrome c, pseudogene 2	17964	0.27
chr7_135526475_135527168	0.08	Clrn3	clarin 3	1833	0.31
chr19_16168628_16168779	0.08	E030024N20Rik	RIKEN cDNA E030024N20 gene	3898	0.26
chr14_22168600_22169219	0.08	Gm7480	predicted gene 7480	132806	0.04
chr2_38914989_38915140	0.08	Nr6a1	nuclear receptor subfamily 6, group A, member 1	11153	0.11
chr3_18241670_18242257	0.08	Cyp7b1	cytochrome P450, family 7, subfamily b, polypeptide 1	1375	0.5
chr5_144098470_144098725	0.08	Lmtk2	lemur tyrosine kinase 2	1839	0.26
chr10_22813360_22814229	0.08	Gm10824	predicted gene 10824	1955	0.28
chr15_27998794_27999022	0.07	Trio	triple functional domain (PTPRF interacting)	3545	0.28
chr3_30514092_30514862	0.07	Mecom	MDS1 and EVI1 complex locus	4655	0.16
chr13_78194785_78195954	0.07	Nr2f1	nuclear receptor subfamily 2, group F, member 1	1004	0.42
chr5_148820568_148820913	0.07	Gm15407	predicted gene 15407	27	0.97
chr18_15060481_15060964	0.07	Kctd1	potassium channel tetramerisation domain containing 1	1167	0.55
chr5_66503946_66504664	0.07	Apbb2	amyloid beta (A4) precursor protein-binding, family B, member 2	10525	0.15
chr18_60646141_60646566	0.07	Synpo	synaptopodin	1919	0.32
chr19_14777221_14777986	0.07	Gm26026	predicted gene, 26026	59123	0.15
chr16_38458401_38458552	0.07	Cd80	CD80 antigen	457	0.72
chr1_79823877_79824635	0.07	Serpine2	serine (or cysteine) peptidase inhibitor, clade E, member 2	2934	0.26
chr11_96863722_96864075	0.07	Gm11524	predicted gene 11524	6297	0.09
chr2_152753689_152753840	0.07	Cox4i2	cytochrome c oxidase subunit 4I2	409	0.74
chr10_45470864_45471317	0.07	Lin28b	lin-28 homolog B (C. elegans)	889	0.65
chr10_78752230_78753214	0.07	Ccdc105	coiled-coil domain containing 105	343	0.81
chr11_63917212_63917744	0.07	Hs3st3b1	heparan sulfate (glucosamine) 3-O-sulfotransferase 3B1	4812	0.25
chr7_66449827_66450975	0.07	Gm44753	predicted gene 44753	8515	0.17
chr13_63276050_63276513	0.07	Aopep	aminopeptidase O	2389	0.12
chr3_107943213_107944057	0.07	Gstm6	glutathione S-transferase, mu 6	80	0.92
chr8_11311242_11311393	0.07	Col4a1	collagen, type IV, alpha 1	1372	0.31
chr11_5972524_5972675	0.07	Camk2b	calcium/calmodulin-dependent protein kinase II, beta	11539	0.13
chr2_170070487_170071222	0.06	Zfp217	zinc finger protein 217	60366	0.14
chr10_41292796_41293533	0.06	Fig4	FIG4 phosphoinositide 5-phosphatase	10096	0.16
chr1_167374494_167374876	0.06	Aldh9a1	aldehyde dehydrogenase 9, subfamily A1	10519	0.13
chr12_95547341_95547492	0.06	Gm22246	predicted gene, 22246	72402	0.11
chr2_91529031_91529182	0.06	Ckap5	cytoskeleton associated protein 5	2128	0.25
chr10_51554019_51554385	0.06	Gm48787	predicted gene, 48787	2755	0.15
chr8_23413505_23413993	0.06	Sfrp1	secreted frizzled-related protein 1	2247	0.39
chr4_149605840_149605991	0.06	Clstn1	calsyntenin 1	18667	0.12
chr16_94180124_94180691	0.06	Hlcs	holocarboxylase synthetase (biotin- [propriony-Coenzyme A-carboxylase (ATP-hydrolysing)] ligase)	5407	0.13
chr2_174283563_174287177	0.06	Gnas	GNAS (guanine nucleotide binding protein, alpha stimulating) complex locus	12	0.53
chr11_76672356_76673645	0.06	Bhlha9	basic helix-loop-helix family, member a9	530	0.76
chr11_96876203_96877056	0.06	Gm11523	predicted gene 11523	2675	0.13
chrX_141726225_141726376	0.06	Irs4	insulin receptor substrate 4	1037	0.41
chr8_27162795_27163172	0.06	Gm45267	predicted gene 45267	3155	0.13
chr5_136051364_136052209	0.06	Upk3bl	uroplakin 3B-like	2706	0.15
chr11_70404123_70404274	0.06	Pelp1	proline, glutamic acid and leucine rich protein 1	5830	0.09
chr14_52306804_52306955	0.06	Mettl3	methyltransferase like 3	1751	0.18
chr8_125361611_125361762	0.06	Sipa1l2	signal-induced proliferation-associated 1 like 2	131024	0.05
chr17_48039617_48039969	0.06	1700122O11Rik	RIKEN cDNA 1700122O11 gene	1500	0.3
chr15_50883181_50884101	0.06	Trps1	transcriptional repressor GATA binding 1	835	0.64
chrX_133689241_133690268	0.06	Pcdh19	protocadherin 19	767	0.77
chr3_95517184_95517335	0.06	Ctss	cathepsin S	9527	0.1
chr17_47989917_47990574	0.06	Gm14871	predicted gene 14871	13327	0.14
chr19_28580015_28580320	0.06	4933413C19Rik	RIKEN cDNA 4933413C19 gene	3127	0.3
chr18_3666230_3667225	0.06	Gm50091	predicted gene, 50091	50446	0.14
chr17_43758947_43759124	0.06	Cyp39a1	cytochrome P450, family 39, subfamily a, polypeptide 1	27092	0.17
chr1_91762985_91763136	0.06	Twist2	twist basic helix-loop-helix transcription factor 2	38401	0.14
chr8_124990881_124991137	0.06	Tsnax	translin-associated factor X	21988	0.13
chr12_59039859_59040384	0.06	Gm22973	predicted gene, 22973	214	0.89
chr18_55258362_55259199	0.06	Gm22597	predicted gene, 22597	78940	0.09
chr6_91712146_91712297	0.06	Gm44981	predicted gene 44981	1057	0.39
chr14_21988628_21988808	0.06	Zfp503	zinc finger protein 503	883	0.5
chr18_74966819_74967388	0.06	Lipg	lipase, endothelial	5840	0.1
chr2_162967542_162967693	0.06	Gm11453	predicted gene 11453	15644	0.11
chr18_50046880_50047192	0.06	Tnfaip8	tumor necrosis factor, alpha-induced protein 8	296	0.91
chr9_56842487_56842638	0.06	Odf3l1	outer dense fiber of sperm tails 3-like 1	9401	0.14
chr12_107960709_107960860	0.06	Bcl11b	B cell leukemia/lymphoma 11B	42630	0.19
chr9_98538219_98538951	0.06	4930579K19Rik	RIKEN cDNA 4930579K19 gene	25007	0.11
chr5_75975002_75975424	0.06	Kdr	kinase insert domain protein receptor	3245	0.23
chr8_26384770_26384921	0.06	Gm31898	predicted gene, 31898	50868	0.1
chr11_18872620_18872876	0.06	8430419K02Rik	RIKEN cDNA 8430419K02 gene	593	0.71
chr3_51357869_51359319	0.06	Gm37203	predicted gene, 37203	11628	0.1
chr14_118322252_118323294	0.06	Gm32093	predicted gene, 32093	204	0.92
chr10_125839451_125839817	0.06	Lrig3	leucine-rich repeats and immunoglobulin-like domains 3	126534	0.06
chr18_55106919_55107352	0.06	AC163347.1	novel transcript	10775	0.17
chr4_116688529_116688680	0.06	Prdx1	peroxiredoxin 1	1292	0.29
chr5_33534271_33535601	0.06	Fam53a	family with sequence similarity 53, member A	93976	0.05
chr15_36779468_36779639	0.06	Ywhaz	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide	12861	0.15
chr4_66414553_66415137	0.06	Astn2	astrotactin 2	10234	0.28
chr14_63255547_63256547	0.06	Gata4	GATA binding protein 4	10776	0.17
chr17_29080873_29081286	0.06	Trp53cor1	tumor protein p53 pathway corepressor 1	1900	0.17
chr17_29397536_29397687	0.06	Fgd2	FYVE, RhoGEF and PH domain containing 2	21110	0.11
chr5_92811720_92812319	0.06	Shroom3	shroom family member 3	2549	0.29
chr1_183144103_183144344	0.06	Disp1	dispatched RND transporter family member 1	3238	0.28
chr3_118548450_118548601	0.06	Gm32444	predicted gene, 32444	11504	0.15
chr1_41131507_41131710	0.05	4930448I06Rik	RIKEN cDNA 4930448I06 gene	49644	0.19
chr11_35972396_35972620	0.05	Wwc1	WW, C2 and coiled-coil domain containing 1	8019	0.23
chr1_87175864_87176092	0.05	Prss56	protease, serine 56	7335	0.1
chr4_148890637_148891853	0.05	Casz1	castor zinc finger 1	1864	0.33
chr3_41522196_41522994	0.05	2400006E01Rik	RIKEN cDNA 2400006E01 gene	622	0.65
chr6_117886217_117886368	0.05	Gm29509	predicted gene 29509	12909	0.11
chr10_116276295_116276851	0.05	Ptprb	protein tyrosine phosphatase, receptor type, B	1023	0.54
chr2_165494605_165494756	0.05	Trp53rka	transformation related protein 53 regulating kinase A	1356	0.36
chr8_26308366_26308822	0.05	Gm31784	predicted gene, 31784	3740	0.18
chr9_54769552_54770224	0.05	Crabp1	cellular retinoic acid binding protein I	5140	0.18
chr3_41284805_41285284	0.05	Gm16508	predicted gene 16508	5546	0.25
chr1_106602971_106603597	0.05	Gm37053	predicted gene, 37053	3586	0.27
chr6_51002449_51002688	0.05	Gm44402	predicted gene, 44402	35300	0.18
chr11_69549158_69549411	0.05	Dnah2	dynein, axonemal, heavy chain 2	174	0.88
chr5_104109155_104109917	0.05	Gm26703	predicted gene, 26703	245	0.88
chr9_60279898_60280278	0.05	2010001M07Rik	RIKEN cDNA 2010001M07 gene	54054	0.14
chr10_100050584_100050771	0.05	Kitl	kit ligand	34761	0.14
chr17_91954712_91954863	0.05	Gm41654	predicted gene, 41654	82648	0.09
chr10_45808506_45808657	0.05	D030045P18Rik	RIKEN cDNA D030045P18 gene	877	0.63
chr9_106397846_106397997	0.05	Dusp7	dual specificity phosphatase 7	23302	0.09
chr11_97047163_97047404	0.05	Osbpl7	oxysterol binding protein-like 7	3345	0.09
chrX_7422152_7422543	0.05	2010204K13Rik	RIKEN cDNA 2010204K13 gene	641	0.67
chr19_56631461_56631906	0.05	Gm32441	predicted gene, 32441	32928	0.14
chr2_95232237_95232956	0.05	Gm13794	predicted gene 13794	161646	0.04
chr8_26808819_26808970	0.05	2310008N11Rik	RIKEN cDNA 2310008N11 gene	15529	0.17
chr12_27566196_27567004	0.05	Gm4166	predicted gene 4166	31601	0.22
chr1_89848531_89848837	0.05	Gm37521	predicted gene, 37521	23203	0.19
chr4_42183593_42183996	0.05	1700045I11Rik	RIKEN cDNA 1700045I11 gene	12949	0.08

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 Hoxb4

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View png image

Gene Ontology Analysis

Gene overrepresentation in biological process category:

Total log-likelihood	Term	Description
0.1	GO:0060399	positive regulation of growth hormone receptor signaling pathway(GO:0060399)
0.1	GO:0036118	hyaluranon cable assembly(GO:0036118) regulation of hyaluranon cable assembly(GO:1900104) positive regulation of hyaluranon cable assembly(GO:1900106)
0.1	GO:0043031	negative regulation of macrophage activation(GO:0043031)
0.1	GO:0021570	rhombomere 4 development(GO:0021570)
0.0	GO:0048369	lateral mesoderm morphogenesis(GO:0048369) lateral mesoderm formation(GO:0048370) lateral mesodermal cell differentiation(GO:0048371)
0.0	GO:0021827	cerebral cortex tangential migration using cell-cell interactions(GO:0021823) postnatal olfactory bulb interneuron migration(GO:0021827)
0.0	GO:2000828	regulation of parathyroid hormone secretion(GO:2000828)
0.1	GO:0090336	positive regulation of brown fat cell differentiation(GO:0090336)
0.0	GO:0035860	glial cell-derived neurotrophic factor receptor signaling pathway(GO:0035860)
0.1	GO:0003344	pericardium morphogenesis(GO:0003344)
0.0	GO:0021776	smoothened signaling pathway involved in ventral spinal cord interneuron specification(GO:0021775) smoothened signaling pathway involved in spinal cord motor neuron cell fate specification(GO:0021776)
0.0	GO:0036166	phenotypic switching(GO:0036166)
0.1	GO:0048251	elastic fiber assembly(GO:0048251)

Gene overrepresentation in cellular component category:

Log-likelihood per target	Total log-likelihood	Term	Description
0.0	0.1	GO:0001939	female pronucleus(GO:0001939)

Gene overrepresentation in molecular function category:

Log-likelihood per target	Total log-likelihood	Term	Description
0.0	0.0	GO:0008449	N-acetylglucosamine-6-sulfatase activity(GO:0008449)
0.0	0.0	GO:0005176	ErbB-2 class receptor binding(GO:0005176)
0.0	0.0	GO:0046976	histone methyltransferase activity (H3-K27 specific)(GO:0046976)
0.0	0.0	GO:0001075	transcription factor activity, RNA polymerase II core promoter sequence-specific binding involved in preinitiation complex assembly(GO:0001075)