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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 Prdm4

Z-value: 0.37

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Transcription factors associated with Prdm4

Gene Symbol	Gene ID	Gene Info
Prdm4 Ensembl NCBI MGI UniProt	ENSMUSG00000035529.9	Prdm4

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
Prdm4	chr10_85917236_85917429	190	0.906396	0.26	4.6e-02	Click!
Prdm4	chr10_85914196_85914347	2385	0.182928	0.11	4.0e-01	Click!
Prdm4	chr10_85915840_85916954	259	0.864648	-0.01	9.5e-01	Click!

Activity of the Prdm4 motif across conditions

Conditions sorted by the z-value of the Prdm4 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
chr15_41710667_41710890	0.87	Oxr1	oxidation resistance 1	174	0.97
chr11_63712018_63712440	0.86	Gm12288	predicted gene 12288	106071	0.07
chr11_76353568_76353719	0.72	Nxn	nucleoredoxin	45425	0.12
chr17_24473380_24473531	0.66	Bricd5	BRICHOS domain containing 5	429	0.59
chr7_120173917_120175138	0.64	Anks4b	ankyrin repeat and sterile alpha motif domain containing 4B	669	0.61
chr14_119908730_119908881	0.64	4930404K13Rik	RIKEN cDNA 4930404K13 gene	109827	0.06
chr2_74680662_74681213	0.58	Hoxd11	homeobox D11	1380	0.15
chr2_154568646_154569144	0.57	E2f1	E2F transcription factor 1	825	0.45
chr12_73476375_73476773	0.54	Gm48656	predicted gene, 48656	19667	0.14
chr3_106545478_106545703	0.51	Cept1	choline/ethanolaminephosphotransferase 1	1992	0.2
chr12_80111226_80112041	0.48	Zfp36l1	zinc finger protein 36, C3H type-like 1	1361	0.31
chr11_83849571_83850989	0.45	Hnf1b	HNF1 homeobox B	217	0.83
chr11_32383101_32383252	0.44	Sh3pxd2b	SH3 and PX domains 2B	35336	0.13
chr5_103428210_103428361	0.42	Ptpn13	protein tyrosine phosphatase, non-receptor type 13	2784	0.29
chr10_87420108_87420324	0.41	Gm23191	predicted gene, 23191	56070	0.12
chr8_121085538_121086180	0.40	Gm27530	predicted gene, 27530	1153	0.3
chr4_98108504_98108946	0.38	Gm12691	predicted gene 12691	37874	0.2
chr6_87993752_87994823	0.35	4933412L11Rik	RIKEN cDNA 4933412L11 gene	108	0.92
chr15_73148296_73148447	0.35	Ago2	argonaute RISC catalytic subunit 2	29476	0.16
chr7_142662290_142664788	0.34	Igf2os	insulin-like growth factor 2, opposite strand	1599	0.21
chr2_172368075_172368471	0.32	Aurka	aurora kinase A	2233	0.19
chr17_43671571_43671722	0.28	Cyp39a1	cytochrome P450, family 39, subfamily a, polypeptide 1	4121	0.18
chr11_98922257_98922979	0.28	Cdc6	cell division cycle 6	2152	0.18
chr3_81039797_81040176	0.27	Gm16000	predicted gene 16000	451	0.78
chr13_63241575_63242090	0.26	Aopep	aminopeptidase O	1724	0.2
chr6_28425695_28425934	0.26	Gcc1	golgi coiled coil 1	1661	0.21
chr8_84200619_84201949	0.26	Gm37352	predicted gene, 37352	415	0.58
chr1_172310298_172310642	0.26	Igsf8	immunoglobulin superfamily, member 8	1301	0.28
chr15_89185418_89185569	0.25	Mir6958	microRNA 6958	44	0.94
chr2_105132016_105133665	0.24	Wt1	Wilms tumor 1 homolog	1957	0.31
chr11_96872293_96874152	0.23	Gm11523	predicted gene 11523	712	0.46
chr17_53482249_53482404	0.22	Rab5a	RAB5A, member RAS oncogene family	3039	0.19
chr8_45913620_45913830	0.22	Pdlim3	PDZ and LIM domain 3	1307	0.32
chr2_32539078_32539941	0.22	Fam102a	family with sequence similarity 102, member A	681	0.5
chr13_35473350_35473501	0.21	Gm48704	predicted gene, 48704	70477	0.1
chr3_129201144_129201586	0.21	Pitx2	paired-like homeodomain transcription factor 2	1396	0.39
chr19_60146143_60147364	0.20	E330013P04Rik	RIKEN cDNA E330013P04 gene	2049	0.34
chr3_89526596_89526945	0.20	Kcnn3	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	6606	0.16
chr11_94939289_94939965	0.20	Col1a1	collagen, type I, alpha 1	615	0.61
chr10_79945094_79946752	0.19	Arid3a	AT rich interactive domain 3A (BRIGHT-like)	356	0.66
chr14_73049116_73049339	0.19	Cysltr2	cysteinyl leukotriene receptor 2	113	0.97
chr11_99435806_99436036	0.18	Krt20	keratin 20	2229	0.16
chr15_103058659_103059955	0.18	5730585A16Rik	RIKEN cDNA 5730585A16 gene	1	0.95
chr10_93309488_93311306	0.18	Elk3	ELK3, member of ETS oncogene family	414	0.82
chr7_45174584_45175709	0.17	Mir7055	microRNA 7055	1843	0.1
chr15_79040318_79041315	0.17	Galr3	galanin receptor 3	1069	0.25
chr3_99261050_99262399	0.17	Gm43120	predicted gene 43120	439	0.81
chr3_95011750_95011901	0.16	Zfp687	zinc finger protein 687	18	0.94
chr1_180943258_180943409	0.16	Tmem63a	transmembrane protein 63a	702	0.5
chr11_95516491_95516808	0.16	Nxph3	neurexophilin 3	2079	0.28
chr19_7153054_7153338	0.16	Otub1	OTU domain, ubiquitin aldehyde binding 1	47268	0.08
chr17_28348327_28348971	0.16	Tead3	TEA domain family member 3	1697	0.21
chrX_64747210_64747361	0.15	Gm14676	predicted gene 14676	3973	0.31
chr5_144965930_144966401	0.15	Smurf1	SMAD specific E3 ubiquitin protein ligase 1	318	0.86
chr17_25415111_25416091	0.15	Cacna1h	calcium channel, voltage-dependent, T type, alpha 1H subunit	17677	0.1
chr3_55517135_55518024	0.14	Gm42608	predicted gene 42608	10	0.97
chr8_110503112_110503371	0.13	Gm47306	predicted gene, 47306	4256	0.24
chr19_55253303_55254683	0.13	Acsl5	acyl-CoA synthetase long-chain family member 5	624	0.71
chr18_14063182_14063853	0.12	Zfp521	zinc finger protein 521	90730	0.09
chr13_63258769_63259476	0.12	Gm47603	predicted gene, 47603	3558	0.11
chr8_36745950_36746830	0.12	Dlc1	deleted in liver cancer 1	13336	0.28
chr13_55182504_55182904	0.11	Fgfr4	fibroblast growth factor receptor 4	26587	0.11
chr14_72600187_72600734	0.11	Fndc3a	fibronectin type III domain containing 3A	2502	0.3
chr1_72873610_72874834	0.11	Igfbp5	insulin-like growth factor binding protein 5	53	0.98
chr12_26454705_26455291	0.10	Rsad2	radical S-adenosyl methionine domain containing 2	156	0.94
chr13_48977850_48978331	0.10	Fam120a	family with sequence similarity 120, member A	10073	0.24
chr8_121396512_121396947	0.10	Gm26747	predicted gene, 26747	24509	0.15
chr3_105914133_105914707	0.10	Tmigd3	transmembrane and immunoglobulin domain containing 3	284	0.84
chr5_17584554_17584705	0.09	Sema3c	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	9730	0.28
chr17_43025342_43025543	0.09	Tnfrsf21	tumor necrosis factor receptor superfamily, member 21	8874	0.29
chr18_42053706_42054633	0.09	Sh3rf2	SH3 domain containing ring finger 2	459	0.84
chr7_19563781_19564198	0.08	Ppp1r37	protein phosphatase 1, regulatory subunit 37	913	0.36
chr12_81816545_81817321	0.08	Gm47080	predicted gene, 47080	10866	0.17
chr10_81280318_81280649	0.08	Tjp3	tight junction protein 3	366	0.64
chr17_56461082_56462187	0.08	Ptprs	protein tyrosine phosphatase, receptor type, S	527	0.73
chr13_3891572_3893506	0.08	Net1	neuroepithelial cell transforming gene 1	894	0.46
chr18_12120723_12121070	0.08	Tmem241	transmembrane protein 241	572	0.72
chr1_66700897_66701735	0.08	Rpe	ribulose-5-phosphate-3-epimerase	409	0.78
chr17_80825543_80826587	0.08	C230072F16Rik	RIKEN cDNA C230072F16 gene	70728	0.1
chr17_68000612_68000868	0.07	Arhgap28	Rho GTPase activating protein 28	3380	0.35
chr7_30584453_30584699	0.07	Kmt2b	lysine (K)-specific methyltransferase 2B	498	0.48
chr17_32319078_32319484	0.07	Akap8	A kinase (PRKA) anchor protein 8	477	0.71
chr1_161070981_161071821	0.07	Cenpl	centromere protein L	385	0.54
chr4_139829324_139829858	0.07	Pax7	paired box 7	3416	0.28
chr9_40325276_40326082	0.06	1700110K17Rik	RIKEN cDNA 1700110K17 gene	2253	0.19
chr3_149093055_149093671	0.06	Gm25127	predicted gene, 25127	64431	0.11
chr7_24904441_24905054	0.06	Arhgef1	Rho guanine nucleotide exchange factor (GEF) 1	307	0.78
chr2_69612307_69612590	0.06	Lrp2	low density lipoprotein receptor-related protein 2	26383	0.15
chr3_129881133_129881711	0.06	Pla2g12a	phospholipase A2, group XIIA	238	0.9
chr7_89903398_89904159	0.06	Ccdc81	coiled-coil domain containing 81	149	0.95
chr4_62406680_62406837	0.06	Cdc26	cell division cycle 26	1244	0.31
chr13_21996613_21997784	0.06	Prss16	protease, serine 16 (thymus)	8024	0.06
chr11_70012013_70013226	0.06	Acadvl	acyl-Coenzyme A dehydrogenase, very long chain	45	0.86
chr12_91683421_91686419	0.06	Gm16876	predicted gene, 16876	255	0.86
chr17_33557999_33558350	0.06	Myo1f	myosin IF	2409	0.22
chr11_25288195_25288807	0.06	Gm12069	predicted gene 12069	12762	0.23
chr16_85132591_85133705	0.05	Gm49226	predicted gene, 49226	15681	0.18
chr15_102971199_102971716	0.05	Mir196a-2	microRNA 196a-2	1893	0.15
chr17_34646272_34646494	0.05	Atf6b	activating transcription factor 6 beta	763	0.3
chr4_11703848_11705053	0.05	Gem	GTP binding protein (gene overexpressed in skeletal muscle)	7	0.98
chr14_99303099_99303560	0.05	Klf5	Kruppel-like factor 5	4175	0.19
chr12_80113642_80114602	0.05	Zfp36l1	zinc finger protein 36, C3H type-like 1	1109	0.34
chr11_74900076_74900873	0.05	Tsr1	TSR1 20S rRNA accumulation	1239	0.27
chr2_102900531_102901984	0.04	Cd44	CD44 antigen	89	0.97
chr11_70525408_70526199	0.04	Psmb6	proteasome (prosome, macropain) subunit, beta type 6	307	0.72
chr12_51377639_51378186	0.04	Scfd1	Sec1 family domain containing 1	320	0.91
chr5_122146089_122146622	0.04	Ccdc63	coiled-coil domain containing 63	5532	0.14
chr8_88523833_88524755	0.04	Nkd1	naked cuticle 1	2940	0.29
chrX_48053949_48055179	0.04	Apln	apelin	19711	0.2
chr17_45279982_45280133	0.04	Gm24979	predicted gene, 24979	70091	0.1
chrX_64781879_64782030	0.04	Gm26111	predicted gene, 26111	18557	0.21
chr19_43618352_43618699	0.04	Gm22646	predicted gene, 22646	3921	0.13
chr14_27044544_27045365	0.04	Il17rd	interleukin 17 receptor D	5698	0.22
chr6_145855324_145856436	0.03	Gm43909	predicted gene, 43909	7417	0.17
chr19_3718944_3720017	0.03	Gm36787	predicted gene, 36787	93	0.93
chr6_135785665_135785816	0.03	Gm22892	predicted gene, 22892	44743	0.15
chr16_13903228_13903614	0.03	Mpv17l	Mpv17 transgene, kidney disease mutant-like	260	0.51
chr11_87853248_87853905	0.03	Mks1	Meckel syndrome, type 1	89	0.94
chr11_18750877_18751932	0.03	Gm28401	predicted gene 28401	5334	0.19
chr12_110447124_110447282	0.03	Ppp2r5c	protein phosphatase 2, regulatory subunit B', gamma	49	0.97
chr10_128547971_128549076	0.03	Rpl41	ribosomal protein L41	579	0.36
chr18_25715120_25715657	0.03	0710001A04Rik	RIKEN cDNA 0710001A04 gene	1618	0.46
chr19_43729441_43730557	0.03	Entpd7	ectonucleoside triphosphate diphosphohydrolase 7	3632	0.16
chr4_127025301_127025452	0.02	Sfpq	splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)	548	0.64
chr9_14717687_14717910	0.02	Piwil4	piwi-like RNA-mediated gene silencing 4	675	0.51
chr5_128703817_128704666	0.02	Piwil1	piwi-like RNA-mediated gene silencing 1	1717	0.34
chr10_85102050_85102712	0.02	Fhl4	four and a half LIM domains 4	114	0.68
chr17_57249307_57250786	0.02	Trip10	thyroid hormone receptor interactor 10	498	0.63
chr3_116807540_116808184	0.02	Agl	amylo-1,6-glucosidase, 4-alpha-glucanotransferase	11	0.96
chr11_75291131_75291523	0.02	Gm47300	predicted gene, 47300	27281	0.12
chr14_45332844_45332995	0.02	Psmc6	proteasome (prosome, macropain) 26S subunit, ATPase, 6	1488	0.29
chr2_80315446_80316199	0.02	Dnajc10	DnaJ heat shock protein family (Hsp40) member C10	356	0.89
chr19_5057787_5057938	0.02	Rin1	Ras and Rab interactor 1	4757	0.07
chr2_39004499_39005146	0.01	Rpl35	ribosomal protein L35	221	0.72
chr3_55347442_55348146	0.01	Dclk1	doublecortin-like kinase 1	6340	0.18
chr16_87454687_87455921	0.01	Usp16	ubiquitin specific peptidase 16	246	0.89
chr2_92374659_92375167	0.01	Large2	LARGE xylosyl- and glucuronyltransferase 2	44	0.74
chr3_9605900_9606819	0.01	Zfp704	zinc finger protein 704	3726	0.28
chr7_135539645_135539955	0.01	Ptpre	protein tyrosine phosphatase, receptor type, E	1961	0.3
chr4_41506381_41507061	0.01	1110017D15Rik	RIKEN cDNA 1110017D15 gene	1033	0.35
chr5_113858981_113859268	0.01	Coro1c	coronin, actin binding protein 1C	350	0.71
chr9_65169040_65169256	0.01	Igdcc3	immunoglobulin superfamily, DCC subclass, member 3	11590	0.13
chr18_61637854_61638670	0.01	Bvht	braveheart long non-coding RNA	1280	0.31
chrX_95163813_95164963	0.00	Arhgef9	CDC42 guanine nucleotide exchange factor (GEF) 9	1437	0.48
chr14_16597821_16598428	0.00	Rarb	retinoic acid receptor, beta	22297	0.21
chr7_127009057_127009208	0.00	Mvp	major vault protein	2733	0.08
chr3_89451824_89451975	0.00	Pmvk	phosphomevalonate kinase	2642	0.13
chrX_109094919_109095373	0.00	Sh3bgrl	SH3-binding domain glutamic acid-rich protein like	219	0.94
chr17_23630249_23630847	0.00	Gm49935	predicted gene, 49935	6048	0.07
chr14_66911778_66912249	0.00	Pnma2	paraneoplastic antigen MA2	771	0.58
chr14_34373115_34373266	0.00	Sncg	synuclein, gamma	1599	0.23
chr6_141249439_141250607	0.00	Gm28523	predicted gene 28523	14	0.53
chr8_57317473_57317624	0.00	Hand2os1	Hand2, opposite strand 1	1276	0.34

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 Prdm4

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View png image

Gene Ontology Analysis

Gene overrepresentation in biological process category:

Log-likelihood per target	Total log-likelihood	Term	Description
0.1	0.8	GO:0071447	cellular response to hydroperoxide(GO:0071447)
0.1	0.4	GO:1900211	mesenchymal cell apoptotic process involved in metanephros development(GO:1900200) regulation of mesenchymal cell apoptotic process involved in metanephros development(GO:1900211) negative regulation of mesenchymal cell apoptotic process involved in metanephros development(GO:1900212)
0.1	0.3	GO:0071930	negative regulation of transcription involved in G1/S transition of mitotic cell cycle(GO:0071930)
0.1	0.4	GO:1904970	brush border assembly(GO:1904970)
0.0	0.1	GO:0034165	positive regulation of toll-like receptor 9 signaling pathway(GO:0034165)
0.0	0.1	GO:1902534	single-organism membrane invagination(GO:1902534)
0.0	0.1	GO:0048371	lateral mesoderm morphogenesis(GO:0048369) lateral mesoderm formation(GO:0048370) lateral mesodermal cell differentiation(GO:0048371)
0.0	0.1	GO:0002074	extraocular skeletal muscle development(GO:0002074) deltoid tuberosity development(GO:0035993) left lung morphogenesis(GO:0060460)
0.0	0.1	GO:0014734	skeletal muscle hypertrophy(GO:0014734)
0.0	0.1	GO:0001957	intramembranous ossification(GO:0001957) direct ossification(GO:0036072)
0.0	0.2	GO:0060710	chorio-allantoic fusion(GO:0060710)
0.0	0.1	GO:0038028	insulin receptor signaling pathway via phosphatidylinositol 3-kinase(GO:0038028)
0.0	0.1	GO:0045039	protein import into mitochondrial inner membrane(GO:0045039)
0.0	0.1	GO:0035279	mRNA cleavage involved in gene silencing by miRNA(GO:0035279) mRNA cleavage involved in gene silencing(GO:0098795)
0.0	0.1	GO:0060282	positive regulation of oocyte development(GO:0060282)
0.0	0.1	GO:0010746	regulation of plasma membrane long-chain fatty acid transport(GO:0010746)
0.0	0.0	GO:1900623	positive regulation of neutrophil apoptotic process(GO:0033031) regulation of monocyte aggregation(GO:1900623) positive regulation of monocyte aggregation(GO:1900625)
0.0	0.0	GO:1902564	negative regulation of neutrophil activation(GO:1902564)
0.0	0.0	GO:2000286	receptor internalization involved in canonical Wnt signaling pathway(GO:2000286)
0.0	0.0	GO:0032696	negative regulation of interleukin-13 production(GO:0032696)
0.0	0.0	GO:0051562	negative regulation of mitochondrial calcium ion concentration(GO:0051562)
0.0	0.1	GO:0009052	pentose-phosphate shunt, non-oxidative branch(GO:0009052)
0.0	0.0	GO:0050883	medulla oblongata development(GO:0021550) musculoskeletal movement, spinal reflex action(GO:0050883)
0.0	0.2	GO:0035335	peptidyl-tyrosine dephosphorylation(GO:0035335)

Gene overrepresentation in cellular component category:

Log-likelihood per target	Total log-likelihood	Term	Description
0.1	0.3	GO:0035189	Rb-E2F complex(GO:0035189)
0.0	0.1	GO:0036454	insulin-like growth factor binding protein complex(GO:0016942) growth factor complex(GO:0036454) insulin-like growth factor ternary complex(GO:0042567)
0.0	0.1	GO:0042585	germinal vesicle(GO:0042585)
0.0	0.0	GO:0010009	cytoplasmic side of endosome membrane(GO:0010009)
0.0	0.1	GO:0005583	fibrillar collagen trimer(GO:0005583) banded collagen fibril(GO:0098643)

Gene overrepresentation in molecular function category:

Total log-likelihood	Term	Description
0.1	GO:0032422	purine-rich negative regulatory element binding(GO:0032422)
0.2	GO:0004974	leukotriene receptor activity(GO:0004974)
0.1	GO:0030943	mitochondrion targeting sequence binding(GO:0030943)
0.1	GO:0017169	CDP-alcohol phosphatidyltransferase activity(GO:0017169)
0.1	GO:0004791	thioredoxin-disulfide reductase activity(GO:0004791)
0.1	GO:0000340	RNA 7-methylguanosine cap binding(GO:0000340)
0.1	GO:0031995	insulin-like growth factor II binding(GO:0031995)
0.1	GO:0070411	I-SMAD binding(GO:0070411)
0.1	GO:0102391	decanoate--CoA ligase activity(GO:0102391)
0.1	GO:0036312	phosphatidylinositol 3-kinase regulatory subunit binding(GO:0036312)
0.0	GO:0004966	galanin receptor activity(GO:0004966)
0.1	GO:0048407	platelet-derived growth factor binding(GO:0048407)

Gene overrepresentation in curated gene sets: canonical pathways category:

Log-likelihood per target	Total log-likelihood	Term	Description
0.0	0.3	SA REG CASCADE OF CYCLIN EXPR	Expression of cyclins regulates progression through the cell cycle by activating cyclin-dependent kinases.

Gene overrepresentation in curated gene sets: REACTOME pathways category:

Total log-likelihood	Term	Description
0.3	REACTOME CDC6 ASSOCIATION WITH THE ORC ORIGIN COMPLEX	Genes involved in CDC6 association with the ORC:origin complex
0.2	REACTOME EICOSANOID LIGAND BINDING RECEPTORS	Genes involved in Eicosanoid ligand-binding receptors
0.4	REACTOME REGULATION OF BETA CELL DEVELOPMENT	Genes involved in Regulation of beta-cell development
0.2	REACTOME REGULATION OF INSULIN LIKE GROWTH FACTOR IGF ACTIVITY BY INSULIN LIKE GROWTH FACTOR BINDING PROTEINS IGFBPS	Genes involved in Regulation of Insulin-like Growth Factor (IGF) Activity by Insulin-like Growth Factor Binding Proteins (IGFBPs)
0.1	REACTOME SYNTHESIS OF PE	Genes involved in Synthesis of PE
0.1	REACTOME PLATELET ADHESION TO EXPOSED COLLAGEN	Genes involved in Platelet Adhesion to exposed collagen