Coexpression cluster:C135

Full id: C135_neuroblastoma_retinoblastoma_carcinoid_choriocarcinoma_testicular_acute_rectum

Phase1 CAGE Peaks

Hg19::chr10:135139802..135139811,-	p9@CALY
Hg19::chr11:71952706..71952712,-	p4@PHOX2A
Hg19::chr11:71952721..71952728,-	p6@PHOX2A
Hg19::chr11:71952772..71952788,-	p@chr11:71952772..71952788 -
Hg19::chr11:71955210..71955227,-	p1@PHOX2A
Hg19::chr11:72070206..72070217,-	p@chr11:72070206..72070217 -
Hg19::chr11:8285219..8285232,-	p8@LMO1
Hg19::chr14:36003132..36003155,-	p@chr14:36003132..36003155 -
Hg19::chr14:36003180..36003191,-	p@chr14:36003180..36003191 -
Hg19::chr14:36003234..36003238,-	p@chr14:36003234..36003238 -
Hg19::chr14:36003363..36003378,+	p1@INSM2
Hg19::chr14:36003405..36003408,+	p3@INSM2
Hg19::chr14:89307203..89307210,+	p5@TTC8
Hg19::chr14:89307222..89307227,+	p7@TTC8
Hg19::chr14:89307231..89307234,+	p8@TTC8
Hg19::chr14:89307240..89307249,+	p4@TTC8
Hg19::chr14:89319304..89319352,+	p@chr14:89319304..89319352 +
Hg19::chr16:55689872..55689912,+	p1@SLC6A2
Hg19::chr17:61509320..61509322,-	p@chr17:61509320..61509322 -
Hg19::chr19:30719524..30719534,+	p@chr19:30719524..30719534 +
Hg19::chr1:109255524..109255546,+	p1@FNDC7
Hg19::chr1:99470368..99470446,-	p1@LPPR5
Hg19::chr20:21086993..21087007,-	p1@LINC00237
Hg19::chr22:45405796..45405814,-	p3@PHF21B
Hg19::chr2:137522983..137523027,+	p4@THSD7B
Hg19::chr2:16080165..16080175,+	p15@MYCN
Hg19::chr2:16080325..16080331,+	p17@MYCN
Hg19::chr2:16080357..16080363,+	p18@MYCN
Hg19::chr2:16080460..16080495,-	p@chr2:16080460..16080495 -
Hg19::chr2:16080635..16080650,+	p4@MYCN
Hg19::chr2:16080659..16080685,+	p1@MYCN
Hg19::chr2:16080823..16080836,+	p5@MYCN
Hg19::chr2:16081024..16081034,+	p10@MYCN
Hg19::chr2:16081392..16081406,-	p3@MYCNOS
Hg19::chr2:16081716..16081740,-	p2@MYCNOS
Hg19::chr2:16081744..16081768,-	p5@MYCNOS
Hg19::chr2:16081783..16081817,-	p1@MYCNOS
Hg19::chr2:16081912..16081931,+	p2@MYCN
Hg19::chr2:16082094..16082106,+	p7@MYCN
Hg19::chr2:16082155..16082169,+	p3@MYCN
Hg19::chr2:16082384..16082391,+	p9@MYCN
Hg19::chr2:16082395..16082415,+	p6@MYCN
Hg19::chr2:16082418..16082429,+	p8@MYCN
Hg19::chr2:16082486..16082491,+	p13@MYCN
Hg19::chr2:16082851..16082860,+	p@chr2:16082851..16082860 +
Hg19::chr2:16082878..16082890,+	p@chr2:16082878..16082890 +
Hg19::chr2:16082902..16082908,+	p@chr2:16082902..16082908 +
Hg19::chr2:16082933..16082942,+	p@chr2:16082933..16082942 +
Hg19::chr2:16083539..16083543,+	p@chr2:16083539..16083543 +
Hg19::chr2:16085596..16085604,+	p@chr2:16085596..16085604 +
Hg19::chr2:16085699..16085709,+	p@chr2:16085699..16085709 +
Hg19::chr2:16085756..16085766,+	p@chr2:16085756..16085766 +
Hg19::chr2:16085836..16085841,-	p@chr2:16085836..16085841 -
Hg19::chr2:16085862..16085895,-	p@chr2:16085862..16085895 -
Hg19::chr2:16085916..16085937,-	p@chr2:16085916..16085937 -
Hg19::chr2:16122765..16122769,-	p@chr2:16122765..16122769 -
Hg19::chr2:16361177..16361195,-	p@chr2:16361177..16361195 -
Hg19::chr2:16383015..16383029,-	p@chr2:16383015..16383029 -
Hg19::chr2:16405283..16405330,+	p1@ENST00000420404
Hg19::chr2:16504184..16504211,+	p@chr2:16504184..16504211 +
Hg19::chr2:173724826..173724840,+	p15@RAPGEF4
Hg19::chr2:173724864..173724875,+	p11@RAPGEF4
Hg19::chr2:173724876..173724893,+	p16@RAPGEF4
Hg19::chr2:192364133..192364143,+	p@chr2:192364133..192364143 +
Hg19::chr2:30099704..30099722,-	p@chr2:30099704..30099722 -
Hg19::chr2:30099741..30099749,-	p@chr2:30099741..30099749 -
Hg19::chr2:74726898..74726903,+	p@chr2:74726898..74726903 +
Hg19::chr2:74735271..74735288,-	p10@PCGF1
Hg19::chr2:74735290..74735299,-	p11@PCGF1
Hg19::chr2:74735317..74735338,-	p5@PCGF1
Hg19::chr2:74740569..74740580,+	p4@TLX2
Hg19::chr2:74741569..74741620,+	p1@TLX2
Hg19::chr2:74743961..74743965,+	p@chr2:74743961..74743965 +
Hg19::chr4:113869733..113869760,+	p@chr4:113869733..113869760 +
Hg19::chr4:113870230..113870237,+	p@chr4:113870230..113870237 +
Hg19::chr4:151509442..151509449,-	p@chr4:151509442..151509449 -
Hg19::chr4:151509505..151509510,-	p@chr4:151509505..151509510 -
Hg19::chr4:151509549..151509560,-	p@chr4:151509549..151509560 -
Hg19::chr4:151509603..151509613,-	p@chr4:151509603..151509613 -
Hg19::chr4:151509614..151509615,-	p@chr4:151509614..151509615 -
Hg19::chr4:151509622..151509629,-	p@chr4:151509622..151509629 -
Hg19::chr4:174427862..174427899,+	p@chr4:174427862..174427899 +
Hg19::chr4:174429225..174429237,+	p@chr4:174429225..174429237 +
Hg19::chr4:174429255..174429289,+	p@chr4:174429255..174429289 +
Hg19::chr4:174429652..174429665,+	p@chr4:174429652..174429665 +
Hg19::chr4:174440390..174440400,-	p@chr4:174440390..174440400 -
Hg19::chr4:174440405..174440414,-	p@chr4:174440405..174440414 -
Hg19::chr4:174930472..174930480,-	p@chr4:174930472..174930480 -
Hg19::chr4:174930493..174930503,-	p@chr4:174930493..174930503 -
Hg19::chr4:174930547..174930558,-	p@chr4:174930547..174930558 -
Hg19::chr4:175028534..175028537,-	p@chr4:175028534..175028537 -
Hg19::chr4:175041663..175041727,-	p1@ENST00000503140
Hg19::chr4:21699314..21699327,-	p7@KCNIP4
Hg19::chr4:21699348..21699355,-	p25@KCNIP4
Hg19::chr4:21699357..21699368,-	p18@KCNIP4
Hg19::chr4:21699380..21699386,-	p20@KCNIP4
Hg19::chr4:41859832..41859854,+	p@chr4:41859832..41859854 +
Hg19::chr4:41875797..41875802,-	p@chr4:41875797..41875802 -
Hg19::chr4:41884582..41884593,-	p1@ENST00000499082
Hg19::chr4:41884620..41884663,-	p1@ENST00000504870
Hg19::chr4:48485220..48485230,+	p10@SLC10A4
Hg19::chr4:48485239..48485249,+	p9@SLC10A4
Hg19::chr4:48485341..48485394,+	p1@SLC10A4
Hg19::chr4:48485400..48485411,+	p3@SLC10A4
Hg19::chr4:48485413..48485423,+	p5@SLC10A4
Hg19::chr4:48485436..48485441,+	p12@SLC10A4
Hg19::chr4:48485486..48485499,+	p2@SLC10A4
Hg19::chr4:95983128..95983134,+	p@chr4:95983128..95983134 +
Hg19::chr5:168271822..168271868,-	p5@SLIT3
Hg19::chr5:168271880..168271889,-	p15@SLIT3
Hg19::chr5:50761081..50761087,-	p@chr5:50761081..50761087 -
Hg19::chr5:51202170..51202198,+	p@chr5:51202170..51202198 +
Hg19::chr6:154360476..154360504,+	p2@OPRM1
Hg19::chr6:154360522..154360525,+	p14@OPRM1
Hg19::chr6:154360530..154360549,+	p3@OPRM1
Hg19::chr6:154360553..154360567,+	p4@OPRM1
Hg19::chr7:133694696..133694724,+	p16@EXOC4
Hg19::chr7:19185493..19185503,-	p2@FERD3L
Hg19::chr7:73919759..73919766,-	p@chr7:73919759..73919766 -
Hg19::chr7:73919790..73919798,-	p@chr7:73919790..73919798 -
Hg19::chr7:73919799..73919805,-	p@chr7:73919799..73919805 -
Hg19::chr7:8276508..8276551,-	p14@ICA1
Hg19::chr7:8276855..8276873,+	p@chr7:8276855..8276873 +
Hg19::chr7:8301962..8301966,-	p17@ICA1
Hg19::chr7:8301975..8301984,-	p11@ICA1
Hg19::chr7:8301994..8301997,-	p19@ICA1
Hg19::chr7:8302002..8302015,-	p10@ICA1
Hg19::chr7:8302097..8302104,-	p15@ICA1
Hg19::chr7:8302126..8302136,-	p12@ICA1
Hg19::chr7:8302298..8302323,-	p9@ICA1
Hg19::chr8:13373093..13373105,-	p55@DLC1
Hg19::chr8:142878006..142878015,+	p@chr8:142878006..142878015 +
Hg19::chr8:73164078..73164082,-	p6@LOC392232
Hg19::chr9:136501478..136501491,+	p1@DBH
Hg19::chr9:137605204..137605213,+	p@chr9:137605204..137605213 +

Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

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No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

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GO ID	GO name	FDR corrected p-value
GO:0032989	cellular structure morphogenesis	0.012351859015746
GO:0000902	cell morphogenesis	0.012351859015746
GO:0032501	multicellular organismal process	0.012351859015746
GO:0030141	secretory granule	0.012351859015746
GO:0032990	cell part morphogenesis	0.012351859015746
GO:0048858	cell projection morphogenesis	0.012351859015746
GO:0030030	cell projection organization and biogenesis	0.012351859015746
GO:0005333	norepinephrine transmembrane transporter activity	0.0185446838572942
GO:0005334	norephinephrine:sodium symporter activity	0.0185446838572942
GO:0042583	chromaffin granule	0.0185446838572942
GO:0015874	norepinephrine transport	0.0185446838572942
GO:0007268	synaptic transmission	0.0200921373067378
GO:0050877	neurological system process	0.0226023037666984
GO:0019226	transmission of nerve impulse	0.0233722017898953
GO:0006836	neurotransmitter transport	0.0233722017898953
GO:0009914	hormone transport	0.023991938083013
GO:0050774	negative regulation of dendrite morphogenesis	0.023991938083013
GO:0015370	solute:sodium symporter activity	0.0247353766381847
GO:0048814	regulation of dendrite morphogenesis	0.0291244924816904
GO:0004988	mu-opioid receptor activity	0.0291244924816904
GO:0030672	synaptic vesicle membrane	0.0291244924816904
GO:0003008	system process	0.0293082164144434
GO:0006887	exocytosis	0.0293082164144434
GO:0015294	solute:cation symporter activity	0.0293082164144434
GO:0050773	regulation of dendrite development	0.0293082164144434
GO:0048813	dendrite morphogenesis	0.0293082164144434
GO:0048667	neuron morphogenesis during differentiation	0.0293082164144434
GO:0048812	neurite morphogenesis	0.0293082164144434
GO:0000904	cellular morphogenesis during differentiation	0.0311410238356019
GO:0032502	developmental process	0.0313272232327204
GO:0048265	response to pain	0.0313272232327204
GO:0008504	monoamine transmembrane transporter activity	0.0313272232327204
GO:0031175	neurite development	0.0313272232327204
GO:0009653	anatomical structure morphogenesis	0.0342713320105026
GO:0015844	monoamine transport	0.0349185433074233
GO:0048666	neuron development	0.0371398780115165
GO:0030667	secretory granule membrane	0.0385248908208417
GO:0008508	bile acid:sodium symporter activity	0.0417582874367942
GO:0004500	dopamine beta-monooxygenase activity	0.0417582874367942
GO:0042423	catecholamine biosynthetic process	0.0496224120078445
GO:0015125	bile acid transmembrane transporter activity	0.0496224120078445

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>

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Cell Type

Ontology term	p-value	n
neural cell	2.02e-07	25

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	1.08e-33	94
nervous system	1.08e-33	94
central nervous system	1.64e-31	82
adult organism	7.62e-29	115
neural tube	2.69e-27	57
neural rod	2.69e-27	57
future spinal cord	2.69e-27	57
neural keel	2.69e-27	57
brain	2.43e-24	69
future brain	2.43e-24	69
regional part of brain	7.85e-23	59
regional part of forebrain	1.38e-21	41
forebrain	1.38e-21	41
future forebrain	1.38e-21	41
neurectoderm	3.26e-21	90
anterior neural tube	4.16e-21	42
neural plate	2.13e-20	86
presumptive neural plate	2.13e-20	86
gray matter	1.00e-18	34
brain grey matter	1.00e-18	34
telencephalon	2.33e-18	34
regional part of telencephalon	6.87e-18	33
cerebral hemisphere	1.41e-17	32
ectoderm	1.74e-17	173
presumptive ectoderm	1.74e-17	173
ectoderm-derived structure	1.11e-16	169
pre-chordal neural plate	6.28e-15	61
cerebral cortex	3.00e-14	25
pallium	3.00e-14	25
regional part of cerebral cortex	3.36e-13	22
neocortex	3.37e-12	20
head	1.96e-10	123
anterior region of body	2.35e-10	129
craniocervical region	2.35e-10	129
tube	1.38e-08	194
posterior neural tube	2.27e-07	15
chordal neural plate	2.27e-07	15
anatomical conduit	4.75e-07	241

Disease

Ontology term	p-value	n
germ cell and embryonal cancer	9.65e-08	22
germ cell cancer	9.65e-08	22

Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

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Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
{{{tfbs_overrepresentation_jaspar}}}

ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
CTBP2#1488	8	3.7165629830713	0.00153685565965633	0.00976977711600508
EP300#2033	42	2.10744853704722	1.16633482712618e-06	4.76009546737908e-05
GATA2#2624	40	3.77627606920118	1.00033832709499e-13	1.56868370185396e-11
RAD21#5885	23	1.76419095996663	0.00519328683404514	0.0240694809470507
REST#5978	29	2.07296913161269	0.000113285334354298	0.00155165993896767

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

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