Coexpression cluster:C3819

Full id: C3819_testicular_Mast_hepatoblastoma_endometrial_cerebellum_cord_H9

Phase1 CAGE Peaks

Hg19::chr19:52408227..52408243,-	p2@ZNF649
Hg19::chr19:52408257..52408278,-	p1@ZNF649
Hg19::chr19:52408285..52408310,-	p3@ZNF649

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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No GOStat results

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><br>uberon_data<br><br>

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Uber Anatomy

Ontology term	p-value	n
adult organism	4.00e-33	114
central nervous system	8.92e-23	81
neural tube	9.71e-23	56
neural rod	9.71e-23	56
future spinal cord	9.71e-23	56
neural keel	9.71e-23	56
nervous system	3.36e-22	89
regional part of nervous system	3.16e-21	53
regional part of brain	3.16e-21	53
regional part of forebrain	4.12e-19	41
forebrain	4.12e-19	41
anterior neural tube	4.12e-19	41
future forebrain	4.12e-19	41
brain	8.91e-17	68
future brain	8.91e-17	68
brain grey matter	5.60e-16	34
gray matter	5.60e-16	34
telencephalon	6.56e-16	34
neurectoderm	6.46e-15	86
regional part of telencephalon	7.25e-15	32
neural plate	1.10e-14	82
presumptive neural plate	1.10e-14	82
cerebral hemisphere	1.13e-14	32
ecto-epithelium	2.43e-12	104
pre-chordal neural plate	9.82e-12	61
cerebral cortex	4.57e-11	25
pallium	4.57e-11	25
regional part of cerebral cortex	7.12e-11	22
ectoderm-derived structure	7.81e-10	171
ectoderm	7.81e-10	171
presumptive ectoderm	7.81e-10	171
neocortex	9.95e-10	20
organ system subdivision	1.64e-07	223

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
BCL3#602	3	34.5471028037383	2.42397750207122e-05	0.000526972910780217
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0279432610998819
CTCFL#140690	3	19.7464743589744	0.000129837200555116	0.0017173337625096
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00437280474162149
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0322221279123257
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0320647675233486
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0462278428525438
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.0076232894211796
NR3C1#2908	3	14.973023331173	0.000297833119467548	0.00309014436360732
REST#5978	3	9.65002871612802	0.00111263624711459	0.0076752058792867
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0276764969603463
SIRT6#51548	3	153.638403990025	2.75057764221434e-07	1.3978957585169e-05
SIX5#147912	3	17.086715355459	0.000200406054632501	0.00239722917647048
SP2#6668	3	26.1535304938446	5.58768218891694e-05	0.000940486607781299
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00542987189938173
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00613779006919833
TRIM28#10155	3	18.5905250452625	0.000155596929725528	0.00197046050001265
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0329391800651266
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.00242734354041181
ZNF143#7702	3	13.5008765522279	0.000406280496299717	0.00389065915579003

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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This analysis result is provided for C0 - C305 clusters.