Coexpression cluster:C2314

Full id: C2314_salivary_pituitary_cerebellum_breast_small_occipital_brain

Phase1 CAGE Peaks

Hg19::chr14:77648077..77648103,+	p3@TMEM63C
Hg19::chr14:77648123..77648162,+	p1@TMEM63C
Hg19::chr14:77648167..77648183,+	p2@TMEM63C
Hg19::chr14:77648188..77648205,+	p4@TMEM63C

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
neural tube	2.57e-36	56
neural rod	2.57e-36	56
future spinal cord	2.57e-36	56
neural keel	2.57e-36	56
regional part of nervous system	1.35e-34	53
regional part of brain	1.35e-34	53
central nervous system	1.90e-34	81
brain	3.01e-33	68
future brain	3.01e-33	68
nervous system	4.88e-33	89
regional part of forebrain	5.01e-31	41
forebrain	5.01e-31	41
anterior neural tube	5.01e-31	41
future forebrain	5.01e-31	41
neural plate	4.83e-27	82
presumptive neural plate	4.83e-27	82
telencephalon	1.55e-25	34
brain grey matter	1.88e-25	34
gray matter	1.88e-25	34
neurectoderm	2.05e-25	86
pre-chordal neural plate	2.89e-25	61
ecto-epithelium	8.64e-25	104
cerebral hemisphere	2.16e-24	32
regional part of telencephalon	4.67e-24	32
ectoderm-derived structure	1.53e-22	171
ectoderm	1.53e-22	171
presumptive ectoderm	1.53e-22	171
adult organism	7.99e-22	114
organ system subdivision	9.50e-21	223
regional part of cerebral cortex	5.28e-20	22
cerebral cortex	3.87e-19	25
pallium	3.87e-19	25
neocortex	5.48e-19	20
structure with developmental contribution from neural crest	2.13e-13	132
organ part	2.06e-09	218
basal ganglion	8.61e-08	9
nuclear complex of neuraxis	8.61e-08	9
aggregate regional part of brain	8.61e-08	9
collection of basal ganglia	8.61e-08	9
cerebral subcortex	8.61e-08	9
neural nucleus	9.60e-08	9
nucleus of brain	9.60e-08	9
organ	1.86e-07	503
temporal lobe	4.71e-07	6
embryo	5.90e-07	592
posterior neural tube	6.25e-07	15
chordal neural plate	6.25e-07	15
diencephalon	7.03e-07	7
future diencephalon	7.03e-07	7
anatomical cluster	9.03e-07	373

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
E2F1#1869	4	4.90738921487932	0.00172402235736179	0.0106365294766368
EBF1#1879	4	8.906466846569	0.0001588790747201	0.00199461133365699
MYC#4609	4	5.2222818716094	0.00134430939527274	0.00886632958212121
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.00795220673347809
SP1#6667	4	5.6983813781409	0.000948260606533398	0.00683474047520646
STAT1#6772	4	20.7065874971992	5.43610708103893e-06	0.000165041159138554
SUZ12#23512	4	50.1157809110629	1.5827390373096e-07	8.79253629348818e-06
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0321677299305749
TRIM28#10155	4	18.5905250452625	8.36730015875654e-06	0.000229905935617042
YY1#7528	4	4.91117074985386	0.0017187183805544	0.0106693550253638
ZEB1#6935	4	16.8884320175439	1.22862303393937e-05	0.000303850724701857
ZNF263#10127	4	8.22184163701068	0.000218787118095832	0.00248314581904049

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.