Coexpression cluster:C3325

Full id: C3325_Mesenchymal_cerebellum_Cardiac_large_brain_vagina_pineal

Phase1 CAGE Peaks

Hg19::chr12:7036797..7036884,+	p@chr12:7036797..7036884 +
Hg19::chr12:7036941..7036986,+	p1@ATN1
Hg19::chr12:7036987..7037005,+	p2@ATN1

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	8.27e-33	115
neural tube	3.20e-30	57
neural rod	3.20e-30	57
future spinal cord	3.20e-30	57
neural keel	3.20e-30	57
organism subdivision	9.30e-30	365
anatomical conduit	1.78e-28	241
neurectoderm	3.32e-28	90
tube	5.64e-28	194
neural plate	5.83e-28	86
presumptive neural plate	5.83e-28	86
cell layer	8.32e-28	312
multi-tissue structure	9.15e-28	347
epithelium	1.62e-27	309
central nervous system	4.94e-27	82
anatomical cluster	5.88e-27	286
regional part of brain	1.88e-26	59
regional part of nervous system	5.16e-26	94
nervous system	5.16e-26	94
brain	5.53e-26	69
future brain	5.53e-26	69
ectoderm	1.75e-24	173
presumptive ectoderm	1.75e-24	173
ectoderm-derived structure	5.71e-24	169
head	4.23e-23	123
anterior neural tube	5.31e-22	42
regional part of forebrain	2.28e-21	41
forebrain	2.28e-21	41
future forebrain	2.28e-21	41
anterior region of body	3.74e-21	129
craniocervical region	3.74e-21	129
multi-cellular organism	1.30e-19	659
pre-chordal neural plate	1.62e-19	61
gray matter	6.14e-18	34
brain grey matter	6.14e-18	34
telencephalon	6.51e-18	34
regional part of telencephalon	2.53e-17	33
cerebral hemisphere	8.29e-17	32
embryo	9.77e-17	612
organ part	3.14e-16	219
anatomical system	2.55e-15	625
anatomical group	3.90e-15	626
embryonic structure	3.91e-15	605
developing anatomical structure	3.91e-15	605
germ layer	7.84e-15	604
embryonic tissue	7.84e-15	604
presumptive structure	7.84e-15	604
epiblast (generic)	7.84e-15	604
regional part of cerebral cortex	6.15e-14	22
cerebral cortex	1.46e-13	25
pallium	1.46e-13	25
neocortex	7.41e-13	20
organ	4.39e-10	511
posterior neural tube	2.55e-09	15
chordal neural plate	2.55e-09	15
compound organ	2.56e-08	69
segmental subdivision of nervous system	2.60e-08	13
trunk	4.38e-08	216
segmental subdivision of hindbrain	6.59e-08	12
hindbrain	6.59e-08	12
presumptive hindbrain	6.59e-08	12

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	3	62.7170003393281	4.049570681927e-06	0.000129179325732979
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0321032870802863
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0319539558172638
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0167081650363209
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156361228949682
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293593553956255
NANOG#79923	3	29.2447784810127	3.99627955670032e-05	0.000735449234576608
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0275827998837857
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00541388436395816
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0328361262781896
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109073695891196

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.