Coexpression cluster:C4664

Full id: C4664_teratocarcinoma_iPS_HES3GFP_Neural_H9_Lens_hepatoblastoma

Phase1 CAGE Peaks

Hg19::chr7:148036524..148036538,+	p7@CNTNAP2
Hg19::chr7:148036546..148036559,+	p4@CNTNAP2
Hg19::chr7:148036562..148036609,+	p3@CNTNAP2

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>cell_data<br>uberon_data<br>disease_data<br>

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Cell Type

Ontology term	p-value	n
neuronal stem cell	2.06e-09	8
ectodermal cell	7.19e-09	72
neural cell	8.26e-09	25
germ line cell	1.55e-07	7
germ cell	1.55e-07	7
B cell	1.63e-07	14
neuron	3.05e-07	6
neuroblast	3.05e-07	6
electrically signaling cell	3.05e-07	6
endodermal cell	4.79e-07	58
embryonic stem cell	5.77e-07	5

Uber Anatomy

Ontology term	p-value	n
central nervous system	1.01e-33	81
nervous system	2.64e-32	89
organ system subdivision	2.42e-27	223
brain	4.86e-25	68
future brain	4.86e-25	68
neural tube	2.61e-24	56
neural rod	2.61e-24	56
future spinal cord	2.61e-24	56
neural keel	2.61e-24	56
regional part of nervous system	8.48e-23	53
regional part of brain	8.48e-23	53
neurectoderm	1.73e-22	86
neural plate	2.36e-21	82
presumptive neural plate	2.36e-21	82
ectoderm-derived structure	7.60e-21	171
ectoderm	7.60e-21	171
presumptive ectoderm	7.60e-21	171
regional part of forebrain	1.15e-19	41
forebrain	1.15e-19	41
anterior neural tube	1.15e-19	41
future forebrain	1.15e-19	41
pre-chordal neural plate	1.16e-19	61
ecto-epithelium	3.95e-19	104
anatomical cluster	1.35e-18	373
cerebral hemisphere	3.57e-17	32
brain grey matter	4.99e-17	34
gray matter	4.99e-17	34
telencephalon	7.66e-17	34
regional part of telencephalon	8.63e-16	32
cerebral cortex	6.65e-13	25
pallium	6.65e-13	25
adult organism	6.98e-13	114
regional part of cerebral cortex	8.18e-11	22
structure with developmental contribution from neural crest	6.22e-10	132
neocortex	1.45e-09	20
embryo	2.60e-08	592
tube	2.79e-08	192
multi-tissue structure	3.22e-08	342
anatomical conduit	6.78e-08	240

Disease

Ontology term	p-value	n
germ cell and embryonal cancer	2.03e-09	22
germ cell cancer	2.03e-09	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	3	62.7170003393281	4.049570681927e-06	0.000130494635127977
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0327607922248298
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0168438675699559
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.0039350043661482
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0157645593024849
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295999475619952
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00486795581484262
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247852294850519
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.0054561605186041
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00617223638770808
TRIM28#10155	3	18.5905250452625	0.000155596929725528	0.00198078836465192
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0331173567650769
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.00243744268704346

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.