Coexpression cluster:C4166

Full id: C4166_neuroectodermal_Neural_small_Neurons_occipital_parietal_duodenum

Phase1 CAGE Peaks

Hg19::chr2:197791393..197791421,-	p3@PGAP1
Hg19::chr2:197791423..197791438,-	p2@PGAP1
Hg19::chr2:197791602..197791620,-	p5@PGAP1

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><br>

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Cell Type

Ontology term	p-value	n
neural cell	9.69e-07	25

Uber Anatomy

Ontology term	p-value	n
nervous system	3.01e-30	89
central nervous system	8.12e-30	81
ectoderm-derived structure	2.81e-25	171
ectoderm	2.81e-25	171
presumptive ectoderm	2.81e-25	171
brain	1.83e-24	68
future brain	1.83e-24	68
neural tube	3.68e-23	56
neural rod	3.68e-23	56
future spinal cord	3.68e-23	56
neural keel	3.68e-23	56
regional part of nervous system	2.83e-22	53
regional part of brain	2.83e-22	53
neurectoderm	2.95e-19	86
regional part of forebrain	3.98e-19	41
forebrain	3.98e-19	41
anterior neural tube	3.98e-19	41
future forebrain	3.98e-19	41
organ system subdivision	1.71e-18	223
neural plate	1.28e-17	82
presumptive neural plate	1.28e-17	82
ecto-epithelium	2.95e-17	104
brain grey matter	5.07e-16	34
gray matter	5.07e-16	34
telencephalon	5.72e-16	34
cerebral hemisphere	2.90e-15	32
regional part of telencephalon	5.00e-15	32
pre-chordal neural plate	9.51e-14	61
anatomical cluster	1.78e-13	373
structure with developmental contribution from neural crest	4.67e-13	132
cerebral cortex	7.33e-13	25
pallium	7.33e-13	25
regional part of cerebral cortex	3.42e-11	22
neocortex	4.53e-10	20
multi-cellular organism	1.10e-09	656
anatomical group	9.04e-09	625
anatomical system	1.21e-08	624
embryo	2.41e-08	592
embryonic structure	3.19e-08	564
anatomical conduit	3.93e-08	240
germ layer	5.92e-08	560
germ layer / neural crest	5.92e-08	560
embryonic tissue	5.92e-08	560
presumptive structure	5.92e-08	560
germ layer / neural crest derived structure	5.92e-08	560
epiblast (generic)	5.92e-08	560
adult organism	8.06e-08	114
tube	1.79e-07	192
epithelium	4.15e-07	306
developing anatomical structure	4.83e-07	581
cell layer	6.12e-07	309
organ	6.30e-07	503

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
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.0066148125181924
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0326217088260608
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0463418722706596
HDAC2#3066	3	13.4156202366263	0.000414076139985721	0.00392108967122756
HNF4A#3172	2	15.4215269086358	0.00544421048668661	0.0246815079662744
NANOG#79923	2	19.4965189873418	0.00342725564850102	0.0174536352971425
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00472018592322358
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0173248915546239
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247049446532772
TRIM28#10155	3	18.5905250452625	0.000155596929725528	0.00197429082050837
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330107145858057
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109652960923358

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.