Coexpression cluster:C3045

Full id: C3045_occipital_brain_hippocampus_medial_cerebellum_temporal_amygdala

Phase1 CAGE Peaks

Hg19::chr10:75255724..75255792,-	p1@PPP3CB
Hg19::chr2:86790580..86790591,-	p4@CHMP3 p4@RNF103-CHMP3
Hg19::chr5:171433662..171433686,-	p2@FBXW11

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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p.value	FDR	nGenes	nPathway	Name
1.58091305570944e-05	0.00879764861457124	2	114	Oocyte meiosis (KEGG):04114
2.77966780871129e-05	0.00879764861457124	2	151	Wnt signaling pathway (KEGG):04310

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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GO ID	GO name	FDR corrected p-value
GO:0005955	calcineurin complex	0.0134222261032357
GO:0008287	protein serine/threonine phosphatase complex	0.03969244056313
GO:0004722	protein serine/threonine phosphatase activity	0.03969244056313
GO:0016567	protein ubiquitination	0.03969244056313
GO:0043687	post-translational protein modification	0.03969244056313
GO:0032446	protein modification by small protein conjugation	0.03969244056313
GO:0000151	ubiquitin ligase complex	0.03969244056313
GO:0006464	protein modification process	0.03969244056313
GO:0043412	biopolymer modification	0.03969244056313
GO:0043234	protein complex	0.03969244056313
GO:0005516	calmodulin binding	0.03969244056313
GO:0016055	Wnt receptor signaling pathway	0.03969244056313
GO:0004842	ubiquitin-protein ligase activity	0.03969244056313
GO:0008639	small protein conjugating enzyme activity	0.03969244056313
GO:0032991	macromolecular complex	0.0485798812421496
GO:0019787	small conjugating protein ligase activity	0.0485798812421496
GO:0006470	protein amino acid dephosphorylation	0.0485798812421496

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	1.37e-27	56
neural rod	1.37e-27	56
future spinal cord	1.37e-27	56
neural keel	1.37e-27	56
adult organism	3.93e-26	114
regional part of nervous system	6.07e-26	53
regional part of brain	6.07e-26	53
nervous system	3.09e-25	89
central nervous system	8.77e-25	81
brain	5.97e-23	68
future brain	5.97e-23	68
neural plate	2.58e-22	82
presumptive neural plate	2.58e-22	82
neurectoderm	5.66e-22	86
regional part of forebrain	1.45e-21	41
forebrain	1.45e-21	41
anterior neural tube	1.45e-21	41
future forebrain	1.45e-21	41
structure with developmental contribution from neural crest	1.66e-18	132
brain grey matter	3.16e-18	34
gray matter	3.16e-18	34
telencephalon	5.71e-18	34
cerebral hemisphere	1.94e-17	32
regional part of telencephalon	4.19e-17	32
ectoderm-derived structure	1.24e-16	171
ectoderm	1.24e-16	171
presumptive ectoderm	1.24e-16	171
pre-chordal neural plate	1.30e-16	61
regional part of cerebral cortex	2.34e-15	22
ecto-epithelium	2.00e-14	104
neocortex	4.18e-14	20
organ system subdivision	2.06e-13	223
cerebral cortex	2.39e-13	25
pallium	2.39e-13	25
tube	1.59e-12	192
anatomical cluster	7.93e-12	373
anatomical conduit	2.23e-11	240
multi-tissue structure	4.31e-11	342
cell layer	2.45e-09	309
epithelium	3.25e-09	306
organ part	5.32e-08	218
posterior neural tube	3.06e-07	15
chordal neural plate	3.06e-07	15

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
BCLAF1#9774	3	21.6526476101218	9.8473954032885e-05	0.0013882993095627
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.031899441353459
ELK4#2005	2	10.823787772312	0.0109128471951648	0.0401722480073249
FAM48A#55578	1	385.05625	0.00259478966140747	0.014348347405503
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127589782211264
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156129227126221
MAX#4149	3	6.45255550900712	0.00372191383426551	0.0185667252071482
MEF2A#4205	2	12.495487273096	0.00823502947802974	0.0324709572113092
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0293159243965195
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0268527451311305
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00469276767888513
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0172223222289507
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00879344366748451
SIX5#147912	2	11.391143570306	0.00987382008142903	0.0370566298506672
STAT1#6772	2	13.8043916647995	0.00677093170844408	0.0287424028247852

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.