Coexpression cluster:C1101

Full id: C1101_testis_cerebellum_parietal_medial_occipital_middle_pituitary

Phase1 CAGE Peaks

Hg19::chr10:102279586..102279637,-	p2@SEC31B
Hg19::chr10:94050794..94050818,-	p2@CPEB3
Hg19::chr10:94050820..94050868,-	p1@CPEB3
Hg19::chr15:76352095..76352145,-	p2@NRG4
Hg19::chr18:76829258..76829280,+	p3@ATP9B
Hg19::chr3:197476560..197476577,-	p5@KIAA0226
Hg19::chr3:197476580..197476657,-	p2@KIAA0226

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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GO ID	GO name	FDR corrected p-value
GO:0015917	aminophospholipid transport	0.0261368651156931
GO:0004012	phospholipid-translocating ATPase activity	0.0478773993503692
GO:0015247	aminophospholipid transporter activity	0.0478773993503692
GO:0015914	phospholipid transport	0.0478773993503692

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	2.09e-56	114
neural tube	5.86e-31	56
neural rod	5.86e-31	56
future spinal cord	5.86e-31	56
neural keel	5.86e-31	56
regional part of nervous system	6.56e-29	53
regional part of brain	6.56e-29	53
central nervous system	1.39e-24	81
nervous system	7.93e-24	89
brain	1.22e-23	68
future brain	1.22e-23	68
regional part of forebrain	2.56e-23	41
forebrain	2.56e-23	41
anterior neural tube	2.56e-23	41
future forebrain	2.56e-23	41
neurectoderm	1.85e-21	86
neural plate	3.18e-21	82
presumptive neural plate	3.18e-21	82
brain grey matter	8.96e-19	34
gray matter	8.96e-19	34
telencephalon	9.74e-19	34
cerebral hemisphere	1.90e-17	32
regional part of telencephalon	2.52e-17	32
regional part of cerebral cortex	1.76e-16	22
organ system subdivision	3.58e-15	223
neocortex	3.87e-15	20
pre-chordal neural plate	4.70e-15	61
structure with developmental contribution from neural crest	2.32e-13	132
ectoderm-derived structure	5.35e-13	171
ectoderm	5.35e-13	171
presumptive ectoderm	5.35e-13	171
ecto-epithelium	6.56e-13	104
cerebral cortex	8.79e-13	25
pallium	8.79e-13	25
posterior neural tube	9.71e-09	15
chordal neural plate	9.71e-09	15
basal ganglion	1.11e-07	9
nuclear complex of neuraxis	1.11e-07	9
aggregate regional part of brain	1.11e-07	9
collection of basal ganglia	1.11e-07	9
cerebral subcortex	1.11e-07	9
neural nucleus	1.20e-07	9
nucleus of brain	1.20e-07	9
segmental subdivision of hindbrain	7.81e-07	12
hindbrain	7.81e-07	12
presumptive hindbrain	7.81e-07	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
ATF3#467	3	9.6270747968609	0.00269612955166033	0.0148380183509434
CTCF#10664	5	3.82875455219645	0.00338737119268134	0.0172893001657925
CTCFL#140690	4	11.2836996336996	0.000203273626505993	0.00241301367113655
E2F1#1869	6	4.20633361275371	0.000413523201700764	0.0039361966516976
E2F4#1874	4	7.23889160873397	0.00111774143052487	0.00766536195827611
ELF1#1997	5	3.04149854200538	0.00971956226937075	0.0365538841862013
GABPB1#2553	4	4.03867647781838	0.0098011349469615	0.0368420937491258
HEY1#23462	5	2.88579360221836	0.0123136694185303	0.0446180938973002
HMGN3#9324	4	4.67345584191462	0.00575188109993887	0.0259031827086592
MYC#4609	5	3.73020133686386	0.00382194422230669	0.0188665705267045
NRF1#4899	5	8.72162817693636	6.71450045004423e-05	0.00107307683626958
PAX5#5079	4	3.81118030353019	0.0120826168155519	0.0438188908118419
RAD21#5885	4	5.91716222597504	0.00239318493722796	0.0135528598665628
SIX5#147912	3	7.32287800948243	0.0058666762526916	0.0263293283982149
SRF#6722	3	5.91307639807192	0.0106686813016745	0.0393872673641905
ZNF143#7702	4	7.71478660127309	0.000877196960661348	0.00654102337387623
ZNF263#10127	4	4.69819522114896	0.0056412295360981	0.0254795818674285

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.