Coexpression cluster:C2485

Full id: C2485_pineal_cerebellum_pituitary_parietal_occipital_CD4_duodenum

Phase1 CAGE Peaks

Hg19::chr19:36980429..36980448,-	p1@ZNF566
Hg19::chr19:38270215..38270251,-	p1@ZNF573
Hg19::chr19:40562072..40562143,-	p1@ZNF780B
Hg19::chr5:179285785..179285846,-	p1@C5orf45

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
1.00202116011964e-05	0.00634279394355734	3	390	{ASH2L,391} (Static Module):NA

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:0006355	regulation of transcription, DNA-dependent	0.00519923459098235
GO:0006351	transcription, DNA-dependent	0.00519923459098235
GO:0032774	RNA biosynthetic process	0.00519923459098235
GO:0003677	DNA binding	0.00519923459098235
GO:0045449	regulation of transcription	0.00519923459098235
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.00519923459098235
GO:0006350	transcription	0.00519923459098235
GO:0010468	regulation of gene expression	0.00519923459098235
GO:0031323	regulation of cellular metabolic process	0.00519923459098235
GO:0019222	regulation of metabolic process	0.00519923459098235
GO:0016070	RNA metabolic process	0.00519923459098235
GO:0008270	zinc ion binding	0.00519923459098235
GO:0046914	transition metal ion binding	0.00784871922371737
GO:0010467	gene expression	0.0100445935106716
GO:0050794	regulation of cellular process	0.0107243941177873
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0108351071276006
GO:0005634	nucleus	0.011147418527857
GO:0050789	regulation of biological process	0.011147418527857
GO:0003676	nucleic acid binding	0.0118316479005403
GO:0043169	cation binding	0.0118867181787075
GO:0065007	biological regulation	0.0125886689188592
GO:0046872	metal ion binding	0.0126208906693392
GO:0043167	ion binding	0.0126967359708667
GO:0043283	biopolymer metabolic process	0.0180817341916611
GO:0043231	intracellular membrane-bound organelle	0.0229336055866812
GO:0043227	membrane-bound organelle	0.0229336055866812
GO:0043229	intracellular organelle	0.0386616181848527
GO:0043226	organelle	0.0386616181848527
GO:0043170	macromolecule metabolic process	0.0413773157609536

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
lymphocyte	8.83e-07	53
common lymphoid progenitor	8.83e-07	53

Uber Anatomy

Ontology term	p-value	n
adult organism	3.64e-38	115
central nervous system	1.85e-26	82
neural tube	1.93e-26	57
neural rod	1.93e-26	57
future spinal cord	1.93e-26	57
neural keel	1.93e-26	57
regional part of nervous system	1.21e-25	94
nervous system	1.21e-25	94
regional part of forebrain	8.40e-23	41
forebrain	8.40e-23	41
future forebrain	8.40e-23	41
brain	1.74e-22	69
future brain	1.74e-22	69
anterior neural tube	9.01e-22	42
regional part of brain	9.45e-22	59
neurectoderm	8.34e-20	90
neural plate	4.04e-19	86
presumptive neural plate	4.04e-19	86
telencephalon	8.58e-19	34
gray matter	1.32e-18	34
brain grey matter	1.32e-18	34
regional part of telencephalon	2.88e-18	33
cerebral hemisphere	1.20e-17	32
pre-chordal neural plate	3.55e-14	61
regional part of cerebral cortex	3.60e-14	22
cerebral cortex	6.92e-14	25
pallium	6.92e-14	25
neocortex	4.98e-13	20
ectoderm	9.93e-13	173
presumptive ectoderm	9.93e-13	173
anterior region of body	1.27e-12	129
craniocervical region	1.27e-12	129
ectoderm-derived structure	4.28e-12	169
head	2.59e-11	123

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
E2F6#1876	4	5.01715573169739	0.0015780219347306	0.00996957430532508
GABPB1#2553	3	5.30076287713663	0.0101267882423427	0.0378604488005023
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0186082610022204
NR2C2#7182	2	16.3073054526204	0.00541182534464822	0.0245538740679315
SETDB1#9869	2	20.1600130890052	0.0035690868540764	0.018086848559022
SIX5#147912	3	12.8150365165942	0.000766447113693038	0.006016307411273
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0322272446945537
TAF7#6879	3	8.57480205369294	0.0025005543351524	0.0140330679317024
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0244258766492212
ZNF143#7702	4	13.5008765522279	3.00867915035614e-05	0.000621117694769806
ZNF263#10127	3	6.16638122775801	0.00653981434797598	0.0279750837881738

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.