Coexpression cluster:C877

Full id: C877_optic_parietal_occipital_temporal_corpus_duodenum_brain

Phase1 CAGE Peaks

Hg19::chr11:113075052..113075072,+	p@chr11:113075052..113075072 +
Hg19::chr11:117667885..117667949,-	p1@DSCAML1
Hg19::chr11:131309852..131309856,+	p@chr11:131309852..131309856 +
Hg19::chr11:131433495..131433499,+	p@chr11:131433495..131433499 +
Hg19::chr11:66059302..66059313,+	p3@TMEM151A
Hg19::chr15:84116080..84116099,+	p2@SH3GL3
Hg19::chr1:147718685..147718722,-	p@chr1:147718685..147718722 -
Hg19::chr2:27170707..27170718,+	p6@DPYSL5
Hg19::chr6:124124993..124125015,+	p6@NKAIN2

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:0007399	nervous system development	0.00235882184034278
GO:0007409	axonogenesis	0.00235882184034278
GO:0048667	neuron morphogenesis during differentiation	0.00235882184034278
GO:0048812	neurite morphogenesis	0.00235882184034278
GO:0000904	cellular morphogenesis during differentiation	0.00235882184034278
GO:0031175	neurite development	0.00235882184034278
GO:0048666	neuron development	0.00263048050948375
GO:0032990	cell part morphogenesis	0.00310783649624717
GO:0048858	cell projection morphogenesis	0.00310783649624717
GO:0030030	cell projection organization and biogenesis	0.00310783649624717
GO:0030182	neuron differentiation	0.00310783649624717
GO:0007417	central nervous system development	0.00348781455915125
GO:0048699	generation of neurons	0.00348781455915125
GO:0022008	neurogenesis	0.00379284252160859
GO:0048731	system development	0.00594289024873574
GO:0042802	identical protein binding	0.00637410169344523
GO:0048704	embryonic skeletal morphogenesis	0.00708727549592255
GO:0048856	anatomical structure development	0.00832386365774856
GO:0048706	embryonic skeletal development	0.00832386365774856
GO:0000902	cell morphogenesis	0.00832386365774856
GO:0032989	cellular structure morphogenesis	0.00832386365774856
GO:0048705	skeletal morphogenesis	0.00912432801082624
GO:0031901	early endosome membrane	0.00989013586888669
GO:0007275	multicellular organismal development	0.0105791378658706
GO:0009953	dorsal/ventral pattern formation	0.014914166630396
GO:0001709	cell fate determination	0.014914166630396
GO:0043025	cell soma	0.0173270730176464
GO:0030425	dendrite	0.018137180821599
GO:0005769	early endosome	0.0225663353440213
GO:0016043	cellular component organization and biogenesis	0.0233626455106897
GO:0032502	developmental process	0.0233626455106897
GO:0007411	axon guidance	0.0233626455106897
GO:0009653	anatomical structure morphogenesis	0.0245951547792637
GO:0045165	cell fate commitment	0.0278535056622883
GO:0043005	neuron projection	0.0289834837544392
GO:0032501	multicellular organismal process	0.0289834837544392
GO:0048468	cell development	0.0289834837544392
GO:0010008	endosome membrane	0.0289834837544392
GO:0044440	endosomal part	0.0289834837544392
GO:0003002	regionalization	0.0289834837544392
GO:0048598	embryonic morphogenesis	0.0294267243002979
GO:0009792	embryonic development ending in birth or egg hatching	0.0294267243002979
GO:0043009	chordate embryonic development	0.0294267243002979
GO:0007389	pattern specification process	0.037472638517259
GO:0007420	brain development	0.0410359049211885
GO:0009986	cell surface	0.042720417716659
GO:0042803	protein homodimerization activity	0.0446103001695871
GO:0048869	cellular developmental process	0.0473024337183543
GO:0030154	cell differentiation	0.0473024337183543
GO:0016020	membrane	0.0474945320108906
GO:0016810	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	0.0483004518974905
GO:0005768	endosome	0.0483004518974905
GO:0010324	membrane invagination	0.0483004518974905
GO:0006897	endocytosis	0.0483004518974905

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
regional part of nervous system	9.79e-38	94
nervous system	9.79e-38	94
central nervous system	1.57e-34	82
neural tube	3.77e-33	57
neural rod	3.77e-33	57
future spinal cord	3.77e-33	57
neural keel	3.77e-33	57
neurectoderm	4.56e-32	90
neural plate	7.14e-31	86
presumptive neural plate	7.14e-31	86
regional part of brain	1.50e-27	59
brain	3.03e-27	69
future brain	3.03e-27	69
regional part of forebrain	8.89e-27	41
forebrain	8.89e-27	41
future forebrain	8.89e-27	41
anterior neural tube	2.83e-26	42
pre-chordal neural plate	1.57e-22	61
telencephalon	1.76e-22	34
gray matter	1.81e-22	34
brain grey matter	1.81e-22	34
adult organism	2.25e-22	115
ectoderm	5.49e-22	173
presumptive ectoderm	5.49e-22	173
regional part of telencephalon	7.71e-22	33
cerebral hemisphere	4.43e-21	32
ectoderm-derived structure	7.30e-21	169
cerebral cortex	1.24e-16	25
pallium	1.24e-16	25
anterior region of body	5.07e-16	129
craniocervical region	5.07e-16	129
head	7.83e-16	123
regional part of cerebral cortex	1.29e-15	22
neocortex	2.68e-14	20
organ part	2.95e-11	219
organism subdivision	5.16e-10	365
multi-tissue structure	6.79e-10	347
tube	9.87e-09	194
organ	3.93e-08	511
epithelium	4.26e-08	309
posterior neural tube	4.87e-08	15
chordal neural plate	4.87e-08	15
cell layer	7.73e-08	312
embryo	1.13e-07	612
nucleus of brain	2.70e-07	9
neural nucleus	2.70e-07	9
basal ganglion	3.50e-07	9
nuclear complex of neuraxis	3.50e-07	9
aggregate regional part of brain	3.50e-07	9
collection of basal ganglia	3.50e-07	9
cerebral subcortex	3.50e-07	9
segmental subdivision of nervous system	8.44e-07	13

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
SUZ12#23512	2	11.1368402024584	0.0130543531390231	0.0463105838140772

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.