Coexpression cluster:C552

Full id: C552_medial_temporal_occipital_parietal_duodenum_brain_spinal

Phase1 CAGE Peaks

Hg19::chr10:105048252..105048262,+	p@chr10:105048252..105048262 +
Hg19::chr10:105048347..105048358,+	p@chr10:105048347..105048358 +
Hg19::chr11:132289875..132289896,-	p12@OPCML
Hg19::chr16:7568144..7568155,+	p@chr16:7568144..7568155 +
Hg19::chr17:44039779..44039792,+	p6@MAPT
Hg19::chr17:44068857..44068869,+	p8@MAPT
Hg19::chr2:149633261..149633270,+	p1@AB384491
Hg19::chr2:50148868..50148876,-	p32@NRXN1
Hg19::chr2:55253343..55253360,-	p29@RTN4
Hg19::chr3:286287..286329,+	p@chr3:286287..286329 +
Hg19::chr3:383640..383650,+	p@chr3:383640..383650 +
Hg19::chr5:71482490..71482501,+	p@chr5:71482490..71482501 +
Hg19::chr5:71482533..71482549,+	p@chr5:71482533..71482549 +
Hg19::chr5:71489693..71489706,+	p@chr5:71489693..71489706 +
Hg19::chr8:80567211..80567218,+	p9@STMN2
Hg19::chr9:111911992..111912002,-	p@chr9:111911992..111912002 -

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:0030516	regulation of axon extension	0.00010362994502982
GO:0030182	neuron differentiation	0.00010362994502982
GO:0048675	axon extension	0.00010362994502982
GO:0030426	growth cone	0.00010362994502982
GO:0030427	site of polarized growth	0.00010362994502982
GO:0048699	generation of neurons	0.00010362994502982
GO:0022008	neurogenesis	0.000112726089605561
GO:0050770	regulation of axonogenesis	0.000123735069240019
GO:0050767	regulation of neurogenesis	0.000237741650507623
GO:0007399	nervous system development	0.00158975368646609
GO:0007409	axonogenesis	0.00166359731717786
GO:0048667	neuron morphogenesis during differentiation	0.00166359731717786
GO:0048812	neurite morphogenesis	0.00166359731717786
GO:0000904	cellular morphogenesis during differentiation	0.00170318642141137
GO:0031175	neurite development	0.00182484678637508
GO:0048666	neuron development	0.00222579120033241
GO:0045298	tubulin complex	0.00304731298129318
GO:0032990	cell part morphogenesis	0.0031203738849544
GO:0048858	cell projection morphogenesis	0.0031203738849544
GO:0030030	cell projection organization and biogenesis	0.0031203738849544
GO:0019987	negative regulation of anti-apoptosis	0.00347582725292053
GO:0030517	negative regulation of axon extension	0.00347582725292053
GO:0048468	cell development	0.00347582725292053
GO:0050793	regulation of developmental process	0.00347582725292053
GO:0042995	cell projection	0.00575468023354051
GO:0045773	positive regulation of axon extension	0.00575468023354051
GO:0050771	negative regulation of axonogenesis	0.00575468023354051
GO:0048731	system development	0.00615746870355665
GO:0031116	positive regulation of microtubule polymerization	0.0062504053506897
GO:0031112	positive regulation of microtubule polymerization or depolymerization	0.00668206759859369
GO:0031113	regulation of microtubule polymerization	0.00668206759859369
GO:0005515	protein binding	0.00719152808698763
GO:0048869	cellular developmental process	0.00720625871783252
GO:0030154	cell differentiation	0.00720625871783252
GO:0046785	microtubule polymerization	0.00739713234206427
GO:0008038	neuron recognition	0.00791035634833841
GO:0050768	negative regulation of neurogenesis	0.00795198723378637
GO:0045767	regulation of anti-apoptosis	0.00795198723378637
GO:0048856	anatomical structure development	0.00795198723378637
GO:0050772	positive regulation of axonogenesis	0.00795198723378637
GO:0000902	cell morphogenesis	0.00795198723378637
GO:0032989	cellular structure morphogenesis	0.00795198723378637
GO:0016020	membrane	0.00795198723378637
GO:0051130	positive regulation of cellular component organization and biogenesis	0.00805275855365829
GO:0004985	opioid receptor activity	0.00805275855365829
GO:0050769	positive regulation of neurogenesis	0.00900202403800668
GO:0007275	multicellular organismal development	0.0104480426339578
GO:0017124	SH3 domain binding	0.0107811353522219
GO:0007026	negative regulation of microtubule depolymerization	0.0113835384307388
GO:0031114	regulation of microtubule depolymerization	0.0113835384307388
GO:0031111	negative regulation of microtubule polymerization or depolymerization	0.0114425685972422
GO:0007019	microtubule depolymerization	0.0114425685972422
GO:0031110	regulation of microtubule polymerization or depolymerization	0.0138883244812153
GO:0008034	lipoprotein binding	0.0138883244812153
GO:0031109	microtubule polymerization or depolymerization	0.0150437531143522
GO:0030424	axon	0.0156967109218176
GO:0008037	cell recognition	0.0172315456118835
GO:0051261	protein depolymerization	0.020489944257951
GO:0008017	microtubule binding	0.0214525192020646
GO:0022610	biological adhesion	0.0216605349071122
GO:0007155	cell adhesion	0.0216605349071122
GO:0051129	negative regulation of cellular component organization and biogenesis	0.0216605349071122
GO:0030176	integral to endoplasmic reticulum membrane	0.0217253746280847
GO:0032502	developmental process	0.0225500834866176
GO:0030334	regulation of cell migration	0.0235007884009187
GO:0009653	anatomical structure morphogenesis	0.0235007884009187
GO:0031227	intrinsic to endoplasmic reticulum membrane	0.0235007884009187
GO:0015631	tubulin binding	0.0254237655144738
GO:0051094	positive regulation of developmental process	0.0254277678098717
GO:0051270	regulation of cell motility	0.0254316124385206
GO:0048523	negative regulation of cellular process	0.0257941112672204
GO:0040012	regulation of locomotion	0.0257941112672204
GO:0040011	locomotion	0.0257941112672204
GO:0048519	negative regulation of biological process	0.0264757184329733
GO:0051093	negative regulation of developmental process	0.0264757184329733
GO:0043005	neuron projection	0.0272872935115342
GO:0032501	multicellular organismal process	0.0272872935115342
GO:0005200	structural constituent of cytoskeleton	0.0280891153272492
GO:0051258	protein polymerization	0.0316265304462711
GO:0051128	regulation of cellular component organization and biogenesis	0.0321914258461296
GO:0000226	microtubule cytoskeleton organization and biogenesis	0.0324260624446285
GO:0051248	negative regulation of protein metabolic process	0.0326548287373963
GO:0048503	GPI anchor binding	0.038874450927321
GO:0019904	protein domain specific binding	0.038874450927321
GO:0031301	integral to organelle membrane	0.042017371296162
GO:0001653	peptide receptor activity	0.0436863081765911
GO:0008528	peptide receptor activity, G-protein coupled	0.0436863081765911
GO:0031300	intrinsic to organelle membrane	0.0443467218518709
GO:0006916	anti-apoptosis	0.0489890794507065

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
non-terminally differentiated cell	7.99e-12	180
fibroblast	3.78e-07	75

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	4.93e-37	94
nervous system	4.93e-37	94
central nervous system	6.36e-37	82
neural tube	8.78e-33	57
neural rod	8.78e-33	57
future spinal cord	8.78e-33	57
neural keel	8.78e-33	57
brain	3.03e-30	69
future brain	3.03e-30	69
regional part of brain	1.68e-28	59
neurectoderm	5.28e-28	90
neural plate	9.15e-27	86
presumptive neural plate	9.15e-27	86
anterior neural tube	1.13e-26	42
regional part of forebrain	3.00e-26	41
forebrain	3.00e-26	41
future forebrain	3.00e-26	41
ectoderm	1.06e-25	173
presumptive ectoderm	1.06e-25	173
ectoderm-derived structure	1.78e-24	169
gray matter	1.62e-22	34
brain grey matter	1.62e-22	34
telencephalon	2.47e-22	34
regional part of telencephalon	1.04e-21	33
head	1.40e-21	123
cerebral hemisphere	2.86e-21	32
pre-chordal neural plate	3.38e-20	61
anterior region of body	4.40e-20	129
craniocervical region	4.40e-20	129
adult organism	3.14e-18	115
organism subdivision	5.60e-18	365
cerebral cortex	4.57e-17	25
pallium	4.57e-17	25
regional part of cerebral cortex	6.57e-16	22
tube	7.30e-15	194
neocortex	1.31e-14	20
anatomical conduit	3.56e-14	241
epithelium	1.26e-13	309
cell layer	1.91e-13	312
anatomical cluster	1.83e-12	286
multi-cellular organism	1.20e-11	659
anatomical system	6.07e-08	625
multi-tissue structure	6.19e-08	347
anatomical group	7.23e-08	626
embryo	9.64e-08	612
posterior neural tube	2.17e-07	15
chordal neural plate	2.17e-07	15
basal ganglion	6.62e-07	9
nuclear complex of neuraxis	6.62e-07	9
aggregate regional part of brain	6.62e-07	9
collection of basal ganglia	6.62e-07	9
cerebral subcortex	6.62e-07	9
nucleus of brain	6.75e-07	9
neural nucleus	6.75e-07	9

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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No analysis results for this cluster

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.