Coexpression cluster:C2113

Full id: C2113_brain_medial_hippocampus_diencephalon_amygdala_substantia_olfactory

Phase1 CAGE Peaks

Hg19::chr11:134281749..134281759,-	p5@B3GAT1
Hg19::chr15:30248510..30248535,-	p32@TJP1
Hg19::chr20:58349377..58349415,+	p@chr20:58349377..58349415 +
Hg19::chr3:58551422..58551434,-	p@chr3:58551422..58551434 -

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:0005918	septate junction	0.00423878488166725
GO:0015018	galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity	0.00953487963183759
GO:0008499	UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity	0.00953487963183759
GO:0048531	beta-1,3-galactosyltransferase activity	0.00953487963183759
GO:0005913	cell-cell adherens junction	0.00953487963183759
GO:0007043	intercellular junction assembly	0.00953487963183759
GO:0035250	UDP-galactosyltransferase activity	0.00953487963183759
GO:0045216	intercellular junction assembly and maintenance	0.00953487963183759
GO:0007028	cytoplasm organization and biogenesis	0.0112995998696127
GO:0015020	glucuronosyltransferase activity	0.014404868632055
GO:0008378	galactosyltransferase activity	0.015404915412871
GO:0005912	adherens junction	0.0190596523614523
GO:0016323	basolateral plasma membrane	0.026911659244122
GO:0005923	tight junction	0.026911659244122
GO:0043296	apical junction complex	0.027774445781206
GO:0016327	apicolateral plasma membrane	0.027774445781206
GO:0008194	UDP-glycosyltransferase activity	0.0343395765145704
GO:0030145	manganese ion binding	0.0345423555680781
GO:0005911	intercellular junction	0.0349728933440095
GO:0006486	protein amino acid glycosylation	0.0349728933440095
GO:0043413	biopolymer glycosylation	0.0349728933440095
GO:0009101	glycoprotein biosynthetic process	0.0349728933440095
GO:0009100	glycoprotein metabolic process	0.0382165680597289
GO:0016758	transferase activity, transferring hexosyl groups	0.0494245767274581

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
neurectodermal cell	5.35e-08	59
neuronal stem cell	1.28e-07	8
neural cell	4.31e-07	25

Uber Anatomy

Ontology term	p-value	n
central nervous system	2.38e-58	82
regional part of nervous system	1.03e-56	94
nervous system	1.03e-56	94
neural tube	4.15e-53	57
neural rod	4.15e-53	57
future spinal cord	4.15e-53	57
neural keel	4.15e-53	57
brain	2.18e-45	69
future brain	2.18e-45	69
regional part of brain	2.66e-43	59
gray matter	4.71e-38	34
brain grey matter	4.71e-38	34
telencephalon	5.90e-38	34
regional part of forebrain	3.47e-37	41
forebrain	3.47e-37	41
future forebrain	3.47e-37	41
regional part of telencephalon	1.30e-36	33
anterior neural tube	5.05e-36	42
adult organism	6.66e-36	115
cerebral hemisphere	5.45e-35	32
neural plate	5.83e-34	86
presumptive neural plate	5.83e-34	86
neurectoderm	3.25e-33	90
ectoderm-derived structure	6.16e-29	169
ectoderm	7.89e-29	173
presumptive ectoderm	7.89e-29	173
cerebral cortex	2.52e-25	25
pallium	2.52e-25	25
regional part of cerebral cortex	1.13e-24	22
pre-chordal neural plate	1.30e-22	61
head	3.82e-22	123
neocortex	7.82e-22	20
anterior region of body	3.41e-21	129
craniocervical region	3.41e-21	129
posterior neural tube	6.54e-18	15
chordal neural plate	6.54e-18	15
segmental subdivision of nervous system	4.73e-15	13
nucleus of brain	2.05e-14	9
neural nucleus	2.05e-14	9
basal ganglion	2.86e-14	9
nuclear complex of neuraxis	2.86e-14	9
aggregate regional part of brain	2.86e-14	9
collection of basal ganglia	2.86e-14	9
cerebral subcortex	2.86e-14	9
segmental subdivision of hindbrain	1.03e-13	12
hindbrain	1.03e-13	12
presumptive hindbrain	1.03e-13	12
telencephalic nucleus	1.42e-11	7
tube	1.97e-11	194
gyrus	3.71e-10	6
regional part of metencephalon	6.24e-10	9
metencephalon	6.24e-10	9
future metencephalon	6.24e-10	9
temporal lobe	6.40e-10	7
brainstem	1.65e-09	8
limbic system	1.28e-08	5
anatomical conduit	6.92e-08	241
corpus striatum	2.53e-07	4
striatum	2.53e-07	4
ventral part of telencephalon	2.53e-07	4
future corpus striatum	2.53e-07	4
organ part	8.32e-07	219

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.