Coexpression cluster:C837

Full id: C837_neuroectodermal_duodenum_temporal_occipital_medial_carcinoid_parietal

Phase1 CAGE Peaks

Hg19::chr15:77907249..77907288,-	p9@LINGO1
Hg19::chr15:77907545..77907560,-	p4@LINGO1
Hg19::chr15:77907829..77907849,-	p11@LINGO1
Hg19::chr15:77907867..77907879,-	p12@LINGO1
Hg19::chr15:77907974..77907985,-	p8@LINGO1
Hg19::chr15:77908039..77908050,-	p14@LINGO1
Hg19::chr15:78111788..78111799,-	p@chr15:78111788..78111799 -
Hg19::chr3:51741072..51741106,+	p1@GRM2
Hg19::chr6:110422944..110422955,-	p7@AK056044
Hg19::chr8:50823900..50823915,+	p6@SNTG1

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:0014047	glutamate secretion	0.00759426602163143
GO:0016013	syntrophin complex	0.00759426602163143
GO:0042734	presynaptic membrane	0.0189784004164746
GO:0031280	negative regulation of cyclase activity	0.0189784004164746
GO:0007194	negative regulation of adenylate cyclase activity	0.0189784004164746
GO:0051350	negative regulation of lyase activity	0.0189784004164746
GO:0016010	dystrophin-associated glycoprotein complex	0.0238536438879483
GO:0030424	axon	0.0245064420408919
GO:0005605	basal lamina	0.0245064420408919
GO:0007269	neurotransmitter secretion	0.0245064420408919
GO:0045761	regulation of adenylate cyclase activity	0.0245064420408919
GO:0031279	regulation of cyclase activity	0.0245064420408919
GO:0051339	regulation of lyase activity	0.0245064420408919
GO:0045055	regulated secretory pathway	0.0287065807247769
GO:0008067	metabotropic glutamate, GABA-B-like receptor activity	0.0288115129303549
GO:0003001	generation of a signal involved in cell-cell signaling	0.029956787610063
GO:0005604	basement membrane	0.029956787610063
GO:0001505	regulation of neurotransmitter levels	0.029956787610063
GO:0043005	neuron projection	0.029956787610063
GO:0007188	G-protein signaling, coupled to cAMP nucleotide second messenger	0.029956787610063
GO:0043086	negative regulation of catalytic activity	0.029956787610063
GO:0019933	cAMP-mediated signaling	0.029956787610063
GO:0008066	glutamate receptor activity	0.0309534539371326
GO:0007187	G-protein signaling, coupled to cyclic nucleotide second messenger	0.0368968572996878
GO:0019935	cyclic-nucleotide-mediated signaling	0.0369292580465969
GO:0044420	extracellular matrix part	0.0381182985017164
GO:0044459	plasma membrane part	0.0412763404122513
GO:0044456	synapse part	0.0434629625940273

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
neuron	4.26e-13	6
neuroblast	4.26e-13	6
electrically signaling cell	4.26e-13	6
embryonic stem cell	2.44e-11	5
neuronal stem cell	1.27e-09	8

Uber Anatomy

Ontology term	p-value	n
central nervous system	2.68e-67	81
neural tube	5.46e-64	56
neural rod	5.46e-64	56
future spinal cord	5.46e-64	56
neural keel	5.46e-64	56
nervous system	9.60e-62	89
regional part of nervous system	1.00e-61	53
regional part of brain	1.00e-61	53
telencephalon	1.05e-54	34
brain grey matter	2.18e-54	34
gray matter	2.18e-54	34
regional part of forebrain	1.09e-53	41
forebrain	1.09e-53	41
anterior neural tube	1.09e-53	41
future forebrain	1.09e-53	41
brain	8.82e-53	68
future brain	8.82e-53	68
cerebral hemisphere	3.31e-51	32
regional part of telencephalon	7.97e-51	32
neurectoderm	8.11e-49	86
regional part of cerebral cortex	1.00e-47	22
neocortex	2.00e-43	20
neural plate	7.38e-42	82
presumptive neural plate	7.38e-42	82
cerebral cortex	2.15e-41	25
pallium	2.15e-41	25
pre-chordal neural plate	4.33e-35	61
ectoderm-derived structure	1.39e-33	171
ectoderm	1.39e-33	171
presumptive ectoderm	1.39e-33	171
ecto-epithelium	5.26e-32	104
adult organism	5.27e-31	114
structure with developmental contribution from neural crest	6.56e-24	132
organ system subdivision	9.17e-22	223
basal ganglion	4.43e-15	9
nuclear complex of neuraxis	4.43e-15	9
aggregate regional part of brain	4.43e-15	9
collection of basal ganglia	4.43e-15	9
cerebral subcortex	4.43e-15	9
gyrus	7.53e-15	6
neural nucleus	3.59e-14	9
nucleus of brain	3.59e-14	9
temporal lobe	5.88e-13	6
occipital lobe	1.23e-12	5
parietal lobe	1.42e-12	5
limbic system	2.11e-12	5
tube	7.44e-12	192
posterior neural tube	1.01e-11	15
chordal neural plate	1.01e-11	15
telencephalic nucleus	8.89e-11	7
segmental subdivision of hindbrain	1.35e-09	12
hindbrain	1.35e-09	12
presumptive hindbrain	1.35e-09	12
segmental subdivision of nervous system	9.38e-09	13
anatomical cluster	1.45e-08	373
frontal cortex	3.26e-08	3
brainstem	4.07e-08	6
regional part of metencephalon	1.02e-07	9
metencephalon	1.02e-07	9
future metencephalon	1.02e-07	9
anatomical conduit	2.52e-07	240
organ part	9.53e-07	218

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.