Coexpression cluster:C1328

Full id: C1328_extraskeletal_cerebellum_brain_duodenum_occipital_parietal_temporal

Phase1 CAGE Peaks

Hg19::chr11:105480958..105480979,+	p7@GRIA4
Hg19::chr21:17442864..17442881,+	p11@LINC00478
Hg19::chr21:17442981..17443002,+	p7@LINC00478
Hg19::chr5:140743720..140743735,+	p3@PCDHGA5
Hg19::chr5:140743737..140743773,+	p1@PCDHGA5
Hg19::chr5:140743798..140743812,+	p5@PCDHGA5

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:0007215	glutamate signaling pathway	0.0359506809929164
GO:0004970	ionotropic glutamate receptor activity	0.0359506809929164
GO:0005234	extracellular-glutamate-gated ion channel activity	0.0359506809929164
GO:0005231	excitatory extracellular ligand-gated ion channel activity	0.0452696791342411
GO:0008066	glutamate receptor activity	0.0452696791342411
GO:0005230	extracellular ligand-gated ion channel activity	0.0452696791342411
GO:0045211	postsynaptic membrane	0.0452696791342411
GO:0044456	synapse part	0.0452696791342411
GO:0015276	ligand-gated ion channel activity	0.0452696791342411
GO:0022834	ligand-gated channel activity	0.0452696791342411
GO:0007156	homophilic cell adhesion	0.0494071807938995
GO:0005886	plasma membrane	0.0494071807938995

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	3.09e-08	180

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	9.40e-42	94
nervous system	9.40e-42	94
central nervous system	2.73e-41	82
neural tube	5.72e-40	57
neural rod	5.72e-40	57
future spinal cord	5.72e-40	57
neural keel	5.72e-40	57
regional part of brain	2.69e-37	59
neurectoderm	2.37e-35	90
adult organism	2.84e-35	115
neural plate	3.41e-35	86
presumptive neural plate	3.41e-35	86
brain	1.02e-34	69
future brain	1.02e-34	69
anterior neural tube	1.10e-29	42
regional part of forebrain	1.94e-29	41
forebrain	1.94e-29	41
future forebrain	1.94e-29	41
ectoderm	1.28e-26	173
presumptive ectoderm	1.28e-26	173
ectoderm-derived structure	4.46e-26	169
pre-chordal neural plate	4.13e-25	61
telencephalon	4.92e-25	34
gray matter	6.64e-25	34
brain grey matter	6.64e-25	34
regional part of telencephalon	2.50e-24	33
cerebral hemisphere	8.26e-24	32
head	9.31e-24	123
anterior region of body	9.91e-24	129
craniocervical region	9.91e-24	129
cerebral cortex	7.14e-19	25
pallium	7.14e-19	25
organism subdivision	7.81e-19	365
regional part of cerebral cortex	4.18e-17	22
multi-cellular organism	4.38e-16	659
neocortex	8.39e-16	20
cell layer	7.64e-14	312
epithelium	1.93e-13	309
multi-tissue structure	2.73e-13	347
anatomical system	5.98e-12	625
anatomical group	8.92e-12	626
posterior neural tube	3.42e-11	15
chordal neural plate	3.42e-11	15
anatomical cluster	7.56e-11	286
tube	1.23e-10	194
anatomical conduit	2.26e-10	241
embryo	3.41e-10	612
embryonic structure	1.33e-09	605
developing anatomical structure	1.33e-09	605
segmental subdivision of nervous system	2.69e-09	13
germ layer	2.79e-09	604
embryonic tissue	2.79e-09	604
presumptive structure	2.79e-09	604
epiblast (generic)	2.79e-09	604
segmental subdivision of hindbrain	3.72e-09	12
hindbrain	3.72e-09	12
presumptive hindbrain	3.72e-09	12
organ part	1.38e-08	219
organ	1.70e-08	511
basal ganglion	1.55e-07	9
nuclear complex of neuraxis	1.55e-07	9
aggregate regional part of brain	1.55e-07	9
collection of basal ganglia	1.55e-07	9
cerebral subcortex	1.55e-07	9
nucleus of brain	1.83e-07	9
neural nucleus	1.83e-07	9
regional part of metencephalon	2.70e-07	9
metencephalon	2.70e-07	9
future metencephalon	2.70e-07	9
tissue	3.49e-07	787

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.