Coexpression cluster:C561

Full id: C561_brain_Neural_spinal_Neurons_parietal_temporal_occipital

Phase1 CAGE Peaks

Hg19::chr11:65816664..65816675,-	p2@GAL3ST3
Hg19::chr13:36705425..36705445,-	p5@DCLK1
Hg19::chr13:53422767..53422780,-	p1@PCDH8
Hg19::chr19:19322758..19322773,+	p1@NCAN
Hg19::chr19:19322805..19322812,+	p2@NCAN
Hg19::chr1:156391550..156391569,-	p2@C1orf61
Hg19::chr1:156399211..156399225,-	p1@C1orf61
Hg19::chr1:156400037..156400063,-	p@chr1:156400037..156400063 -
Hg19::chr22:42372970..42372971,+	p5@SEPT3
Hg19::chr2:26395939..26396015,+	p2@FAM59B
Hg19::chr3:26664252..26664268,+	p5@LRRC3B
Hg19::chr3:65387362..65387385,-	p14@MAGI1
Hg19::chr4:150999554..150999573,+	p6@DCLK2
Hg19::chr5:140787600..140787637,+	p2@PCDHGB6
Hg19::chr5:87968909..87968913,-	p2@LINC00461
Hg19::chr5:87969130..87969153,-	p1@LINC00461

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:0022610	biological adhesion	0.00364590195774595
GO:0007155	cell adhesion	0.00364590195774595
GO:0016337	cell-cell adhesion	0.00364590195774595
GO:0050698	proteoglycan sulfotransferase activity	0.0170795551236903
GO:0030309	poly-N-acetyllactosamine metabolic process	0.0170795551236903
GO:0050694	galactose 3-O-sulfotransferase activity	0.0170795551236903
GO:0001733	galactosylceramide sulfotransferase activity	0.0170795551236903
GO:0017076	purine nucleotide binding	0.0170795551236903
GO:0007156	homophilic cell adhesion	0.0170795551236903
GO:0050656	3'-phosphoadenosine 5'-phosphosulfate binding	0.0170795551236903
GO:0007158	neuron adhesion	0.0217324972662446
GO:0000166	nucleotide binding	0.0271439940753673
GO:0030554	adenyl nucleotide binding	0.0468748694812944
GO:0030166	proteoglycan biosynthetic process	0.0468748694812944
GO:0005509	calcium ion binding	0.0468748694812944
GO:0009311	oligosaccharide metabolic process	0.0468748694812944

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
neural cell	5.18e-10	25
neurectodermal cell	2.13e-08	59

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	9.48e-46	94
nervous system	9.48e-46	94
central nervous system	2.73e-44	82
brain	4.32e-36	69
future brain	4.32e-36	69
neural tube	3.78e-34	57
neural rod	3.78e-34	57
future spinal cord	3.78e-34	57
neural keel	3.78e-34	57
regional part of brain	5.13e-32	59
neurectoderm	2.05e-31	90
neural plate	1.03e-29	86
presumptive neural plate	1.03e-29	86
ectoderm	1.01e-25	173
presumptive ectoderm	1.01e-25	173
anterior neural tube	1.85e-25	42
regional part of forebrain	1.98e-25	41
forebrain	1.98e-25	41
future forebrain	1.98e-25	41
ectoderm-derived structure	3.42e-24	169
pre-chordal neural plate	2.07e-22	61
telencephalon	2.26e-22	34
gray matter	2.58e-22	34
brain grey matter	2.58e-22	34
regional part of telencephalon	1.01e-21	33
cerebral hemisphere	3.14e-21	32
head	4.71e-21	123
anterior region of body	1.94e-20	129
craniocervical region	1.94e-20	129
adult organism	3.03e-20	115
cerebral cortex	5.65e-17	25
pallium	5.65e-17	25
regional part of cerebral cortex	2.78e-15	22
neocortex	4.82e-14	20
posterior neural tube	1.03e-09	15
chordal neural plate	1.03e-09	15
segmental subdivision of nervous system	1.88e-08	13
segmental subdivision of hindbrain	5.88e-08	12
hindbrain	5.88e-08	12
presumptive hindbrain	5.88e-08	12
organ	9.59e-08	511
basal ganglion	6.84e-07	9
nuclear complex of neuraxis	6.84e-07	9
aggregate regional part of brain	6.84e-07	9
collection of basal ganglia	6.84e-07	9
cerebral subcortex	6.84e-07	9
nucleus of brain	8.66e-07	9
neural nucleus	8.66e-07	9

Disease

Ontology term	p-value	n
germ cell and embryonal cancer	7.70e-08	22
germ cell cancer	7.70e-08	22

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.