Coexpression cluster:C2114

Full id: C2114_neuroblastoma_parietal_occipital_Neurons_brain_medial_amygdala

Phase1 CAGE Peaks

Hg19::chr11:1411252..1411304,+	p2@BRSK2
Hg19::chr20:42875893..42875921,+	p2@GDAP1L1
Hg19::chr3:111717807..111717818,+	p8@TAGLN3
Hg19::chr9:23826199..23826217,-	p4@ELAVL2

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:0030010	establishment of cell polarity	0.0247211503997304
GO:0003730	mRNA 3'-UTR binding	0.0247211503997304
GO:0007399	nervous system development	0.0306167527140869
GO:0007163	establishment and/or maintenance of cell polarity	0.0419937964321619
GO:0003729	mRNA binding	0.0419937964321619

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	2.00e-08	25
neuronal stem cell	1.42e-07	8

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	7.99e-48	94
nervous system	7.99e-48	94
central nervous system	2.85e-46	82
neural tube	1.01e-39	57
neural rod	1.01e-39	57
future spinal cord	1.01e-39	57
neural keel	1.01e-39	57
brain	2.93e-36	69
future brain	2.93e-36	69
neurectoderm	1.34e-32	90
regional part of brain	3.78e-32	59
regional part of forebrain	8.12e-32	41
forebrain	8.12e-32	41
future forebrain	8.12e-32	41
neural plate	5.68e-31	86
presumptive neural plate	5.68e-31	86
anterior neural tube	1.33e-30	42
ectoderm	6.78e-28	173
presumptive ectoderm	6.78e-28	173
telencephalon	8.98e-27	34
gray matter	9.06e-27	34
brain grey matter	9.06e-27	34
ectoderm-derived structure	2.25e-26	169
regional part of telencephalon	7.37e-26	33
cerebral hemisphere	1.79e-25	32
pre-chordal neural plate	1.80e-23	61
regional part of cerebral cortex	3.90e-21	22
adult organism	4.69e-21	115
cerebral cortex	4.44e-20	25
pallium	4.44e-20	25
head	6.81e-20	123
neocortex	1.36e-19	20
anterior region of body	2.34e-18	129
craniocervical region	2.34e-18	129
embryo	4.70e-11	612
posterior neural tube	4.33e-10	15
chordal neural plate	4.33e-10	15
organ part	3.07e-09	219
epithelium	6.12e-09	309
embryonic structure	9.01e-09	605
developing anatomical structure	9.01e-09	605
segmental subdivision of nervous system	1.44e-08	13
cell layer	1.55e-08	312
germ layer	1.65e-08	604
embryonic tissue	1.65e-08	604
presumptive structure	1.65e-08	604
epiblast (generic)	1.65e-08	604
tube	2.27e-08	194
organism subdivision	2.40e-08	365
basal ganglion	3.13e-08	9
nuclear complex of neuraxis	3.13e-08	9
aggregate regional part of brain	3.13e-08	9
collection of basal ganglia	3.13e-08	9
cerebral subcortex	3.13e-08	9
multi-tissue structure	3.40e-08	347
temporal lobe	4.03e-08	7
nucleus of brain	4.12e-08	9
neural nucleus	4.12e-08	9
segmental subdivision of hindbrain	6.21e-08	12
hindbrain	6.21e-08	12
presumptive hindbrain	6.21e-08	12
multi-cellular organism	1.82e-07	659
organ	6.59e-07	511
gyrus	8.76e-07	6

Disease

Ontology term	p-value	n
cell type cancer	5.40e-08	143

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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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
PBX3#5090	2	10.9572563433721	0.0117453018068803	0.0428066574333046

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.