Coexpression cluster:C2412

Full id: C2412_neuroblastoma_cerebellum_Neurons_migratory_thalamus_parietal_amygdala

Phase1 CAGE Peaks

Hg19::chr17:43861598..43861616,+	p4@CRHR1
Hg19::chr17:43861631..43861669,+	p2@CRHR1
Hg19::chr17:43861680..43861705,+	p1@CRHR1
Hg19::chr7:31726822..31726846,+	p1@PPP1R17

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:0015056	corticotrophin-releasing factor receptor activity	0.00264924055104203
GO:0001636	corticotrophin-releasing factor gastric inhibitory peptide-like receptor activity	0.00264924055104203
GO:0007567	parturition	0.00353232073472271
GO:0007190	adenylate cyclase activation	0.00463617096432356
GO:0031281	positive regulation of cyclase activity	0.00463617096432356
GO:0045762	positive regulation of adenylate cyclase activity	0.00463617096432356
GO:0051349	positive regulation of lyase activity	0.00463617096432356
GO:0007189	G-protein signaling, adenylate cyclase activating pathway	0.00463617096432356
GO:0001633	secretin-like receptor activity	0.00463617096432356
GO:0045761	regulation of adenylate cyclase activity	0.00463617096432356
GO:0031279	regulation of cyclase activity	0.00463617096432356
GO:0051339	regulation of lyase activity	0.00463617096432356
GO:0007565	female pregnancy	0.0076827975980219
GO:0007188	G-protein signaling, coupled to cAMP nucleotide second messenger	0.0076827975980219
GO:0019933	cAMP-mediated signaling	0.0076827975980219
GO:0007187	G-protein signaling, coupled to cyclic nucleotide second messenger	0.00950609844785671
GO:0019935	cyclic-nucleotide-mediated signaling	0.00950609844785671
GO:0043085	positive regulation of catalytic activity	0.018684117570507
GO:0019932	second-messenger-mediated signaling	0.018684117570507
GO:0022414	reproductive process	0.0202004592016955
GO:0051704	multi-organism process	0.0210046929404047
GO:0050790	regulation of catalytic activity	0.036427057576828
GO:0065009	regulation of a molecular function	0.0386443567336784

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
CD14-positive, CD16-negative classical monocyte	1.12e-21	42
classical monocyte	2.30e-19	45
myeloid lineage restricted progenitor cell	8.24e-12	70
monopoietic cell	1.62e-11	63
monocyte	1.62e-11	63
monoblast	1.62e-11	63
promonocyte	1.62e-11	63
granulocyte monocyte progenitor cell	1.79e-11	71
macrophage dendritic cell progenitor	8.11e-11	65
myeloid leukocyte	9.64e-11	76
neuronal stem cell	3.25e-08	8

Uber Anatomy

Ontology term	p-value	n
central nervous system	4.89e-44	82
regional part of nervous system	1.74e-40	94
nervous system	1.74e-40	94
neural tube	9.52e-40	57
neural rod	9.52e-40	57
future spinal cord	9.52e-40	57
neural keel	9.52e-40	57
adult organism	4.87e-36	115
brain	2.60e-33	69
future brain	2.60e-33	69
regional part of brain	1.45e-32	59
neurectoderm	2.59e-32	90
regional part of forebrain	1.76e-31	41
forebrain	1.76e-31	41
future forebrain	1.76e-31	41
neural plate	1.96e-30	86
presumptive neural plate	1.96e-30	86
anterior neural tube	2.25e-30	42
telencephalon	3.16e-27	34
gray matter	4.39e-27	34
brain grey matter	4.39e-27	34
regional part of telencephalon	3.34e-26	33
cerebral hemisphere	1.80e-25	32
regional part of cerebral cortex	5.49e-22	22
cerebral cortex	8.67e-22	25
pallium	8.67e-22	25
pre-chordal neural plate	8.50e-21	61
neocortex	4.19e-20	20
ectoderm	7.64e-20	173
presumptive ectoderm	7.64e-20	173
ectoderm-derived structure	2.27e-18	169
anterior region of body	1.85e-14	129
craniocervical region	1.85e-14	129
head	3.65e-14	123
embryo	1.00e-11	612
posterior neural tube	2.52e-10	15
chordal neural plate	2.52e-10	15
hematopoietic system	5.39e-10	102
blood island	5.39e-10	102
embryonic structure	3.63e-09	605
developing anatomical structure	3.63e-09	605
segmental subdivision of nervous system	6.04e-09	13
bone marrow	7.24e-09	80
germ layer	7.97e-09	604
embryonic tissue	7.97e-09	604
presumptive structure	7.97e-09	604
epiblast (generic)	7.97e-09	604
organ	1.31e-08	511
hemolymphoid system	2.48e-08	112
segmental subdivision of hindbrain	4.01e-08	12
hindbrain	4.01e-08	12
presumptive hindbrain	4.01e-08	12
bone element	6.24e-08	86
multi-cellular organism	6.40e-08	659
gyrus	1.45e-07	6
temporal lobe	3.67e-07	7
basal ganglion	6.97e-07	9
nuclear complex of neuraxis	6.97e-07	9
aggregate regional part of brain	6.97e-07	9
collection of basal ganglia	6.97e-07	9
cerebral subcortex	6.97e-07	9
nucleus of brain	8.40e-07	9
neural nucleus	8.40e-07	9

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
ZNF263#10127	3	6.16638122775801	0.00653981434797598	0.0279693558840403

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.