Coexpression cluster:C1019

Full id: C1019_occipital_medial_amygdala_caudate_hippocampus_cerebellum_parietal

Phase1 CAGE Peaks

Hg19::chr12:53535758..53535789,+	p1@HIGD1AP1
Hg19::chr12:6773757..6773767,+	p@chr12:6773757..6773767 +
Hg19::chr13:41745362..41745368,-	p1@CALM2P3
Hg19::chr15:90808919..90808930,+	p2@NGRN
Hg19::chr17:43697693..43697718,+	p3@CRHR1
Hg19::chr2:130737223..130737244,+	p1@RAB6C
Hg19::chr7:72569000..72569055,+	p1@GTF2IP1
Hg19::chr9:116843080..116843085,+	p@chr9:116843080..116843085 +

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	0.0169536422372063
GO:0001636	corticotrophin-releasing factor gastric inhibitory peptide-like receptor activity	0.0169536422372063
GO:0007567	parturition	0.0226021946511821
GO:0007190	adenylate cyclase activation	0.0296356973517762
GO:0031281	positive regulation of cyclase activity	0.0296356973517762
GO:0051349	positive regulation of lyase activity	0.0296356973517762
GO:0045762	positive regulation of adenylate cyclase activity	0.0296356973517762
GO:0007189	G-protein signaling, adenylate cyclase activating pathway	0.0296356973517762
GO:0001633	secretin-like receptor activity	0.0296356973517762
GO:0045761	regulation of adenylate cyclase activity	0.0296356973517762
GO:0031279	regulation of cyclase activity	0.0296356973517762
GO:0051339	regulation of lyase activity	0.0296356973517762
GO:0042493	response to drug	0.041008671075108
GO:0007565	female pregnancy	0.0459801856340502
GO:0007188	G-protein signaling, coupled to cAMP nucleotide second messenger	0.0459801856340502
GO:0019933	cAMP-mediated signaling	0.0459801856340502

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
classical monocyte	9.10e-13	45
CD14-positive, CD16-negative classical monocyte	1.07e-12	42
granulocyte monocyte progenitor cell	2.83e-09	71
myeloid lineage restricted progenitor cell	3.20e-09	70
myeloid leukocyte	5.07e-09	76
macrophage dendritic cell progenitor	2.62e-08	65
monopoietic cell	1.01e-07	63
monocyte	1.01e-07	63
monoblast	1.01e-07	63
promonocyte	1.01e-07	63

Uber Anatomy

Ontology term	p-value	n
neural tube	3.99e-14	57
neural rod	3.99e-14	57
future spinal cord	3.99e-14	57
neural keel	3.99e-14	57
central nervous system	9.04e-13	82
anterior neural tube	2.04e-12	42
regional part of forebrain	2.06e-12	41
forebrain	2.06e-12	41
future forebrain	2.06e-12	41
regional part of brain	1.04e-11	59
brain	5.86e-11	69
future brain	5.86e-11	69
regional part of nervous system	6.55e-11	94
nervous system	6.55e-11	94
gray matter	7.06e-11	34
brain grey matter	7.06e-11	34
telencephalon	3.04e-10	34
regional part of telencephalon	4.07e-10	33
cerebral hemisphere	5.16e-10	32
bone marrow	1.25e-08	80
regional part of cerebral cortex	2.58e-08	22
neural plate	2.94e-08	86
presumptive neural plate	2.94e-08	86
adult organism	3.52e-08	115
cerebral cortex	5.33e-08	25
pallium	5.33e-08	25
pre-chordal neural plate	6.91e-08	61
neocortex	1.62e-07	20
bone element	1.94e-07	86
neurectoderm	2.12e-07	90
skeletal element	6.40e-07	101
skeletal system	6.40e-07	101

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)
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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.