Coexpression cluster:C4209

Full id: C4209_amniotic_endometrioid_Placental_pancreatic_chorionic_heart_placenta

Phase1 CAGE Peaks

Hg19::chr2:241396106..241396123,-	p1@PP14571
Hg19::chr2:241396134..241396151,-	p1@ENST00000404327
Hg19::chr2:241397690..241397720,+	p16@GPC1

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:0048503	GPI anchor binding	0.0454491934534322
GO:0035091	phosphoinositide binding	0.0454491934534322
GO:0005543	phospholipid binding	0.0454491934534322
GO:0005578	proteinaceous extracellular matrix	0.0454491934534322
GO:0005615	extracellular space	0.0454491934534322
GO:0008289	lipid binding	0.0454491934534322

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
epithelial cell	4.65e-09	254
endo-epithelial cell	1.40e-07	43
kidney tubule cell	7.02e-07	12
nephron tubule epithelial cell	7.02e-07	12
germ line cell	7.20e-07	7
germ cell	7.20e-07	7

Uber Anatomy

Ontology term	p-value	n
adult organism	3.50e-20	115
organ part	7.13e-15	219
extraembryonic membrane	1.62e-13	14
membranous layer	1.62e-13	14
chorion	2.83e-10	7
anatomical space	6.71e-10	104
anterior region of body	1.05e-09	129
craniocervical region	1.05e-09	129
organ	1.41e-09	511
endoderm-derived structure	3.18e-09	169
endoderm	3.18e-09	169
presumptive endoderm	3.18e-09	169
neural tube	7.18e-09	57
neural rod	7.18e-09	57
future spinal cord	7.18e-09	57
neural keel	7.18e-09	57
anatomical conduit	1.40e-08	241
renal system	1.66e-08	45
head	2.06e-08	123
ectoderm-derived structure	2.24e-08	169
regional part of brain	2.33e-08	59
urinary system structure	5.81e-08	44
anterior neural tube	7.31e-08	42
ectoderm	7.68e-08	173
presumptive ectoderm	7.68e-08	173
duct	8.49e-08	26
multi-tissue structure	8.92e-08	347
immaterial anatomical entity	1.11e-07	126
intermediate mesoderm	1.11e-07	37
multi-cellular organism	1.33e-07	659
extraembryonic structure	1.66e-07	24
organism subdivision	1.92e-07	365
neural plate	1.92e-07	86
presumptive neural plate	1.92e-07	86
respiratory system	2.08e-07	72
gray matter	2.20e-07	34
brain grey matter	2.20e-07	34
regional part of forebrain	2.55e-07	41
forebrain	2.55e-07	41
future forebrain	2.55e-07	41
telencephalon	3.13e-07	34
cerebral hemisphere	3.24e-07	32
orifice	3.41e-07	35
urogenital ridge	3.67e-07	20
mesonephros	4.32e-07	18
pronephros	4.32e-07	18
nephrogenic cord	4.32e-07	18
pronephric mesoderm	4.32e-07	18
rostral part of nephrogenic cord	4.32e-07	18
presumptive pronephric mesoderm	4.32e-07	18
renal tubule	7.02e-07	12
nephron tubule	7.02e-07	12
nephron tubule epithelium	7.02e-07	12
reproductive structure	9.50e-07	59
reproductive system	9.50e-07	59

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.