Coexpression cluster:C1469

Full id: C1469_kidney_amniotic_liver_Hepatocyte_Placental_Amniotic_tongue

Phase1 CAGE Peaks

Hg19::chr1:204120903..204120917,-	p6@ETNK2
Hg19::chr1:204120920..204120929,-	p12@ETNK2
Hg19::chr1:204120931..204120942,-	p10@ETNK2
Hg19::chr1:204120945..204120958,-	p11@ETNK2
Hg19::chr1:47603109..47603120,+	p1@CYP4A22
Hg19::chr2:135595876..135595891,+	p3@ACMSD

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

---

p.value	FDR	nGenes	nPathway	Name
6.31961929821581e-05	0.0400031901577061	3	1138	Metabolic pathways (KEGG):01100

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

---

GO ID	GO name	FDR corrected p-value
GO:0046874	quinolinate metabolic process	0.00141292829388908
GO:0001760	aminocarboxymuconate-semialdehyde decarboxylase activity	0.00141292829388908
GO:0004305	ethanolamine kinase activity	0.00211926766548736
GO:0004103	choline kinase activity	0.00211926766548736
GO:0043648	dicarboxylic acid metabolic process	0.00903874877915148
GO:0016831	carboxy-lyase activity	0.0263319827971826
GO:0016830	carbon-carbon lyase activity	0.0330240233239064

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>

---

Cell Type

Ontology term	p-value	n
extraembryonic cell	9.00e-12	19
placental epithelial cell	9.73e-08	3
astrocyte of the cerebellum	7.92e-07	3

Uber Anatomy

Ontology term	p-value	n
extraembryonic membrane	4.54e-14	14
membranous layer	4.54e-14	14
abdomen element	4.12e-10	54
abdominal segment element	4.12e-10	54
gland	1.35e-09	59
reproductive structure	1.39e-09	59
reproductive system	1.39e-09	59
endoderm-derived structure	1.43e-09	160
endoderm	1.43e-09	160
presumptive endoderm	1.43e-09	160
male organism	6.54e-09	22
male reproductive system	6.54e-09	22
extraembryonic structure	9.65e-09	24
male reproductive organ	1.07e-08	11
subdivision of digestive tract	1.26e-08	118
abdominal segment of trunk	1.41e-08	60
abdomen	1.41e-08	60
digestive system	1.82e-08	145
digestive tract	1.82e-08	145
primitive gut	1.82e-08	145
reproductive organ	3.76e-08	48
organ	3.83e-08	503
urinary system structure	4.18e-08	47
amnion	4.59e-08	7
trunk region element	4.82e-08	101
renal system	7.52e-08	48
adult organism	7.66e-08	114
liver	9.05e-08	19
digestive gland	9.05e-08	19
liver bud	9.05e-08	19
chorion	1.26e-07	7
exocrine gland	1.63e-07	31
exocrine system	1.63e-07	31
gut epithelium	2.01e-07	54
mixed endoderm/mesoderm-derived structure	2.35e-07	29
organ system subdivision	4.89e-07	223
somatic layer of lateral plate mesoderm	5.59e-07	8
immaterial anatomical entity	5.83e-07	117
endocrine gland	6.90e-07	35
segmental subdivision of hindbrain	8.03e-07	12
hindbrain	8.03e-07	12
presumptive hindbrain	8.03e-07	12

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

---

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

---

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

TF	#promoters	Enrichment	p-value	q-value
CEBPB#1051	4	5.31409841721654	0.00300804729391746	0.0159811502354993
NR3C1#2908	4	9.98201555411536	0.000267321918040192	0.00286082936757861
ZBTB7A#51341	4	4.90127287191726	0.00407962811884375	0.0194891721299022

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

---

This analysis result is provided for C0 - C305 clusters.