Coexpression cluster:C3028

Full id: C3028_Smooth_CD14_renal_heart_normal_meningioma_Renal

Phase1 CAGE Peaks

Hg19::chr10:6019461..6019494,-	p2@IL15RA
Hg19::chr10:6019499..6019551,-	p1@IL15RA
Hg19::chr10:6019552..6019585,-	p3@IL15RA

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

---

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

---

No GOStat results

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
CD14-positive, CD16-negative classical monocyte	6.05e-16	42
classical monocyte	9.39e-15	45
meso-epithelial cell	8.27e-13	44
lining cell	2.39e-12	57
barrier cell	2.39e-12	57
endothelial cell	5.54e-12	35
monopoietic cell	1.06e-10	63
monocyte	1.06e-10	63
monoblast	1.06e-10	63
promonocyte	1.06e-10	63
endothelial cell of vascular tree	6.81e-10	24
macrophage dendritic cell progenitor	1.51e-09	65
nongranular leukocyte	3.36e-09	119
myeloid lineage restricted progenitor cell	6.68e-09	70
squamous epithelial cell	4.42e-08	62
blood vessel endothelial cell	1.21e-07	18
embryonic blood vessel endothelial progenitor cell	1.21e-07	18
mesodermal cell	1.96e-07	119
myeloid leukocyte	2.84e-07	76
granulocyte monocyte progenitor cell	3.21e-07	71
hematopoietic lineage restricted progenitor cell	5.83e-07	124

Uber Anatomy

Ontology term	p-value	n
lateral plate mesoderm	3.42e-14	216
epithelial tube	4.68e-12	118
mesoderm	6.01e-11	448
mesoderm-derived structure	6.01e-11	448
presumptive mesoderm	6.01e-11	448
hemolymphoid system	1.84e-10	112
immune system	7.75e-10	115
circulatory system	2.93e-09	113
vessel	4.19e-09	69
cardiovascular system	1.59e-08	110
splanchnic layer of lateral plate mesoderm	6.25e-08	84
hematopoietic system	9.05e-08	102
blood island	9.05e-08	102
endothelium	1.21e-07	18
blood vessel endothelium	1.21e-07	18
cardiovascular system endothelium	1.21e-07	18
compound organ	6.11e-07	69

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
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0189059410051234
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0320249590881071
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.00759520818628811
FOS#2353	3	8.9979553088944	0.00137249927241713	0.00894604328228
FOSL1#8061	3	39.713579716373	1.59554825631833e-05	0.000370058770467756
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0108263470776253
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0127575895643762
JUNB#3726	3	30.6106326598211	3.4847716247536e-05	0.000679510947941825
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156097280893242
MAFK#7975	3	27.1007331378299	5.02195559325033e-05	0.000855887761428642
SMARCB1#6598	3	18.2527157811574	0.00016439776067989	0.00202542617997488
TFAP2A#7020	3	16.518634373045	0.000221803388076634	0.00247303555538973
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00612820260617463
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.013958423848304
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0108896689777544

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.