Coexpression cluster:C2095

Full id: C2095_Mast_Retinal_CD14_bile_lung_cervical_Gingival

Phase1 CAGE Peaks

Hg19::chr11:112034761..112034772,-	p4@IL18
Hg19::chr11:112034780..112034795,-	p3@IL18
Hg19::chr11:112034803..112034824,-	p1@IL18
Hg19::chr11:112034831..112034848,-	p2@IL18

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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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>disease_data<br>

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Cell Type

Ontology term	p-value	n
myeloid cell	2.98e-23	112
common myeloid progenitor	2.98e-23	112
granulocyte monocyte progenitor cell	6.51e-23	71
myeloid leukocyte	4.09e-22	76
myeloid lineage restricted progenitor cell	6.29e-22	70
macrophage dendritic cell progenitor	7.05e-21	65
monopoietic cell	7.81e-20	63
monocyte	7.81e-20	63
monoblast	7.81e-20	63
promonocyte	7.81e-20	63
classical monocyte	3.56e-15	45
CD14-positive, CD16-negative classical monocyte	1.28e-13	42
epithelial cell	1.92e-13	254
endo-epithelial cell	9.76e-13	43
endodermal cell	5.95e-09	59
mesothelial cell	6.43e-08	19
hematopoietic stem cell	2.93e-07	172
angioblastic mesenchymal cell	2.93e-07	172
hematopoietic oligopotent progenitor cell	7.55e-07	165
hematopoietic multipotent progenitor cell	7.55e-07	165

Uber Anatomy

Ontology term	p-value	n
bone marrow	3.00e-18	80
organ	1.20e-17	511
hematopoietic system	4.42e-16	102
blood island	4.42e-16	102
bone element	2.98e-14	86
hemolymphoid system	6.38e-14	112
immune system	2.21e-11	115
skeletal element	2.40e-11	101
skeletal system	2.40e-11	101
endoderm-derived structure	2.03e-10	169
endoderm	2.03e-10	169
presumptive endoderm	2.03e-10	169
subdivision of digestive tract	2.73e-09	129
endodermal part of digestive tract	2.73e-09	129
digestive system	4.53e-09	155
digestive tract	4.53e-09	155
primitive gut	4.53e-09	155
respiratory tract	1.73e-08	53
respiratory system	3.58e-08	72
respiratory primordium	1.03e-07	38
endoderm of foregut	1.03e-07	38
larynx	3.02e-07	9
adult organism	3.35e-07	115
segment of respiratory tract	9.40e-07	46
foregut	9.51e-07	98

Disease

Ontology term	p-value	n
carcinoma	1.08e-10	106
squamous cell carcinoma	5.90e-07	14

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
CEBPB#1051	4	7.97114762582482	0.000247638578809083	0.00267512676171305
CTCF#10664	4	5.36025637307503	0.00121114538164362	0.00815491022587056
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0160528546879233
GATA3#2625	4	27.236516357206	1.81561517799785e-06	6.74567888918239e-05
GTF2F1#2962	4	12.7396608767577	3.79492332235515e-05	0.000716446125928145
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0185492598433945
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.032118301949735
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0243452490030484

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.