Coexpression cluster:C2163

Full id: C2163_granulocyte_acute_oral_Bronchial_amniotic_skeletal_throat

Phase1 CAGE Peaks

Hg19::chr11:72929319..72929342,+	p1@P2RY2
Hg19::chr11:72929350..72929369,+	p3@P2RY2
Hg19::chr11:72929402..72929420,+	p4@P2RY2
Hg19::chr11:72929601..72929643,+	p2@P2RY2

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><br>

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Cell Type

Ontology term	p-value	n
defensive cell	7.16e-25	48
phagocyte	7.16e-25	48
monopoietic cell	6.83e-24	59
monocyte	6.83e-24	59
monoblast	6.83e-24	59
promonocyte	6.83e-24	59
classical monocyte	8.87e-24	42
CD14-positive, CD16-negative classical monocyte	8.87e-24	42
macrophage dendritic cell progenitor	2.68e-23	61
myeloid leukocyte	2.39e-22	72
granulocyte monocyte progenitor cell	1.85e-20	67
myeloid lineage restricted progenitor cell	1.58e-19	66
myeloid cell	3.10e-18	108
common myeloid progenitor	3.10e-18	108
endo-epithelial cell	8.67e-14	42
endodermal cell	3.35e-12	58
epithelial cell	1.01e-08	253
stuff accumulating cell	1.20e-08	87
respiratory epithelial cell	5.04e-08	13
epithelial cell of alimentary canal	9.69e-07	20

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	5.76e-20	98
blood island	5.76e-20	98
hemolymphoid system	7.04e-19	108
bone marrow	7.15e-17	76
immune system	1.85e-15	93
bone element	5.49e-14	82
organ	1.83e-13	503
developing anatomical structure	2.08e-13	581
embryonic structure	2.18e-13	564
anatomical system	4.28e-13	624
anatomical group	6.22e-13	625
embryo	7.82e-13	592
skeletal element	9.95e-13	90
adult organism	1.59e-12	114
germ layer	2.18e-12	560
germ layer / neural crest	2.18e-12	560
embryonic tissue	2.18e-12	560
presumptive structure	2.18e-12	560
germ layer / neural crest derived structure	2.18e-12	560
epiblast (generic)	2.18e-12	560
multi-cellular organism	2.32e-12	656
skeletal system	1.63e-10	100
endoderm-derived structure	6.25e-10	160
endoderm	6.25e-10	160
presumptive endoderm	6.25e-10	160
lateral plate mesoderm	2.22e-09	203
digestive system	5.61e-08	145
digestive tract	5.61e-08	145
primitive gut	5.61e-08	145
respiratory system	5.85e-07	74

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
CTCF#10664	4	5.36025637307503	0.00121114538164362	0.00815859213838224
E2F1#1869	4	4.90738921487932	0.00172402235736179	0.0106283673325369
E2F6#1876	4	5.01715573169739	0.0015780219347306	0.00995211550974209
MAX#4149	4	6.45255550900712	0.000576761319564549	0.00484565806886026
MYC#4609	4	5.2222818716094	0.00134430939527274	0.00885849762968574
SMARCC1#6599	3	32.7475194897236	4.71941722862287e-05	0.000824646504835442
USF1#7391	4	6.36149927720796	0.000610501139914083	0.00507038795638067

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.