Coexpression cluster:C2769

Full id: C2769_CD14_amniotic_chorionic_immature_Mast_Smooth_granulosa

Phase1 CAGE Peaks

Hg19::chr4:108745993..108746041,+	p5@SGMS2
Hg19::chr4:108746054..108746072,+	p6@SGMS2
Hg19::chr4:108746081..108746096,+	p3@SGMS2
Hg19::chr4:108746105..108746178,+	p1@SGMS2

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
CD14-positive, CD16-negative classical monocyte	8.49e-18	42
classical monocyte	2.71e-16	45
macrophage dendritic cell progenitor	1.39e-11	65
granulocyte monocyte progenitor cell	1.51e-11	71
monopoietic cell	1.15e-10	63
monocyte	1.15e-10	63
monoblast	1.15e-10	63
promonocyte	1.15e-10	63
myeloid leukocyte	7.06e-10	76
animal cell	9.50e-10	679
eukaryotic cell	9.50e-10	679
myeloid lineage restricted progenitor cell	2.01e-09	70
somatic cell	2.98e-09	591

Uber Anatomy

Ontology term	p-value	n
mesoderm	1.26e-25	448
mesoderm-derived structure	1.26e-25	448
presumptive mesoderm	1.26e-25	448
anatomical group	1.57e-20	626
anatomical system	2.24e-20	625
multi-cellular organism	5.31e-19	659
musculoskeletal system	1.91e-18	167
organ	1.37e-15	511
germ layer	4.42e-15	604
embryonic tissue	4.42e-15	604
presumptive structure	4.42e-15	604
epiblast (generic)	4.42e-15	604
embryonic structure	4.46e-15	605
developing anatomical structure	4.46e-15	605
skeletal element	6.21e-14	101
skeletal system	6.21e-14	101
embryo	9.24e-14	612
bone element	4.61e-12	86
bone marrow	2.98e-11	80
lateral plate mesoderm	2.26e-10	216

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	0.00268428910557777
CTCF#10664	4	5.36025637307503	0.00121114538164362	0.00818975801317438
E2F1#1869	4	4.90738921487932	0.00172402235736179	0.0106699360581042
EGR1#1958	4	4.98817909481014	0.00161501150007605	0.0101596305298424
EP300#2033	4	6.7739417262232	0.000474845982144264	0.00434945093221933
FOS#2353	4	8.9979553088944	0.000152514771116863	0.00195226010303641
FOSL2#2355	4	16.9302006045617	1.2165416097647e-05	0.000304176177118065
FOXA1#3169	4	11.0814197493855	6.62943068949433e-05	0.00107244596000635
GATA2#2624	3	9.5586988001655	0.00181815161835744	0.010905463868001
GATA3#2625	4	27.236516357206	1.81561517799785e-06	6.78186815360934e-05
JUN#3725	4	12.5128291923363	4.07770316866756e-05	0.00074453014201481
JUND#3727	4	6.99466394187103	0.00041768421781858	0.00392218324265012
MYC#4609	4	5.2222818716094	0.00134430939527274	0.00889047169027921
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.032298205135995
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0244810091877965

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.