Coexpression cluster:C2707

Full id: C2707_Neutrophils_Eosinophils_CD14_Mesenchymal_blood_Whole_heart

Phase1 CAGE Peaks

Hg19::chr2:96931679..96931756,-	p1@TMEM127
Hg19::chr3:122513887..122513992,+	p1@DIRC2
Hg19::chr3:122513994..122514005,+	p6@DIRC2
Hg19::chr9:33817124..33817197,+	p1@UBE2R2

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	6.71e-27	42
classical monocyte	5.96e-26	45
monopoietic cell	6.08e-26	63
monocyte	6.08e-26	63
monoblast	6.08e-26	63
promonocyte	6.08e-26	63
myeloid leukocyte	1.05e-25	76
macrophage dendritic cell progenitor	1.72e-25	65
granulocyte monocyte progenitor cell	1.89e-21	71
myeloid lineage restricted progenitor cell	2.94e-19	70

Uber Anatomy

Ontology term	p-value	n
anatomical system	5.79e-21	625
multi-cellular organism	1.34e-20	659
anatomical group	1.57e-20	626
embryonic structure	2.35e-18	605
developing anatomical structure	2.35e-18	605
germ layer	2.81e-18	604
embryonic tissue	2.81e-18	604
presumptive structure	2.81e-18	604
epiblast (generic)	2.81e-18	604
hematopoietic system	1.38e-17	102
blood island	1.38e-17	102
hemolymphoid system	1.50e-17	112
embryo	1.88e-17	612
organ	3.39e-17	511
bone marrow	4.40e-17	80
immune system	1.99e-16	115
bone element	4.40e-15	86
skeletal element	2.95e-13	101
skeletal system	2.95e-13	101
lateral plate mesoderm	5.23e-13	216
adult organism	7.28e-11	115
mesoderm	1.13e-09	448
mesoderm-derived structure	1.13e-09	448
presumptive mesoderm	1.13e-09	448
musculoskeletal system	9.75e-07	167

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
BRCA1#672	3	15.1381729824178	0.000468218442143119	0.00430308569860834
E2F1#1869	4	4.90738921487932	0.00172402235736179	0.0106642484589261
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0161155643328409
EP300#2033	3	5.0804562946674	0.0114429840539824	0.0419066488398157
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0186401184016915
NRF1#4899	4	12.2102794477109	4.49717228915276e-05	0.000794721111179061
STAT1#6772	3	15.5299406228994	0.00043408865517555	0.00405145532241995
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0322819936816796
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0244680144467759

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.