Coexpression cluster:C2369

Full id: C2369_CD14CD16_Natural_CD8_CD14_Basophils_CD4_Whole

Phase1 CAGE Peaks

Hg19::chr16:30484054..30484084,+	p1@ITGAL
Hg19::chr8:21771173..21771178,-	p2@DOK2
Hg19::chr8:21771182..21771208,-	p1@DOK2
Hg19::chr8:21771214..21771223,-	p4@DOK2

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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GO ID	GO name	FDR corrected p-value
GO:0005069	transmembrane receptor protein tyrosine kinase docking protein activity	0.00847732021019322
GO:0005066	transmembrane receptor protein tyrosine kinase signaling protein activity	0.012714857326154
GO:0005158	insulin receptor binding	0.021657885290216
GO:0008305	integrin complex	0.038793191786861
GO:0007229	integrin-mediated signaling pathway	0.038793191786861
GO:0007166	cell surface receptor linked signal transduction	0.038793191786861
GO:0032403	protein complex binding	0.038793191786861
GO:0043235	receptor complex	0.038793191786861
GO:0005057	receptor signaling protein activity	0.0493003668503964
GO:0004871	signal transducer activity	0.0493003668503964
GO:0060089	molecular transducer activity	0.0493003668503964
GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	0.0493003668503964

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
hematopoietic stem cell	7.65e-79	172
angioblastic mesenchymal cell	7.65e-79	172
hematopoietic oligopotent progenitor cell	1.94e-74	165
hematopoietic multipotent progenitor cell	1.94e-74	165
hematopoietic cell	9.46e-74	182
leukocyte	1.82e-66	140
nongranular leukocyte	3.99e-56	119
hematopoietic lineage restricted progenitor cell	4.24e-56	124
myeloid cell	6.07e-47	112
common myeloid progenitor	6.07e-47	112
myeloid leukocyte	1.95e-35	76
granulocyte monocyte progenitor cell	2.11e-31	71
myeloid lineage restricted progenitor cell	8.20e-31	70
macrophage dendritic cell progenitor	1.16e-29	65
monopoietic cell	3.82e-29	63
monocyte	3.82e-29	63
monoblast	3.82e-29	63
promonocyte	3.82e-29	63
CD14-positive, CD16-negative classical monocyte	2.13e-26	42
classical monocyte	7.82e-24	45
lymphocyte	5.37e-23	53
common lymphoid progenitor	5.37e-23	53
lymphoid lineage restricted progenitor cell	8.85e-23	52
T cell	9.75e-16	25
pro-T cell	9.75e-16	25
mesenchymal cell	1.23e-14	358
mature alpha-beta T cell	1.69e-13	18
alpha-beta T cell	1.69e-13	18
immature T cell	1.69e-13	18
mature T cell	1.69e-13	18
immature alpha-beta T cell	1.69e-13	18
connective tissue cell	1.73e-13	365
motile cell	1.05e-09	390
CD8-positive, alpha-beta T cell	4.09e-09	11
intermediate monocyte	2.25e-08	9
CD14-positive, CD16-positive monocyte	2.25e-08	9
lymphocyte of B lineage	5.83e-07	24
pro-B cell	5.83e-07	24

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	8.30e-41	102
blood island	8.30e-41	102
hemolymphoid system	3.51e-36	112
bone marrow	1.20e-27	80
bone element	4.48e-24	86
immune system	3.69e-22	115
adult organism	2.01e-17	115
skeletal element	3.61e-17	101
skeletal system	3.61e-17	101
connective tissue	4.94e-12	375
lateral plate mesoderm	2.39e-10	216
blood	2.49e-10	15
haemolymphatic fluid	2.49e-10	15
organism substance	2.49e-10	15

Disease

Ontology term	p-value	n
hematologic cancer	1.70e-13	51
immune system cancer	1.70e-13	51
leukemia	1.82e-12	39
myeloid leukemia	1.41e-10	31

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
MEF2A#4205	4	18.7432309096441	8.0978922767748e-06	0.000224392616474949
SPI1#6688	4	8.20432350852273	0.00022066188152768	0.00249385415483924
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0321850656846371
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0243914102918363
ZEB1#6935	3	12.6663240131579	0.00079333607591285	0.00613151975373804

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.