Coexpression cluster:C1809

Full id: C1809_CD4_Peripheral_normal_Neutrophils_CD8_Natural_CD14

Phase1 CAGE Peaks

Hg19::chr19:12902603..12902655,-	p@chr19:12902603..12902655 -
Hg19::chr19:12902681..12902688,-	p@chr19:12902681..12902688 -
Hg19::chr19:12903127..12903178,-	p1@CU678639 p1@CU679368
Hg19::chr19:12903214..12903252,-	p3@CU678639 p3@CU679368
Hg19::chr19:12903367..12903458,-	p2@CU678639 p2@CU679368

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
leukocyte	7.90e-24	136
myeloid leukocyte	4.29e-23	72
defensive cell	1.32e-20	48
phagocyte	1.32e-20	48
macrophage dendritic cell progenitor	3.13e-19	61
nongranular leukocyte	3.22e-19	115
granulocyte monocyte progenitor cell	9.77e-19	67
classical monocyte	1.17e-18	42
CD14-positive, CD16-negative classical monocyte	1.17e-18	42
monopoietic cell	1.18e-18	59
monocyte	1.18e-18	59
monoblast	1.18e-18	59
promonocyte	1.18e-18	59
hematopoietic lineage restricted progenitor cell	1.20e-18	120
myeloid lineage restricted progenitor cell	2.08e-18	66
hematopoietic stem cell	2.77e-15	168
angioblastic mesenchymal cell	2.77e-15	168
hematopoietic cell	6.94e-15	177
hematopoietic oligopotent progenitor cell	1.40e-13	161
hematopoietic multipotent progenitor cell	1.40e-13	161
myeloid cell	1.33e-11	108
common myeloid progenitor	1.33e-11	108
stuff accumulating cell	4.47e-10	87
intermediate monocyte	9.45e-07	9
CD14-positive, CD16-positive monocyte	9.45e-07	9

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	9.81e-24	98
blood island	9.81e-24	98
hemolymphoid system	3.84e-21	108
bone marrow	2.51e-17	76
skeletal element	9.65e-16	90
bone element	1.12e-15	82
immune system	4.23e-15	93
skeletal system	6.52e-14	100
blood	5.27e-08	15
haemolymphatic fluid	5.27e-08	15
organism substance	5.27e-08	15
lateral plate mesoderm	3.15e-07	203

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
ETS1#2113	5	9.72876092220234	1.14685159850452e-05	0.000292207938756315
GABPB1#2553	5	7.06768383618217	5.6685482528729e-05	0.000948290102485652
MAX#4149	4	5.1620444072057	0.00252630900948518	0.0139985773897295
NANOG#79923	3	17.5468670886076	0.000379420009068183	0.00376139025411219
NR2C2#7182	3	19.5687665431445	0.000275017170096661	0.00293146746557717
TAF7#6879	3	6.85984164295435	0.00584328640701904	0.0262469136408181
TCF12#6938	3	6.38067894131185	0.00718516865325884	0.0298315177490638
TCF7L2#6934	3	6.46210593788241	0.00693010875568919	0.0293227577010664
USF1#7391	4	5.08919942176637	0.0026686777536004	0.0147195160236743
USF2#7392	4	10.3937579080557	0.000164617972868753	0.00202646587322486

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.