Coexpression cluster:C813

Full id: C813_CD19_CD14CD16_CD14_Macrophage_Monocytederived_pancreatic_choriocarcinoma

Phase1 CAGE Peaks

Hg19::chr12:109027413..109027428,-	p@chr12:109027413..109027428 -
Hg19::chr15:42566384..42566475,+	p2@GANC
Hg19::chr19:3178856..3178869,+	p3@S1PR4
Hg19::chr1:198609269..198609281,+	p@chr1:198609269..198609281 +
Hg19::chr3:46968478..46968499,-	p@chr3:46968478..46968499 -
Hg19::chr4:164534657..164534701,-	p1@MARCH1
Hg19::chr5:122110718..122110800,+	p1@SNX2
Hg19::chr6:36973462..36973468,+	p2@FGD2
Hg19::chr6:36973470..36973478,+	p3@FGD2
Hg19::chr7:18330064..18330080,+	p3@HDAC9

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:0004558	alpha-glucosidase activity	0.0453431196630803
GO:0045843	negative regulation of striated muscle development	0.0453431196630803
GO:0032488	Cdc42 protein signal transduction	0.0453431196630803
GO:0043088	regulation of Cdc42 GTPase activity	0.0453431196630803
GO:0032489	regulation of Cdc42 protein signal transduction	0.0453431196630803
GO:0032319	regulation of Rho GTPase activity	0.0453431196630803
GO:0016202	regulation of striated muscle development	0.0453431196630803
GO:0016566	specific transcriptional repressor activity	0.0453431196630803
GO:0015926	glucosidase activity	0.0453431196630803

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	1.17e-72	136
nongranular leukocyte	1.01e-65	115
hematopoietic stem cell	1.19e-65	168
angioblastic mesenchymal cell	1.19e-65	168
hematopoietic oligopotent progenitor cell	9.34e-61	161
hematopoietic multipotent progenitor cell	9.34e-61	161
hematopoietic lineage restricted progenitor cell	1.94e-60	120
hematopoietic cell	6.63e-60	177
macrophage dendritic cell progenitor	2.58e-49	61
monopoietic cell	2.11e-47	59
monocyte	2.11e-47	59
monoblast	2.11e-47	59
promonocyte	2.11e-47	59
granulocyte monocyte progenitor cell	2.88e-47	67
myeloid leukocyte	5.82e-47	72
myeloid lineage restricted progenitor cell	1.94e-42	66
myeloid cell	3.82e-41	108
common myeloid progenitor	3.82e-41	108
defensive cell	4.54e-41	48
phagocyte	4.54e-41	48
classical monocyte	4.76e-36	42
CD14-positive, CD16-negative classical monocyte	4.76e-36	42
lymphocyte of B lineage	5.78e-20	24
pro-B cell	5.78e-20	24
lymphocyte	1.18e-16	53
common lymphoid progenitor	1.18e-16	53
lymphoid lineage restricted progenitor cell	4.61e-16	52
nucleate cell	1.49e-15	55
B cell	1.78e-14	14
stuff accumulating cell	3.32e-14	87
dendritic cell	3.52e-11	10
intermediate monocyte	2.44e-10	9
CD14-positive, CD16-positive monocyte	2.44e-10	9
mesenchymal cell	2.68e-10	354
connective tissue cell	1.84e-09	361
conventional dendritic cell	3.39e-09	8
immature conventional dendritic cell	2.31e-07	5
common dendritic progenitor	2.31e-07	5

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	4.80e-51	98
blood island	4.80e-51	98
hemolymphoid system	1.54e-46	108
bone marrow	1.91e-41	76
immune system	1.74e-38	93
bone element	1.60e-36	82
skeletal element	4.97e-31	90
skeletal system	1.78e-26	100
adult organism	1.91e-24	114
lateral plate mesoderm	1.66e-14	203
connective tissue	1.07e-08	371
musculoskeletal system	1.07e-08	167
blood	1.81e-08	15
haemolymphatic fluid	1.81e-08	15
organism substance	1.81e-08	15

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
EBF1#1879	5	4.4532334232845	0.00275908025703869	0.0151278655483444
IRF4#3662	4	8.76580507469765	0.00072866783536506	0.00580970608883819
NFKB1#4790	6	3.2928380545163	0.0039127525205927	0.0190696700965132
SPI1#6688	6	4.92259410511364	0.000443419790230525	0.00412858335311454
SRF#6722	4	5.51887130486712	0.00405805946662648	0.019413662802208

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.