Coexpression cluster:C1238

Full id: C1238_CD34_CD14_Eosinophils_CD8_Natural_CD19_Peripheral

Phase1 CAGE Peaks

Hg19::chr19:1248314..1248335,+	p9@MIDN
Hg19::chr1:2222149..2222184,-	p@chr1:2222149..2222184 -
Hg19::chr1:2232428..2232442,-	p@chr1:2232428..2232442 -
Hg19::chr1:2232455..2232495,-	p@chr1:2232455..2232495 -
Hg19::chr1:2232583..2232594,-	p@chr1:2232583..2232594 -
Hg19::chr3:114866901..114866924,+	p@chr3:114866901..114866924 +
Hg19::chr8:41997529..41997538,+	p@chr8:41997529..41997538 +

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	8.12e-59	136
hematopoietic stem cell	1.07e-50	168
angioblastic mesenchymal cell	1.07e-50	168
hematopoietic cell	3.62e-47	177
hematopoietic lineage restricted progenitor cell	1.49e-46	120
classical monocyte	4.40e-46	42
CD14-positive, CD16-negative classical monocyte	4.40e-46	42
myeloid leukocyte	1.40e-45	72
nongranular leukocyte	1.98e-43	115
hematopoietic oligopotent progenitor cell	8.90e-43	161
hematopoietic multipotent progenitor cell	8.90e-43	161
granulocyte monocyte progenitor cell	1.91e-39	67
defensive cell	4.48e-39	48
phagocyte	4.48e-39	48
myeloid lineage restricted progenitor cell	4.89e-38	66
myeloid cell	3.33e-32	108
common myeloid progenitor	3.33e-32	108
macrophage dendritic cell progenitor	3.77e-32	61
monopoietic cell	1.73e-31	59
monocyte	1.73e-31	59
monoblast	1.73e-31	59
promonocyte	1.73e-31	59
intermediate monocyte	5.51e-19	9
CD14-positive, CD16-positive monocyte	5.51e-19	9
stuff accumulating cell	2.67e-17	87
mesenchymal cell	2.33e-14	354
CD4-positive, alpha-beta T cell	6.89e-14	6
connective tissue cell	9.80e-14	361
histamine secreting cell	1.28e-11	5
biogenic amine secreting cell	1.28e-11	5
granulocytopoietic cell	1.28e-11	5
mast cell	1.28e-11	5
mast cell progenitor	1.28e-11	5
basophil mast progenitor cell	1.28e-11	5
motile cell	1.49e-11	386
T cell	1.77e-10	25
pro-T cell	1.77e-10	25
lymphoid lineage restricted progenitor cell	5.69e-10	52
stem cell	7.36e-10	441
lymphocyte	1.08e-09	53
common lymphoid progenitor	1.08e-09	53
mature alpha-beta T cell	3.05e-09	18
alpha-beta T cell	3.05e-09	18
immature T cell	3.05e-09	18
mature T cell	3.05e-09	18
immature alpha-beta T cell	3.05e-09	18
nucleate cell	3.60e-09	55
multi fate stem cell	6.30e-09	427
somatic stem cell	1.43e-08	433
natural killer cell	2.65e-08	3
pro-NK cell	2.65e-08	3
single nucleate cell	6.38e-08	3
mononuclear cell	6.38e-08	3
basophil	6.53e-08	3
naive T cell	2.04e-07	3
plasmacytoid dendritic cell	2.96e-07	3
granulocyte	4.49e-07	8
non-classical monocyte	9.30e-07	3
CD14-low, CD16-positive monocyte	9.30e-07	3

Uber Anatomy

Ontology term	p-value	n
bone marrow	1.50e-35	76
hematopoietic system	1.47e-33	98
blood island	1.47e-33	98
bone element	4.12e-32	82
immune system	2.90e-30	93
hemolymphoid system	2.87e-29	108
skeletal element	3.04e-28	90
skeletal system	2.75e-24	100
connective tissue	6.91e-13	371
musculoskeletal system	2.90e-10	167
lateral plate mesoderm	5.89e-10	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
EBF1#1879	5	6.36176203326358	0.000307843991861182	0.00316976423799566
ELF1#1997	5	3.04149854200538	0.00971956226937075	0.036568369316287
FOS#2353	6	7.71253312190949	1.19258382729196e-05	0.000301433355127166
FOSL1#8061	2	11.3467370618209	0.0122366479067572	0.0443651763776231
PAX5#5079	5	4.76397537941274	0.00121882104700747	0.00820130476956465
RFX5#5993	4	6.88452047268291	0.00135220703152858	0.0089037986360137
SPI1#6688	4	4.68818486201299	0.00568568052914417	0.0256681416436106

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.