Coexpression cluster:C3240

Full id: C3240_immature_CD14_Mast_Hair_Basophils_CD34_embryonic

Phase1 CAGE Peaks

Hg19::chr12:111843149..111843189,-	p@chr12:111843149..111843189 -
Hg19::chr17:75319211..75319234,-	p@chr17:75319211..75319234 -
Hg19::chr3:5022272..5022321,+	p7@BHLHE40

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	1.99e-22	42
classical monocyte	4.12e-20	45
myeloid leukocyte	3.36e-19	76
granulocyte monocyte progenitor cell	1.31e-17	71
myeloid lineage restricted progenitor cell	1.74e-17	70
mesenchymal cell	9.07e-17	358
connective tissue cell	4.17e-16	365
macrophage dendritic cell progenitor	1.38e-15	65
leukocyte	5.09e-15	140
motile cell	7.84e-15	390
monopoietic cell	1.89e-14	63
monocyte	1.89e-14	63
monoblast	1.89e-14	63
promonocyte	1.89e-14	63
somatic cell	8.74e-14	591
multi fate stem cell	1.17e-13	430
somatic stem cell	5.39e-13	436
myeloid cell	5.83e-13	112
common myeloid progenitor	5.83e-13	112
stem cell	1.52e-12	444
animal cell	1.91e-11	679
eukaryotic cell	1.91e-11	679
hematopoietic lineage restricted progenitor cell	3.04e-11	124
hematopoietic cell	3.24e-11	182
hematopoietic stem cell	3.33e-10	172
angioblastic mesenchymal cell	3.33e-10	172
nongranular leukocyte	3.12e-09	119
hematopoietic oligopotent progenitor cell	3.76e-09	165
hematopoietic multipotent progenitor cell	3.76e-09	165
native cell	2.34e-08	722

Uber Anatomy

Ontology term	p-value	n
bone marrow	3.66e-16	80
connective tissue	6.63e-16	375
bone element	1.06e-15	86
skeletal element	8.08e-14	101
skeletal system	8.08e-14	101
lateral plate mesoderm	1.72e-11	216
hematopoietic system	4.01e-11	102
blood island	4.01e-11	102
immune system	1.18e-09	115
hemolymphoid system	1.84e-09	112
musculoskeletal system	9.08e-09	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
BATF#10538	2	16.2385345282024	0.00491746240780997	0.022993143642965
CTCF#10664	3	5.36025637307503	0.006492509252767	0.027856017330118
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.032074646779179
EBF1#1879	3	8.906466846569	0.0014152328356098	0.00912830423161144
JUNB#3726	2	20.4070884398808	0.00313146219943874	0.0164452547215358
JUND#3727	3	6.99466394187103	0.00292184504273499	0.0156265144622183
NR3C1#2908	2	9.98201555411536	0.0127847436554717	0.0460152959518148
RXRA#6256	2	13.3830780927555	0.00719643442946573	0.0298178376330624
SMARCB1#6598	3	18.2527157811574	0.00016439776067989	0.00202638235898112
SMC3#9126	2	10.0299552299552	0.012665637976747	0.0457157962555203
TFAP2A#7020	2	11.0124229153633	0.0105499065521556	0.0389970160119128
YY1#7528	3	4.91117074985386	0.00844145534180826	0.032820235069731
ZEB1#6935	2	11.2589546783626	0.0101022267664633	0.0378010985368729

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.