Coexpression cluster:C883

Full id: C883_CD14_CD14CD16_Monocytederived_spleen_Macrophage_Basophils_Peripheral

Phase1 CAGE Peaks

Hg19::chr11:60145301..60145329,-	p@chr11:60145301..60145329 -
Hg19::chr11:60145332..60145348,-	p@chr11:60145332..60145348 -
Hg19::chr11:60145948..60145960,+	p2@MS4A14 p2@MS4A7
Hg19::chr11:60145967..60145978,+	p3@MS4A7
Hg19::chr11:60145997..60146040,+	p1@MS4A14 p1@MS4A7
Hg19::chr11:60146052..60146068,+	p4@MS4A7
Hg19::chr11:60146080..60146091,+	p5@MS4A7
Hg19::chr11:60150636..60150652,+	p7@MS4A7
Hg19::chr11:60161612..60161616,+	p@chr11:60161612..60161616 +

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	4.77e-43	140
nongranular leukocyte	2.20e-42	119
hematopoietic stem cell	5.60e-42	172
angioblastic mesenchymal cell	5.60e-42	172
macrophage dendritic cell progenitor	1.90e-41	65
monopoietic cell	1.44e-40	63
monocyte	1.44e-40	63
monoblast	1.44e-40	63
promonocyte	1.44e-40	63
granulocyte monocyte progenitor cell	5.79e-40	71
hematopoietic oligopotent progenitor cell	3.61e-39	165
hematopoietic multipotent progenitor cell	3.61e-39	165
hematopoietic lineage restricted progenitor cell	6.73e-39	124
myeloid leukocyte	1.62e-37	76
hematopoietic cell	7.43e-37	182
myeloid lineage restricted progenitor cell	9.07e-37	70
CD14-positive, CD16-negative classical monocyte	3.82e-36	42
myeloid cell	2.67e-34	112
common myeloid progenitor	2.67e-34	112
classical monocyte	3.30e-32	45
intermediate monocyte	3.43e-09	9
CD14-positive, CD16-positive monocyte	3.43e-09	9
lymphocyte of B lineage	1.44e-07	24
pro-B cell	1.44e-07	24

Uber Anatomy

Ontology term	p-value	n
adult organism	8.30e-47	115
hematopoietic system	4.26e-42	102
blood island	4.26e-42	102
hemolymphoid system	2.63e-37	112
bone marrow	9.89e-35	80
bone element	7.30e-31	86
immune system	6.58e-27	115
skeletal element	7.92e-24	101
skeletal system	7.92e-24	101
neural tube	6.71e-15	57
neural rod	6.71e-15	57
future spinal cord	6.71e-15	57
neural keel	6.71e-15	57
anterior neural tube	4.46e-12	42
lateral plate mesoderm	1.24e-11	216
regional part of forebrain	1.39e-11	41
forebrain	1.39e-11	41
future forebrain	1.39e-11	41
regional part of brain	3.57e-11	59
central nervous system	2.29e-09	82
gray matter	4.62e-09	34
brain grey matter	4.62e-09	34
telencephalon	5.42e-09	34
regional part of telencephalon	9.71e-09	33
neural plate	1.30e-08	86
presumptive neural plate	1.30e-08	86
musculoskeletal system	1.54e-08	167
tissue	1.76e-08	787
brain	2.67e-08	69
future brain	2.67e-08	69
cerebral hemisphere	3.28e-08	32
regional part of cerebral cortex	1.21e-07	22
neurectoderm	1.46e-07	90
regional part of nervous system	5.31e-07	94
nervous system	5.31e-07	94
neocortex	7.71e-07	20

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
BCL11A#53335	5	15.7608083908928	6.07835896292738e-06	0.000180859752629394
BCLAF1#9774	5	12.0292486722899	2.26104873625909e-05	0.000494020227962684
EBF1#1879	7	6.92725199177589	6.58055964035478e-06	0.000192727725260519
MEF2A#4205	5	10.4129060609134	4.53864389110116e-05	0.000798267816340038
NFKB1#4790	5	3.04892412455213	0.0131687302649851	0.046599207838476
PAX5#5079	7	5.18743985758276	4.62776729125731e-05	0.000812438036866066
SPI1#6688	7	6.38114050662879	1.14766724697107e-05	0.000292273151929802
SRF#6722	7	10.7311386483527	3.31352184322677e-07	1.65658644224395e-05
ZEB1#6935	5	9.3824622319688	7.48833020047875e-05	0.00116017462959175

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.