Coexpression cluster:C623

Full id: C623_Dendritic_Neutrophils_Eosinophils_Whole_Macrophage_CD14_Basophils

Phase1 CAGE Peaks

Hg19::chr11:85779986..85780014,-	p3@PICALM
Hg19::chr11:85780015..85780042,-	p2@PICALM
Hg19::chr12:15114191..15114233,-	p5@ARHGDIB
Hg19::chr12:8276205..8276219,+	p2@CLEC4A
Hg19::chr12:8276224..8276237,+	p3@CLEC4A
Hg19::chr14:93581500..93581509,-	p12@ITPK1
Hg19::chr16:28192360..28192372,-	p3@AB384470
Hg19::chr16:31271322..31271339,+	p2@ITGAM
Hg19::chr16:8738211..8738249,+	p@chr16:8738211..8738249 +
Hg19::chr16:8738462..8738501,+	p@chr16:8738462..8738501 +
Hg19::chr16:90023641..90023698,+	p@chr16:90023641..90023698 +
Hg19::chr3:149531627..149531651,+	p7@RNF13
Hg19::chr5:142193841..142193874,+	p@chr5:142193841..142193874 +
Hg19::chr8:38662960..38663003,+	p9@TACC1

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:0035300	inositol trisphosphate 5/6-kinase activity	0.0113730683144134
GO:0043647	inositol phosphate metabolic process	0.0113730683144134
GO:0051765	inositol tetrakisphosphate kinase activity	0.0113730683144134
GO:0032957	inositol trisphosphate metabolic process	0.0113730683144134
GO:0047325	inositol tetrakisphosphate 1-kinase activity	0.0113730683144134
GO:0022610	biological adhesion	0.0142547691685994
GO:0007155	cell adhesion	0.0142547691685994
GO:0001948	glycoprotein binding	0.0213169715519573
GO:0048268	clathrin cage assembly	0.0227340873511213
GO:0006901	vesicle coating	0.0227340873511213
GO:0006900	membrane budding	0.02324871800575
GO:0030276	clathrin binding	0.0260425749057417
GO:0006020	inositol metabolic process	0.0266215290817958
GO:0051766	inositol trisphosphate kinase activity	0.0266215290817958
GO:0031410	cytoplasmic vesicle	0.0266215290817958
GO:0031982	vesicle	0.0266215290817958
GO:0016050	vesicle organization and biogenesis	0.0266215290817958
GO:0000287	magnesium ion binding	0.0266215290817958
GO:0005545	phosphatidylinositol binding	0.0269705183200261
GO:0005094	Rho GDP-dissociation inhibitor activity	0.0269705183200261
GO:0007162	negative regulation of cell adhesion	0.0351278293777307
GO:0005092	GDP-dissociation inhibitor activity	0.036104050016986
GO:0006898	receptor-mediated endocytosis	0.0487274734501486
GO:0044459	plasma membrane part	0.0487274734501486
GO:0005905	coated pit	0.0487274734501486

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
myeloid leukocyte	3.78e-66	72
macrophage dendritic cell progenitor	2.71e-62	61
monopoietic cell	2.09e-60	59
monocyte	2.09e-60	59
monoblast	2.09e-60	59
promonocyte	2.09e-60	59
defensive cell	4.41e-57	48
phagocyte	4.41e-57	48
granulocyte monocyte progenitor cell	1.73e-56	67
myeloid lineage restricted progenitor cell	1.88e-53	66
classical monocyte	1.12e-49	42
CD14-positive, CD16-negative classical monocyte	1.12e-49	42
leukocyte	2.84e-42	136
myeloid cell	1.39e-41	108
common myeloid progenitor	1.39e-41	108
nongranular leukocyte	1.74e-34	115
hematopoietic lineage restricted progenitor cell	1.37e-31	120
hematopoietic stem cell	6.35e-31	168
angioblastic mesenchymal cell	6.35e-31	168
hematopoietic cell	5.75e-28	177
hematopoietic oligopotent progenitor cell	6.07e-28	161
hematopoietic multipotent progenitor cell	6.07e-28	161
stuff accumulating cell	3.03e-24	87
intermediate monocyte	6.56e-12	9
CD14-positive, CD16-positive monocyte	6.56e-12	9
granulocyte	2.49e-11	8
macrophage	1.39e-08	6
immature conventional dendritic cell	3.87e-08	5
common dendritic progenitor	3.87e-08	5
blood cell	1.26e-07	11

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	2.43e-59	98
blood island	2.43e-59	98
hemolymphoid system	1.36e-54	108
bone marrow	3.25e-47	76
immune system	2.63e-43	93
bone element	3.53e-42	82
skeletal element	1.57e-36	90
adult organism	1.82e-34	114
skeletal system	4.93e-32	100
lateral plate mesoderm	4.74e-22	203
musculoskeletal system	4.21e-15	167
blood	1.13e-11	15
haemolymphatic fluid	1.13e-11	15
organism substance	1.13e-11	15
mesoderm	3.81e-11	315
mesoderm-derived structure	3.81e-11	315
presumptive mesoderm	3.81e-11	315
neural tube	2.22e-08	56
neural rod	2.22e-08	56
future spinal cord	2.22e-08	56
neural keel	2.22e-08	56
tissue	8.71e-08	773
germ layer	1.10e-07	560
germ layer / neural crest	1.10e-07	560
embryonic tissue	1.10e-07	560
presumptive structure	1.10e-07	560
germ layer / neural crest derived structure	1.10e-07	560
epiblast (generic)	1.10e-07	560
embryonic structure	2.15e-07	564
regional part of nervous system	5.45e-07	53
regional part of brain	5.45e-07	53
telencephalon	5.98e-07	34
developing anatomical structure	7.68e-07	581

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
NFE2#4778	2	11.0291800930899	0.0137623173564868	0.0484452682056733
SPI1#6688	7	4.10216175426136	0.000625554480566112	0.005149545550236

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.