Coexpression cluster:C446

Full id: C446_Neutrophils_Mast_Eosinophils_Whole_CD14_immature_optic

Phase1 CAGE Peaks

Hg19::chr11:59521653..59521681,+	p@chr11:59521653..59521681 +
Hg19::chr14:75746340..75746368,+	p3@FOS
Hg19::chr14:93118094..93118129,+	p8@RIN3
Hg19::chr14:93118130..93118140,+	p18@RIN3
Hg19::chr16:27325997..27326036,+	p@chr16:27325997..27326036 +
Hg19::chr17:3819751..3819767,-	p1@P2RX1
Hg19::chr17:4802910..4802929,+	p5@C17orf107
Hg19::chr1:231665876..231665886,-	p@chr1:231665876..231665886 -
Hg19::chr1:231666076..231666093,+	p@chr1:231666076..231666093 +
Hg19::chr20:34357224..34357250,+	p@chr20:34357224..34357250 +
Hg19::chr2:208029288..208029307,+	p@chr2:208029288..208029307 +
Hg19::chr2:232469321..232469404,-	p@chr2:232469321..232469404 -
Hg19::chr2:43358229..43358245,-	p@chr2:43358229..43358245 -
Hg19::chr2:43453036..43453081,-	p@chr2:43453036..43453081 -
Hg19::chr2:43453083..43453099,-	p@chr2:43453083..43453099 -
Hg19::chr4:141074616..141074637,-	p7@MAML3
Hg19::chr4:160024275..160024320,+	p@chr4:160024275..160024320 +
Hg19::chr4:160024323..160024354,+	p@chr4:160024323..160024354 +
Hg19::chr4:160025300..160025318,+	p9@RAPGEF2
Hg19::chr4:6918626..6918641,+	p@chr4:6918626..6918641 +
Hg19::chr6:138188551..138188562,+	p5@TNFAIP3
Hg19::chr7:28725740..28725778,+	p1@CREB5

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:0005515	protein binding	0.0198265617681682
GO:0006366	transcription from RNA polymerase II promoter	0.0222516553977654
GO:0065007	biological regulation	0.0222516553977654
GO:0017034	Rap guanyl-nucleotide exchange factor activity	0.0222516553977654
GO:0046582	Rap GTPase activator activity	0.023800322236145
GO:0004931	ATP-gated cation channel activity	0.023800322236145
GO:0035249	synaptic transmission, glutamatergic	0.023800322236145
GO:0045893	positive regulation of transcription, DNA-dependent	0.023800322236145
GO:0043124	negative regulation of I-kappaB kinase/NF-kappaB cascade	0.0265035690185179
GO:0007165	signal transduction	0.0265035690185179
GO:0045941	positive regulation of transcription	0.0265035690185179
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0265035690185179
GO:0007154	cell communication	0.0296771541767025
GO:0050794	regulation of cellular process	0.0296771541767025
GO:0005096	GTPase activator activity	0.0296771541767025
GO:0031325	positive regulation of cellular metabolic process	0.0296771541767025
GO:0046983	protein dimerization activity	0.0296771541767025
GO:0007243	protein kinase cascade	0.0296771541767025
GO:0009893	positive regulation of metabolic process	0.0303613989977837
GO:0050789	regulation of biological process	0.0315500390975979
GO:0006357	regulation of transcription from RNA polymerase II promoter	0.0320551948780199
GO:0042310	vasoconstriction	0.0323260544063619
GO:0044451	nucleoplasm part	0.0323557424108025
GO:0008047	enzyme activator activity	0.0323557424108025
GO:0007270	nerve-nerve synaptic transmission	0.0337717794615979
GO:0005654	nucleoplasm	0.0364885636811877
GO:0006305	DNA alkylation	0.0364885636811877
GO:0006306	DNA methylation	0.0364885636811877
GO:0006304	DNA modification	0.0428701763320134

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	1.02e-26	76
CD14-positive, CD16-negative classical monocyte	3.71e-26	42
granulocyte monocyte progenitor cell	4.08e-23	71
myeloid cell	2.79e-22	112
common myeloid progenitor	2.79e-22	112
classical monocyte	2.37e-21	45
myeloid lineage restricted progenitor cell	6.45e-21	70
macrophage dendritic cell progenitor	1.18e-19	65
monopoietic cell	1.09e-18	63
monocyte	1.09e-18	63
monoblast	1.09e-18	63
promonocyte	1.09e-18	63
leukocyte	2.52e-18	140
hematopoietic stem cell	4.65e-18	172
angioblastic mesenchymal cell	4.65e-18	172
hematopoietic oligopotent progenitor cell	2.50e-16	165
hematopoietic multipotent progenitor cell	2.50e-16	165
hematopoietic cell	3.77e-16	182
hematopoietic lineage restricted progenitor cell	2.10e-14	124
nongranular leukocyte	1.84e-12	119
granulocyte	7.87e-07	8

Uber Anatomy

Ontology term	p-value	n
adult organism	3.97e-29	115
hematopoietic system	6.66e-26	102
blood island	6.66e-26	102
hemolymphoid system	1.94e-25	112
bone marrow	4.82e-20	80
bone element	4.79e-19	86
skeletal element	1.24e-15	101
skeletal system	1.24e-15	101
immune system	2.45e-13	115
lateral plate mesoderm	2.15e-11	216
neural tube	1.26e-10	57
neural rod	1.26e-10	57
future spinal cord	1.26e-10	57
neural keel	1.26e-10	57
anterior neural tube	5.89e-09	42
regional part of forebrain	1.10e-08	41
forebrain	1.10e-08	41
future forebrain	1.10e-08	41
regional part of brain	1.27e-08	59
gray matter	4.04e-08	34
brain grey matter	4.04e-08	34
central nervous system	4.30e-08	82
telencephalon	4.81e-08	34
regional part of telencephalon	8.14e-08	33
cerebral hemisphere	1.66e-07	32
blood	3.30e-07	15
haemolymphatic fluid	3.30e-07	15
organism substance	3.30e-07	15
brain	3.56e-07	69
future brain	3.56e-07	69
regional part of cerebral cortex	7.41e-07	22

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
BCL3#602	4	6.28129141886151	0.003378044720939	0.017250971229287
CEBPB#1051	9	3.26092402874652	0.00081695470974557	0.00622424372126623
EBF1#1879	9	3.64355461905096	0.000356518273109663	0.00356753970732012
EGR1#1958	10	2.26735413400461	0.00624618072445826	0.0275634794727552
FOS#2353	7	2.86298578010277	0.00785702226201148	0.0322643631511114
FOSL2#2355	5	3.84777286467311	0.00811118198034043	0.0320346292105874
GATA2#2624	6	3.47589047278745	0.00579111909679269	0.0260372244758678
JUN#3725	8	4.55011970630412	0.000190744449962844	0.00230542293827907
MAX#4149	8	2.34638382145714	0.0137898248043718	0.0485110318224126
POLR2A#5430	19	1.85461865248197	0.000132350848337639	0.00173956585068395
SMARCA4#6597	2	14.2514457552625	0.00862929986819234	0.0328714100351657
SMARCB1#6598	5	4.14834449571759	0.00592460468593055	0.0265721802282015
SMARCC1#6599	4	7.93879260356936	0.00144444001092748	0.00926234851729937
SMARCC2#6601	3	12.8393692400315	0.0015840021469931	0.00998259716568986
SPI1#6688	10	3.72923795841942	0.000115237226647339	0.00157612109924325
TCF12#6938	7	3.38369337796841	0.00310034136711275	0.016302313565597
ZNF263#10127	7	2.61604052086703	0.0127364095875261	0.0459410748398026

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.