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Coexpression cluster:C446

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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

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

GO IDGO nameFDR corrected p-value
GO:0005515protein binding0.0198265617681682
GO:0006366transcription from RNA polymerase II promoter0.0222516553977654
GO:0065007biological regulation0.0222516553977654
GO:0017034Rap guanyl-nucleotide exchange factor activity0.0222516553977654
GO:0046582Rap GTPase activator activity0.023800322236145
GO:0004931ATP-gated cation channel activity0.023800322236145
GO:0035249synaptic transmission, glutamatergic0.023800322236145
GO:0045893positive regulation of transcription, DNA-dependent0.023800322236145
GO:0043124negative regulation of I-kappaB kinase/NF-kappaB cascade0.0265035690185179
GO:0007165signal transduction0.0265035690185179
GO:0045941positive regulation of transcription0.0265035690185179
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0265035690185179
GO:0007154cell communication0.0296771541767025
GO:0050794regulation of cellular process0.0296771541767025
GO:0005096GTPase activator activity0.0296771541767025
GO:0031325positive regulation of cellular metabolic process0.0296771541767025
GO:0046983protein dimerization activity0.0296771541767025
GO:0007243protein kinase cascade0.0296771541767025
GO:0009893positive regulation of metabolic process0.0303613989977837
GO:0050789regulation of biological process0.0315500390975979
GO:0006357regulation of transcription from RNA polymerase II promoter0.0320551948780199
GO:0042310vasoconstriction0.0323260544063619
GO:0044451nucleoplasm part0.0323557424108025
GO:0008047enzyme activator activity0.0323557424108025
GO:0007270nerve-nerve synaptic transmission0.0337717794615979
GO:0005654nucleoplasm0.0364885636811877
GO:0006305DNA alkylation0.0364885636811877
GO:0006306DNA methylation0.0364885636811877
GO:0006304DNA modification0.0428701763320134



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>

Uber Anatomy
Ontology termp-valuen
adult organism3.97e-29115
hematopoietic system6.66e-26102
blood island6.66e-26102
hemolymphoid system1.94e-25112
bone marrow4.82e-2080
bone element4.79e-1986
skeletal element1.24e-15101
skeletal system1.24e-15101
immune system2.45e-13115
lateral plate mesoderm2.15e-11216
neural tube1.26e-1057
neural rod1.26e-1057
future spinal cord1.26e-1057
neural keel1.26e-1057
anterior neural tube5.89e-0942
regional part of forebrain1.10e-0841
forebrain1.10e-0841
future forebrain1.10e-0841
regional part of brain1.27e-0859
gray matter4.04e-0834
brain grey matter4.04e-0834
central nervous system4.30e-0882
telencephalon4.81e-0834
regional part of telencephalon8.14e-0833
cerebral hemisphere1.66e-0732
blood3.30e-0715
haemolymphatic fluid3.30e-0715
organism substance3.30e-0715
brain3.56e-0769
future brain3.56e-0769
regional part of cerebral cortex7.41e-0722


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

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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
BCL3#60246.281291418861510.0033780447209390.017250971229287
CEBPB#105193.260924028746520.000816954709745570.00622424372126623
EBF1#187993.643554619050960.0003565182731096630.00356753970732012
EGR1#1958102.267354134004610.006246180724458260.0275634794727552
FOS#235372.862985780102770.007857022262011480.0322643631511114
FOSL2#235553.847772864673110.008111181980340430.0320346292105874
GATA2#262463.475890472787450.005791119096792690.0260372244758678
JUN#372584.550119706304120.0001907444499628440.00230542293827907
MAX#414982.346383821457140.01378982480437180.0485110318224126
POLR2A#5430191.854618652481970.0001323508483376390.00173956585068395
SMARCA4#6597214.25144575526250.008629299868192340.0328714100351657
SMARCB1#659854.148344495717590.005924604685930550.0265721802282015
SMARCC1#659947.938792603569360.001444440010927480.00926234851729937
SMARCC2#6601312.83936924003150.00158400214699310.00998259716568986
SPI1#6688103.729237958419420.0001152372266473390.00157612109924325
TCF12#693873.383693377968410.003100341367112750.016302313565597
ZNF263#1012772.616040520867030.01273640958752610.0459410748398026



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

This analysis result is provided for C0 - C305 clusters.

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