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Difference between revisions of "Coexpression cluster:C1999"

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|full_id=C1999_Neutrophils_Alveolar_Olfactory_Smooth_Monocytederived_Renal_Dendritic
 
|full_id=C1999_Neutrophils_Alveolar_Olfactory_Smooth_Monocytederived_Renal_Dendritic
 
|id=C1999
 
|id=C1999
|ontology_enrichment_celltype=CL:0002371!8.24e-22!591;CL:0000144!9.41e-22!625;CL:0000548!4.66e-19!679;CL:0000004!4.66e-19!679;CL:0000255!4.66e-19!679;CL:0000012!3.73e-18!682;CL:0000003!1.77e-13!722;CL:0000222!2.63e-11!119;CL:0000723!5.31e-11!436;CL:0000048!9.81e-11!430;CL:0000034!3.92e-10!444;CL:0000055!6.61e-10!180;CL:0000192!1.05e-09!42;CL:0000514!1.05e-09!42;CL:0000393!1.24e-09!60;CL:0000211!1.24e-09!60;CL:0000220!2.88e-09!246;CL:0000183!3.23e-09!59;CL:0002321!4.72e-09!248;CL:0000680!1.50e-08!57;CL:0000056!1.50e-08!57;CL:0000355!1.50e-08!57;CL:0000063!2.59e-08!578;CL:0000187!3.00e-08!54;CL:0000359!2.54e-07!32;CL:0000766!3.08e-07!76;CL:0002009!5.44e-07!65;CL:0002194!5.68e-07!63;CL:0000576!5.68e-07!63;CL:0000040!5.68e-07!63;CL:0000559!5.68e-07!63
+
|ontology_enrichment_celltype=CL:0002371!9.55e-22!588;CL:0000548!2.67e-18!679;CL:0000255!2.67e-18!679;CL:0000003!5.91e-13!722;CL:0000222!3.70e-11!121;CL:0000723!1.07e-10!433;CL:0000048!2.00e-10!427;CL:0000034!8.84e-10!441;CL:0000192!7.74e-09!43;CL:0000514!7.74e-09!43;CL:0000393!8.24e-09!61;CL:0000211!8.24e-09!61;CL:0002321!1.31e-08!250;CL:0000183!3.54e-08!59;CL:0000473!9.31e-08!48;CL:0000234!9.31e-08!48;CL:0000766!1.04e-07!72;CL:0000680!1.28e-07!58;CL:0000056!1.28e-07!58;CL:0000355!1.28e-07!58;CL:0000187!1.61e-07!55;CL:0000359!2.18e-07!32;CL:0002009!2.75e-07!61;CL:0002194!3.24e-07!59;CL:0000576!3.24e-07!59;CL:0000040!3.24e-07!59;CL:0000559!3.24e-07!59;CL:0000055!6.67e-07!106
 
|ontology_enrichment_disease=
 
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003081!1.04e-11!216;UBERON:0002204!5.97e-11!167;UBERON:0005256!6.67e-09!143;UBERON:0002049!1.04e-08!79;UBERON:0007798!1.04e-08!79;UBERON:0000914!2.27e-08!83;UBERON:0002329!2.27e-08!83;UBERON:0003077!2.27e-08!83;UBERON:0003059!2.27e-08!83;UBERON:0007282!2.27e-08!83;UBERON:0009618!2.27e-08!83;UBERON:0007285!2.27e-08!83;UBERON:0000486!2.32e-08!82;UBERON:0004290!4.58e-08!70;UBERON:0002385!1.30e-07!63;UBERON:0001015!1.30e-07!63;UBERON:0000383!1.30e-07!63;UBERON:0001134!2.12e-07!61;UBERON:0002036!2.12e-07!61;UBERON:0003082!2.12e-07!61;UBERON:0004535!2.91e-07!110;UBERON:0000055!2.94e-07!69;UBERON:0001637!3.04e-07!42;UBERON:0003509!3.04e-07!42;UBERON:0004572!3.04e-07!42;UBERON:0001981!8.98e-07!60;UBERON:0007500!8.98e-07!60;UBERON:0004537!8.98e-07!60;UBERON:0006965!8.98e-07!60
+
|ontology_enrichment_uberon=UBERON:0000926!2.06e-11!315;UBERON:0004120!2.06e-11!315;UBERON:0006603!2.06e-11!315;UBERON:0003081!1.15e-10!203;UBERON:0002204!6.29e-10!167;UBERON:0007503!1.35e-09!78;UBERON:0002049!1.02e-08!78;UBERON:0007798!1.02e-08!78;UBERON:0000486!1.53e-07!83;UBERON:0002329!3.31e-07!71;UBERON:0003059!3.31e-07!71;UBERON:0007282!3.31e-07!71;UBERON:0004290!3.31e-07!71;UBERON:0009618!3.31e-07!71;UBERON:0001637!3.40e-07!42;UBERON:0003509!3.40e-07!42;UBERON:0004572!3.40e-07!42;UBERON:0000055!3.53e-07!68;UBERON:0004535!4.20e-07!109;UBERON:0007524!4.35e-07!73;UBERON:0003077!6.98e-07!72;UBERON:0007285!6.98e-07!72;UBERON:0002385!7.19e-07!64;UBERON:0001015!7.19e-07!64;UBERON:0000383!7.19e-07!64
 
|tf_chipseq_enrich=BCLAF1#9774;5:21.6526476101218:2.09874458450681e-07:1.12118048931615e-05!CTCF#10664;4:4.28820509846002:0.00515201558824328:0.0239462107708295!EBF1#1879;5:8.906466846569:1.78355672307702e-05:0.000406798166851804!ETS1#2113;5:9.72876092220234:1.14685159850452e-05:0.000292421958242709!HEY1#23462;5:4.04011104310571:0.000928885220517799:0.00675052839368579!JUND#3727;5:6.99466394187103:5.97069468343598e-05:0.000985575125720515!MYC#4609;5:5.2222818716094:0.000257394484885061:0.00276791830796034!POU2F2#5452;4:7.28489924619402:0.000663122328874386:0.00542757311170157!SIN3A#25942;4:4.32710778145211:0.00497705285576288:0.0232509582753184!SP1#6667;5:5.6983813781409:0.00016639184371255:0.00204565011954032!TAF7#6879;5:11.4330694049239:5.11611886715123e-06:0.000157570727916959!ZBTB33#10009;5:31.6647250299812:3.13617771034015e-08:2.11588671763705e-06
 
|tf_chipseq_enrich=BCLAF1#9774;5:21.6526476101218:2.09874458450681e-07:1.12118048931615e-05!CTCF#10664;4:4.28820509846002:0.00515201558824328:0.0239462107708295!EBF1#1879;5:8.906466846569:1.78355672307702e-05:0.000406798166851804!ETS1#2113;5:9.72876092220234:1.14685159850452e-05:0.000292421958242709!HEY1#23462;5:4.04011104310571:0.000928885220517799:0.00675052839368579!JUND#3727;5:6.99466394187103:5.97069468343598e-05:0.000985575125720515!MYC#4609;5:5.2222818716094:0.000257394484885061:0.00276791830796034!POU2F2#5452;4:7.28489924619402:0.000663122328874386:0.00542757311170157!SIN3A#25942;4:4.32710778145211:0.00497705285576288:0.0232509582753184!SP1#6667;5:5.6983813781409:0.00016639184371255:0.00204565011954032!TAF7#6879;5:11.4330694049239:5.11611886715123e-06:0.000157570727916959!ZBTB33#10009;5:31.6647250299812:3.13617771034015e-08:2.11588671763705e-06
 
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}}
 
}}

Revision as of 02:55, 19 October 2012


Full id: C1999_Neutrophils_Alveolar_Olfactory_Smooth_Monocytederived_Renal_Dendritic



Phase1 CAGE Peaks

  Short description
Hg19::chr7:5567947..5567983,- p10@ACTB
Hg19::chr7:5567987..5568010,- p7@ACTB
Hg19::chr7:5568016..5568065,- p3@ACTB
Hg19::chr7:5568084..5568101,- p14@ACTB
Hg19::chr7:5568284..5568346,- p4@ACTB


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Cell Type
Ontology termp-valuen
somatic cell9.55e-22588
animal cell2.67e-18679
eukaryotic cell2.67e-18679
native cell5.91e-13722
mesodermal cell3.70e-11121
somatic stem cell1.07e-10433
multi fate stem cell2.00e-10427
stem cell8.84e-10441
smooth muscle cell7.74e-0943
smooth muscle myoblast7.74e-0943
electrically responsive cell8.24e-0961
electrically active cell8.24e-0961
embryonic cell1.31e-08250
contractile cell3.54e-0859
defensive cell9.31e-0848
phagocyte9.31e-0848
myeloid leukocyte1.04e-0772
muscle precursor cell1.28e-0758
myoblast1.28e-0758
multi-potent skeletal muscle stem cell1.28e-0758
muscle cell1.61e-0755
vascular associated smooth muscle cell2.18e-0732
macrophage dendritic cell progenitor2.75e-0761
monopoietic cell3.24e-0759
monocyte3.24e-0759
monoblast3.24e-0759
promonocyte3.24e-0759
non-terminally differentiated cell6.67e-07106
Uber Anatomy
Ontology termp-valuen
mesoderm2.06e-11315
mesoderm-derived structure2.06e-11315
presumptive mesoderm2.06e-11315
lateral plate mesoderm1.15e-10203
musculoskeletal system6.29e-10167
epithelial vesicle1.35e-0978
vasculature1.02e-0878
vascular system1.02e-0878
multilaminar epithelium1.53e-0783
somite3.31e-0771
presomitic mesoderm3.31e-0771
presumptive segmental plate3.31e-0771
dermomyotome3.31e-0771
trunk paraxial mesoderm3.31e-0771
artery3.40e-0742
arterial blood vessel3.40e-0742
arterial system3.40e-0742
vessel3.53e-0768
cardiovascular system4.20e-07109
dense mesenchyme tissue4.35e-0773
paraxial mesoderm6.98e-0772
presumptive paraxial mesoderm6.98e-0772
muscle tissue7.19e-0764
musculature7.19e-0764
musculature of body7.19e-0764


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


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

TF#promotersEnrichmentp-valueq-value
BCLAF1#9774521.65264761012182.09874458450681e-071.12118048931615e-05
CTCF#1066444.288205098460020.005152015588243280.0239462107708295
EBF1#187958.9064668465691.78355672307702e-050.000406798166851804
ETS1#211359.728760922202341.14685159850452e-050.000292421958242709
HEY1#2346254.040111043105710.0009288852205177990.00675052839368579
JUND#372756.994663941871035.97069468343598e-050.000985575125720515
MYC#460955.22228187160940.0002573944848850610.00276791830796034
POU2F2#545247.284899246194020.0006631223288743860.00542757311170157
SIN3A#2594244.327107781452110.004977052855762880.0232509582753184
SP1#666755.69838137814090.000166391843712550.00204565011954032
TAF7#6879511.43306940492395.11611886715123e-060.000157570727916959
ZBTB33#10009531.66472502998123.13617771034015e-082.11588671763705e-06



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.