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Coexpression cluster:C632: Difference between revisions

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|full_id=C632_Monocytederived_Macrophage_Dendritic_CD14_Keratinocyte_basal_tenocyte
|full_id=C632_Monocytederived_Macrophage_Dendritic_CD14_Keratinocyte_basal_tenocyte
|id=C632
|id=C632
|ontology_enrichment_celltype=CL:0002371!4.36e-17!591;CL:0000055!5.80e-16!180;CL:0000222!3.22e-14!119;CL:0000144!4.16e-14!625;CL:0000220!6.60e-12!246;CL:0002321!3.17e-11!248;CL:0002194!1.55e-10!63;CL:0000576!1.55e-10!63;CL:0000040!1.55e-10!63;CL:0000559!1.55e-10!63;CL:0002009!4.51e-10!65;CL:0000680!7.39e-10!57;CL:0000056!7.39e-10!57;CL:0000355!7.39e-10!57;CL:0000183!2.15e-09!59;CL:0000187!4.40e-09!54;CL:0000057!5.60e-09!75;CL:0000192!9.55e-09!42;CL:0000514!9.55e-09!42;CL:0000839!1.96e-08!70;CL:0000048!4.48e-08!430;CL:0002057!6.93e-08!42;CL:0000557!9.27e-08!71;CL:0000115!1.11e-07!35;CL:0000723!1.41e-07!436;CL:0000548!4.99e-07!679;CL:0000004!4.99e-07!679;CL:0000255!4.99e-07!679;CL:0000393!6.03e-07!60;CL:0000211!6.03e-07!60
|ontology_enrichment_celltype=CL:0002371!2.66e-17!588;CL:0002194!7.15e-13!59;CL:0000576!7.15e-13!59;CL:0000040!7.15e-13!59;CL:0000559!7.15e-13!59;CL:0000222!1.20e-12!121;CL:0002009!3.79e-12!61;CL:0000473!4.67e-11!48;CL:0000234!4.67e-11!48;CL:0002321!7.96e-11!250;CL:0000839!3.04e-10!66;CL:0000325!7.52e-10!87;CL:0000680!2.37e-09!58;CL:0000056!2.37e-09!58;CL:0000355!2.37e-09!58;CL:0000557!4.16e-09!67;CL:0000183!8.92e-09!59;CL:0000187!1.56e-08!55;CL:0000057!2.04e-08!76;CL:0000192!2.74e-08!43;CL:0000514!2.74e-08!43;CL:0000048!4.60e-08!427;CL:0000860!6.91e-08!42;CL:0002057!6.91e-08!42;CL:0000723!1.17e-07!433;CL:0000055!1.31e-07!106;CL:0000548!2.54e-07!679;CL:0000255!2.54e-07!679;CL:0000393!7.74e-07!61;CL:0000211!7.74e-07!61
|ontology_enrichment_disease=DOID:2394!3.31e-07!14
|ontology_enrichment_disease=DOID:2394!8.89e-07!14
|ontology_enrichment_uberon=UBERON:0000468!5.53e-21!659;UBERON:0000467!2.23e-19!625;UBERON:0000480!4.28e-19!626;UBERON:0003081!2.91e-18!216;UBERON:0000926!1.28e-17!448;UBERON:0004120!1.28e-17!448;UBERON:0006603!1.28e-17!448;UBERON:0002204!1.82e-17!167;UBERON:0002050!7.32e-13!605;UBERON:0005423!7.32e-13!605;UBERON:0000923!8.49e-13!604;UBERON:0005291!8.49e-13!604;UBERON:0006598!8.49e-13!604;UBERON:0002532!8.49e-13!604;UBERON:0004872!3.72e-12!84;UBERON:0000922!4.99e-12!612;UBERON:0000486!8.94e-12!82;UBERON:0000914!4.08e-11!83;UBERON:0002329!4.08e-11!83;UBERON:0003077!4.08e-11!83;UBERON:0003059!4.08e-11!83;UBERON:0007282!4.08e-11!83;UBERON:0009618!4.08e-11!83;UBERON:0007285!4.08e-11!83;UBERON:0001009!6.05e-11!113;UBERON:0002049!7.75e-11!79;UBERON:0007798!7.75e-11!79;UBERON:0004535!9.00e-11!110;UBERON:0000055!1.11e-10!69;UBERON:0003914!1.17e-10!118;UBERON:0000490!1.76e-10!138;UBERON:0005256!4.49e-10!143;UBERON:0001637!5.06e-10!42;UBERON:0003509!5.06e-10!42;UBERON:0004572!5.06e-10!42;UBERON:0004290!6.06e-10!70;UBERON:0001981!7.50e-10!60;UBERON:0007500!7.50e-10!60;UBERON:0004537!7.50e-10!60;UBERON:0006965!7.50e-10!60;UBERON:0002405!9.43e-09!115;UBERON:0001134!1.73e-08!61;UBERON:0002036!1.73e-08!61;UBERON:0003082!1.73e-08!61;UBERON:0002385!2.10e-08!63;UBERON:0001015!2.10e-08!63;UBERON:0000383!2.10e-08!63;UBERON:0004573!2.16e-08!33;UBERON:0004571!2.16e-08!33;UBERON:0004765!3.14e-08!101;UBERON:0001434!3.14e-08!101;UBERON:0002371!3.22e-08!80;UBERON:0001474!5.99e-07!86;UBERON:0000062!8.34e-07!511
|ontology_enrichment_uberon=UBERON:0000926!1.85e-24!315;UBERON:0004120!1.85e-24!315;UBERON:0006603!1.85e-24!315;UBERON:0002204!9.51e-19!167;UBERON:0000468!9.57e-19!656;UBERON:0000467!8.93e-18!624;UBERON:0000480!1.80e-17!625;UBERON:0003081!2.10e-16!203;UBERON:0002050!2.94e-12!564;UBERON:0005423!9.47e-12!581;UBERON:0000923!1.25e-11!560;UBERON:0010316!1.25e-11!560;UBERON:0005291!1.25e-11!560;UBERON:0006598!1.25e-11!560;UBERON:0010317!1.25e-11!560;UBERON:0002532!1.25e-11!560;UBERON:0000486!1.64e-10!83;UBERON:0004872!3.11e-10!83;UBERON:0000922!5.17e-10!592;UBERON:0001434!6.97e-10!100;UBERON:0000490!7.14e-10!148;UBERON:0002371!2.69e-09!76;UBERON:0001637!3.07e-09!42;UBERON:0003509!3.07e-09!42;UBERON:0004572!3.07e-09!42;UBERON:0004765!3.14e-09!90;UBERON:0003914!3.64e-09!117;UBERON:0002049!5.94e-09!78;UBERON:0007798!5.94e-09!78;UBERON:0001009!7.28e-09!112;UBERON:0007503!9.57e-09!78;UBERON:0002405!1.00e-08!93;UBERON:0004535!1.21e-08!109;UBERON:0007524!1.37e-08!73;UBERON:0000055!1.59e-08!68;UBERON:0002329!1.74e-08!71;UBERON:0003059!1.74e-08!71;UBERON:0007282!1.74e-08!71;UBERON:0004290!1.74e-08!71;UBERON:0009618!1.74e-08!71;UBERON:0003077!2.39e-08!72;UBERON:0007285!2.39e-08!72;UBERON:0007500!3.58e-08!59;UBERON:0001981!3.58e-08!59;UBERON:0004537!3.58e-08!59;UBERON:0006965!3.58e-08!59;UBERON:0001474!6.29e-08!82;UBERON:0002385!1.07e-07!64;UBERON:0001015!1.07e-07!64;UBERON:0000383!1.07e-07!64;UBERON:0001134!1.10e-07!62;UBERON:0002036!1.10e-07!62;UBERON:0003082!1.10e-07!62;UBERON:0005256!1.12e-07!122;UBERON:0004573!1.75e-07!33;UBERON:0004571!1.75e-07!33;UBERON:0002193!8.70e-07!108
|tf_chipseq_enrich=BCL3#602;3:7.40295060080107:0.00694426632847338:0.0293731412692654!FOSL2#2355;4:4.83720017273191:0.00754162287399241:0.0310914440191408!POLR2A#5430;12:1.84067415133549:0.00308514162916731:0.0162625097970325
|tf_chipseq_enrich=BCL3#602;3:7.40295060080107:0.00694426632847338:0.0293731412692654!FOSL2#2355;4:4.83720017273191:0.00754162287399241:0.0310914440191408!POLR2A#5430;12:1.84067415133549:0.00308514162916731:0.0162625097970325
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}}
}}

Revision as of 16:30, 19 October 2012


Full id: C632_Monocytederived_Macrophage_Dendritic_CD14_Keratinocyte_basal_tenocyte



Phase1 CAGE Peaks

Hg19::chr18:3466261..3466312,+p@chr18:3466261..3466312
+
Hg19::chr20:57571799..57571828,+p@chr20:57571799..57571828
+
Hg19::chr8:11702366..11702398,+p@chr8:11702366..11702398
+
Hg19::chr8:11702610..11702625,+p@chr8:11702610..11702625
+
Hg19::chr8:11704610..11704653,+p@chr8:11704610..11704653
+
Hg19::chr8:11705180..11705213,+p@chr8:11705180..11705213
+
Hg19::chr8:11705214..11705244,+p@chr8:11705214..11705244
+
Hg19::chr8:11705265..11705300,+p@chr8:11705265..11705300
+
Hg19::chr8:11706577..11706604,+p@chr8:11706577..11706604
+
Hg19::chr8:11710161..11710184,+p@chr8:11710161..11710184
+
Hg19::chr8:11710828..11710871,+p@chr8:11710828..11710871
+
Hg19::chr8:11710864..11710931,-p3@CTSB
Hg19::chr8:11710941..11710962,-p8@CTSB
Hg19::chr8:11725589..11725605,-p1@CTSB


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


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>disease_data<br>


Cell Type
Ontology termp-valuen
somatic cell2.66e-17588
monopoietic cell7.15e-1359
monocyte7.15e-1359
monoblast7.15e-1359
promonocyte7.15e-1359
mesodermal cell1.20e-12121
macrophage dendritic cell progenitor3.79e-1261
defensive cell4.67e-1148
phagocyte4.67e-1148
embryonic cell7.96e-11250
myeloid lineage restricted progenitor cell3.04e-1066
stuff accumulating cell7.52e-1087
muscle precursor cell2.37e-0958
myoblast2.37e-0958
multi-potent skeletal muscle stem cell2.37e-0958
granulocyte monocyte progenitor cell4.16e-0967
contractile cell8.92e-0959
muscle cell1.56e-0855
fibroblast2.04e-0876
smooth muscle cell2.74e-0843
smooth muscle myoblast2.74e-0843
multi fate stem cell4.60e-08427
classical monocyte6.91e-0842
CD14-positive, CD16-negative classical monocyte6.91e-0842
somatic stem cell1.17e-07433
non-terminally differentiated cell1.31e-07106
animal cell2.54e-07679
eukaryotic cell2.54e-07679
electrically responsive cell7.74e-0761
electrically active cell7.74e-0761
Uber Anatomy
Ontology termp-valuen
mesoderm1.85e-24315
mesoderm-derived structure1.85e-24315
presumptive mesoderm1.85e-24315
musculoskeletal system9.51e-19167
multi-cellular organism9.57e-19656
anatomical system8.93e-18624
anatomical group1.80e-17625
lateral plate mesoderm2.10e-16203
embryonic structure2.94e-12564
developing anatomical structure9.47e-12581
germ layer1.25e-11560
germ layer / neural crest1.25e-11560
embryonic tissue1.25e-11560
presumptive structure1.25e-11560
germ layer / neural crest derived structure1.25e-11560
epiblast (generic)1.25e-11560
multilaminar epithelium1.64e-1083
splanchnic layer of lateral plate mesoderm3.11e-1083
embryo5.17e-10592
skeletal system6.97e-10100
unilaminar epithelium7.14e-10148
bone marrow2.69e-0976
artery3.07e-0942
arterial blood vessel3.07e-0942
arterial system3.07e-0942
skeletal element3.14e-0990
epithelial tube3.64e-09117
vasculature5.94e-0978
vascular system5.94e-0978
circulatory system7.28e-09112
epithelial vesicle9.57e-0978
immune system1.00e-0893
cardiovascular system1.21e-08109
dense mesenchyme tissue1.37e-0873
vessel1.59e-0868
somite1.74e-0871
presomitic mesoderm1.74e-0871
presumptive segmental plate1.74e-0871
dermomyotome1.74e-0871
trunk paraxial mesoderm1.74e-0871
paraxial mesoderm2.39e-0872
presumptive paraxial mesoderm2.39e-0872
epithelial tube open at both ends3.58e-0859
blood vessel3.58e-0859
blood vasculature3.58e-0859
vascular cord3.58e-0859
bone element6.29e-0882
muscle tissue1.07e-0764
musculature1.07e-0764
musculature of body1.07e-0764
skeletal muscle tissue1.10e-0762
striated muscle tissue1.10e-0762
myotome1.10e-0762
trunk mesenchyme1.12e-07122
systemic artery1.75e-0733
systemic arterial system1.75e-0733
hemolymphoid system8.70e-07108
Disease
Ontology termp-valuen
ovarian cancer8.89e-0714


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)

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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#60237.402950600801070.006944266328473380.0293731412692654
FOSL2#235544.837200172731910.007541622873992410.0310914440191408
POLR2A#5430121.840674151335490.003085141629167310.0162625097970325



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.