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Coexpression cluster:C1972: Difference between revisions

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|full_id=C1972_Fibroblast_Synoviocyte_Endothelial_osteosarcoma_mature_cerebellum_alveolar
|full_id=C1972_Fibroblast_Synoviocyte_Endothelial_osteosarcoma_mature_cerebellum_alveolar
|id=C1972
|id=C1972
|ontology_enrichment_celltype=CL:0000222!6.00e-24!119;CL:0000055!8.47e-22!180;CL:0002139!2.28e-13!24;CL:0002078!2.52e-13!44;CL:0000213!1.12e-12!57;CL:0000215!1.12e-12!57;CL:0000220!2.88e-12!246;CL:0002321!3.12e-12!248;CL:0000680!8.84e-12!57;CL:0000056!8.84e-12!57;CL:0000355!8.84e-12!57;CL:0000115!2.02e-11!35;CL:0000183!2.82e-11!59;CL:0000187!4.97e-11!54;CL:0000071!5.91e-10!18;CL:0002546!5.91e-10!18;CL:0000057!5.55e-09!75;CL:0000393!6.54e-09!60;CL:0000211!6.54e-09!60;CL:0000192!1.31e-07!42;CL:0000514!1.31e-07!42
|ontology_enrichment_celltype=CL:0000222!4.73e-21!121;CL:0002078!1.63e-12!45;CL:0002139!2.45e-12!24;CL:0000055!1.89e-11!106;CL:0002321!4.48e-11!250;CL:0000213!6.92e-11!58;CL:0000215!6.92e-11!58;CL:0000115!8.27e-11!36;CL:0000680!1.17e-10!58;CL:0000056!1.17e-10!58;CL:0000355!1.17e-10!58;CL:0000183!3.80e-10!59;CL:0000187!6.85e-10!55;CL:0000057!1.51e-09!76;CL:0000071!3.36e-09!18;CL:0002546!3.36e-09!18;CL:0000393!5.26e-08!61;CL:0000211!5.26e-08!61;CL:0000192!7.48e-07!43;CL:0000514!7.48e-07!43
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000119!4.08e-25!312;UBERON:0000483!7.38e-24!309;UBERON:0002049!2.66e-23!79;UBERON:0007798!2.66e-23!79;UBERON:0000477!3.44e-22!286;UBERON:0003914!1.09e-19!118;UBERON:0000055!7.98e-19!69;UBERON:0000481!1.58e-18!347;UBERON:0000490!4.36e-18!138;UBERON:0004872!7.05e-17!84;UBERON:0004111!7.38e-17!241;UBERON:0001981!1.66e-16!60;UBERON:0007500!1.66e-16!60;UBERON:0004537!1.66e-16!60;UBERON:0006965!1.66e-16!60;UBERON:0005256!4.85e-16!143;UBERON:0004535!7.36e-16!110;UBERON:0001009!8.34e-16!113;UBERON:0000025!3.24e-15!194;UBERON:0000468!1.10e-14!659;UBERON:0000475!1.18e-14!365;UBERON:0002100!7.87e-14!216;UBERON:0000486!3.29e-13!82;UBERON:0000467!4.47e-13!625;UBERON:0000914!5.63e-13!83;UBERON:0002329!5.63e-13!83;UBERON:0003077!5.63e-13!83;UBERON:0003059!5.63e-13!83;UBERON:0007282!5.63e-13!83;UBERON:0009618!5.63e-13!83;UBERON:0007285!5.63e-13!83;UBERON:0000480!8.19e-13!626;UBERON:0003104!2.01e-12!238;UBERON:0009142!2.01e-12!238;UBERON:0004290!2.26e-12!70;UBERON:0001134!1.02e-11!61;UBERON:0002036!1.02e-11!61;UBERON:0003082!1.02e-11!61;UBERON:0002385!1.63e-11!63;UBERON:0001015!1.63e-11!63;UBERON:0000383!1.63e-11!63;UBERON:0001637!7.30e-11!42;UBERON:0003509!7.30e-11!42;UBERON:0004572!7.30e-11!42;UBERON:0006914!1.09e-10!25;UBERON:0000922!2.09e-10!612;UBERON:0001986!5.91e-10!18;UBERON:0004638!5.91e-10!18;UBERON:0004852!5.91e-10!18;UBERON:0002050!6.98e-10!605;UBERON:0005423!6.98e-10!605;UBERON:0000923!1.36e-09!604;UBERON:0005291!1.36e-09!604;UBERON:0006598!1.36e-09!604;UBERON:0002532!1.36e-09!604;UBERON:0000487!3.80e-09!22;UBERON:0004573!6.32e-09!33;UBERON:0004571!6.32e-09!33;UBERON:0003103!5.99e-07!69;UBERON:0000947!9.32e-07!21;UBERON:0010191!9.32e-07!21
|ontology_enrichment_uberon=UBERON:0000119!8.03e-22!309;UBERON:0000483!1.05e-20!306;UBERON:0002049!2.43e-20!78;UBERON:0007798!2.43e-20!78;UBERON:0000477!1.41e-17!373;UBERON:0000490!4.29e-17!148;UBERON:0003914!4.40e-17!117;UBERON:0000055!6.94e-16!68;UBERON:0003104!1.02e-14!160;UBERON:0009142!1.02e-14!160;UBERON:0004111!2.45e-14!240;UBERON:0000481!8.29e-14!342;UBERON:0007500!9.96e-14!59;UBERON:0001981!9.96e-14!59;UBERON:0004537!9.96e-14!59;UBERON:0006965!9.96e-14!59;UBERON:0004535!1.02e-13!109;UBERON:0001009!1.04e-13!112;UBERON:0004872!1.49e-13!83;UBERON:0005256!6.06e-13!122;UBERON:0000486!9.54e-13!83;UBERON:0007503!9.84e-13!78;UBERON:0000475!3.98e-12!264;UBERON:0000025!4.29e-12!192;UBERON:0000468!9.18e-12!656;UBERON:0002100!1.19e-11!199;UBERON:0002329!1.75e-11!71;UBERON:0003059!1.75e-11!71;UBERON:0007282!1.75e-11!71;UBERON:0004290!1.75e-11!71;UBERON:0009618!1.75e-11!71;UBERON:0007524!1.97e-11!73;UBERON:0003077!2.68e-11!72;UBERON:0007285!2.68e-11!72;UBERON:0001134!6.64e-11!62;UBERON:0002036!6.64e-11!62;UBERON:0003082!6.64e-11!62;UBERON:0002385!7.13e-11!64;UBERON:0001015!7.13e-11!64;UBERON:0000383!7.13e-11!64;UBERON:0000467!9.20e-11!624;UBERON:0000480!1.53e-10!625;UBERON:0006914!8.02e-10!25;UBERON:0004638!3.36e-09!18;UBERON:0001986!3.36e-09!18;UBERON:0004852!3.36e-09!18;UBERON:0001637!3.88e-09!42;UBERON:0003509!3.88e-09!42;UBERON:0004572!3.88e-09!42;UBERON:0000487!2.67e-08!22;UBERON:0004573!2.42e-07!33;UBERON:0004571!2.42e-07!33
|tf_chipseq_enrich=ATF3#467;5:22.4631745260087:1.74638470646713e-07:9.5793420356471e-06!E2F1#1869;4:3.92591137190346:0.00721498454710636:0.029882843080395!E2F6#1876;5:5.01715573169739:0.000314497859929779:0.00323254030048284!EGR1#1958;5:4.98817909481014:0.000323739800059071:0.00331123895586812!GTF2B#2959;5:31.9438299343242:3.00149609204784e-08:2.03951366530504e-06!MAX#4149;5:6.45255550900712:8.93743970843928e-05:0.00130803989028824!POLR3A#11128;5:339.132110091743:2.18870993324884e-13:3.30327567512392e-11!STAT1#6772;5:20.7065874971992:2.62418353652031e-07:1.35542583763919e-05!STAT3#6774;5:10.5194649971542:7.759040745861e-06:0.000220682586181094!TCF7L2#6934;5:10.7701765631373:6.89693748574565e-06:0.000200141498770155!USF1#7391;5:6.36149927720796:9.59569864925045e-05:0.00137076346769124!USF2#7392;5:12.9921973850696:2.69963551658264e-06:9.43914408156594e-05
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}}
}}

Revision as of 11:54, 19 October 2012


Full id: C1972_Fibroblast_Synoviocyte_Endothelial_osteosarcoma_mature_cerebellum_alveolar



Phase1 CAGE Peaks

Hg19::chr6:151646636..151646655,+p5@AKAP12
Hg19::chr6:151646657..151646671,+p8@AKAP12
Hg19::chr6:151646675..151646705,+p4@AKAP12
Hg19::chr6:151646706..151646717,+p11@AKAP12
Hg19::chr6:151646718..151646731,+p10@AKAP12


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><br>

Uber Anatomy
Ontology termp-valuen
cell layer8.03e-22309
epithelium1.05e-20306
vasculature2.43e-2078
vascular system2.43e-2078
anatomical cluster1.41e-17373
unilaminar epithelium4.29e-17148
epithelial tube4.40e-17117
vessel6.94e-1668
mesenchyme1.02e-14160
entire embryonic mesenchyme1.02e-14160
anatomical conduit2.45e-14240
multi-tissue structure8.29e-14342
epithelial tube open at both ends9.96e-1459
blood vessel9.96e-1459
blood vasculature9.96e-1459
vascular cord9.96e-1459
cardiovascular system1.02e-13109
circulatory system1.04e-13112
splanchnic layer of lateral plate mesoderm1.49e-1383
trunk mesenchyme6.06e-13122
multilaminar epithelium9.54e-1383
epithelial vesicle9.84e-1378
organism subdivision3.98e-12264
tube4.29e-12192
multi-cellular organism9.18e-12656
trunk1.19e-11199
somite1.75e-1171
presomitic mesoderm1.75e-1171
presumptive segmental plate1.75e-1171
dermomyotome1.75e-1171
trunk paraxial mesoderm1.75e-1171
dense mesenchyme tissue1.97e-1173
paraxial mesoderm2.68e-1172
presumptive paraxial mesoderm2.68e-1172
skeletal muscle tissue6.64e-1162
striated muscle tissue6.64e-1162
myotome6.64e-1162
muscle tissue7.13e-1164
musculature7.13e-1164
musculature of body7.13e-1164
anatomical system9.20e-11624
anatomical group1.53e-10625
squamous epithelium8.02e-1025
blood vessel endothelium3.36e-0918
endothelium3.36e-0918
cardiovascular system endothelium3.36e-0918
artery3.88e-0942
arterial blood vessel3.88e-0942
arterial system3.88e-0942
simple squamous epithelium2.67e-0822
systemic artery2.42e-0733
systemic arterial system2.42e-0733


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
ATF3#467522.46317452600871.74638470646713e-079.5793420356471e-06
E2F1#186943.925911371903460.007214984547106360.029882843080395
E2F6#187655.017155731697390.0003144978599297790.00323254030048284
EGR1#195854.988179094810140.0003237398000590710.00331123895586812
GTF2B#2959531.94382993432423.00149609204784e-082.03951366530504e-06
MAX#414956.452555509007128.93743970843928e-050.00130803989028824
POLR3A#111285339.1321100917432.18870993324884e-133.30327567512392e-11
STAT1#6772520.70658749719922.62418353652031e-071.35542583763919e-05
STAT3#6774510.51946499715427.759040745861e-060.000220682586181094
TCF7L2#6934510.77017656313736.89693748574565e-060.000200141498770155
USF1#739156.361499277207969.59569864925045e-050.00137076346769124
USF2#7392512.99219738506962.69963551658264e-069.43914408156594e-05



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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