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Coexpression cluster:C1682: Difference between revisions

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|full_id=C1682_schwannoma_Fibroblast_hepatoblastoma_Wilms_adrenal_Aortic_meningioma
|full_id=C1682_schwannoma_Fibroblast_hepatoblastoma_Wilms_adrenal_Aortic_meningioma
|id=C1682
|id=C1682
|ontology_enrichment_celltype=CL:0002321!2.63e-31!248;CL:0000055!5.71e-31!180;CL:0000220!1.25e-30!246;CL:0000012!6.33e-21!682;CL:0000548!3.84e-20!679;CL:0000004!3.84e-20!679;CL:0000255!3.84e-20!679;CL:0000680!7.59e-20!57;CL:0000056!7.59e-20!57;CL:0000355!7.59e-20!57;CL:0000393!8.86e-19!60;CL:0000211!8.86e-19!60;CL:0000187!3.16e-18!54;CL:0000144!3.46e-18!625;CL:0000183!4.93e-18!59;CL:0002371!6.81e-18!591;CL:0000222!2.83e-17!119;CL:0000192!2.21e-16!42;CL:0000514!2.21e-16!42;CL:0000359!3.74e-14!32;CL:0000066!1.77e-13!254;CL:0000057!5.31e-10!75;CL:0000003!1.14e-09!722;CL:0002076!4.52e-09!43;CL:0000223!1.13e-08!59
|ontology_enrichment_celltype=CL:0002321!2.37e-29!250;CL:0000680!9.63e-23!58;CL:0000056!9.63e-23!58;CL:0000355!9.63e-23!58;CL:0000548!7.35e-22!679;CL:0000255!7.35e-22!679;CL:0000393!2.16e-21!61;CL:0000211!2.16e-21!61;CL:0000187!8.64e-21!55;CL:0000183!1.44e-20!59;CL:0002371!5.00e-20!588;CL:0000055!5.51e-20!106;CL:0000192!3.06e-19!43;CL:0000514!3.06e-19!43;CL:0000359!6.15e-17!32;CL:0000222!2.84e-16!121;CL:0000003!7.42e-14!722;CL:0000066!7.33e-10!253;CL:0002076!2.06e-09!42;CL:0000057!7.01e-09!76;CL:0000223!3.10e-08!58;CL:0002539!5.00e-08!10
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000486!3.79e-22!82;UBERON:0000914!4.10e-22!83;UBERON:0002329!4.10e-22!83;UBERON:0003077!4.10e-22!83;UBERON:0003059!4.10e-22!83;UBERON:0007282!4.10e-22!83;UBERON:0009618!4.10e-22!83;UBERON:0007285!4.10e-22!83;UBERON:0005256!6.94e-21!143;UBERON:0004290!2.00e-19!70;UBERON:0000490!6.08e-19!138;UBERON:0001134!1.84e-17!61;UBERON:0002036!1.84e-17!61;UBERON:0003082!1.84e-17!61;UBERON:0002385!1.51e-16!63;UBERON:0001015!1.51e-16!63;UBERON:0000383!1.51e-16!63;UBERON:0002049!2.84e-16!79;UBERON:0007798!2.84e-16!79;UBERON:0003914!2.34e-15!118;UBERON:0002100!2.60e-15!216;UBERON:0001637!2.53e-14!42;UBERON:0003509!2.53e-14!42;UBERON:0004572!2.53e-14!42;UBERON:0003104!4.16e-14!238;UBERON:0009142!4.16e-14!238;UBERON:0001981!4.06e-13!60;UBERON:0007500!4.06e-13!60;UBERON:0004537!4.06e-13!60;UBERON:0006965!4.06e-13!60;UBERON:0004872!1.40e-12!84;UBERON:0000055!1.74e-12!69;UBERON:0000119!2.44e-12!312;UBERON:0000481!4.57e-12!347;UBERON:0000483!8.76e-12!309;UBERON:0004573!2.73e-11!33;UBERON:0004571!2.73e-11!33;UBERON:0000475!3.71e-11!365;UBERON:0004535!3.26e-10!110;UBERON:0000468!6.42e-10!659;UBERON:0001009!2.64e-09!113;UBERON:0003102!5.33e-09!95;UBERON:0000922!1.18e-08!612;UBERON:0000467!4.01e-08!625;UBERON:0000480!6.45e-08!626;UBERON:0000947!1.52e-07!21;UBERON:0010191!1.52e-07!21;UBERON:0002050!1.60e-07!605;UBERON:0005423!1.60e-07!605;UBERON:0000923!1.64e-07!604;UBERON:0005291!1.64e-07!604;UBERON:0006598!1.64e-07!604;UBERON:0002532!1.64e-07!604;UBERON:0000926!2.21e-07!448;UBERON:0004120!2.21e-07!448;UBERON:0006603!2.21e-07!448;UBERON:0001444!3.39e-07!48
|ontology_enrichment_uberon=UBERON:0000486!3.75e-23!83;UBERON:0002329!1.98e-20!71;UBERON:0003059!1.98e-20!71;UBERON:0007282!1.98e-20!71;UBERON:0004290!1.98e-20!71;UBERON:0009618!1.98e-20!71;UBERON:0007524!2.94e-20!73;UBERON:0007503!8.93e-20!78;UBERON:0003077!9.26e-20!72;UBERON:0007285!9.26e-20!72;UBERON:0001134!1.32e-19!62;UBERON:0002036!1.32e-19!62;UBERON:0003082!1.32e-19!62;UBERON:0000490!3.74e-19!148;UBERON:0002385!3.29e-18!64;UBERON:0001015!3.29e-18!64;UBERON:0000383!3.29e-18!64;UBERON:0001637!1.18e-16!42;UBERON:0003509!1.18e-16!42;UBERON:0004572!1.18e-16!42;UBERON:0002049!3.53e-16!78;UBERON:0007798!3.53e-16!78;UBERON:0000475!3.09e-15!264;UBERON:0003104!1.04e-14!160;UBERON:0009142!1.04e-14!160;UBERON:0005256!4.38e-14!122;UBERON:0003914!4.70e-14!117;UBERON:0007500!1.05e-13!59;UBERON:0001981!1.05e-13!59;UBERON:0004537!1.05e-13!59;UBERON:0006965!1.05e-13!59;UBERON:0004573!2.32e-13!33;UBERON:0004571!2.32e-13!33;UBERON:0000119!1.64e-12!309;UBERON:0000055!2.29e-12!68;UBERON:0000483!5.30e-12!306;UBERON:0004872!7.65e-12!83;UBERON:0004535!3.18e-11!109;UBERON:0001009!2.99e-10!112;UBERON:0002100!1.05e-09!199;UBERON:0003102!2.69e-09!99;UBERON:0000947!1.20e-08!21;UBERON:0010191!1.20e-08!21;UBERON:0000033!1.65e-08!56;UBERON:0000481!3.00e-08!342;UBERON:0004237!5.00e-08!10;UBERON:0004695!5.00e-08!10;UBERON:0002111!5.00e-08!10;UBERON:0004178!5.00e-08!10;UBERON:0001444!5.37e-08!49;UBERON:0000467!1.47e-07!624;UBERON:0000480!2.02e-07!625;UBERON:0000468!3.59e-07!656;UBERON:0000922!4.91e-07!592;UBERON:0000153!8.85e-07!62;UBERON:0007811!8.85e-07!62
|tf_chipseq_enrich=CTCF#10664;4:4.28820509846002:0.00515201558824328:0.0239249157857065!JUNB#3726;3:18.3663795958927:0.000331631981170089:0.00337773673507148!TCF7L2#6934;3:6.46210593788241:0.00693010875568919:0.0293156315904015!TFAP2C#7022;3:6.48553716591613:0.00685895151794:0.029055813968611!ZZZ3#26009;3:143.64792746114:7.21371177912933e-07:3.21550509816683e-05
|tf_chipseq_enrich=CTCF#10664;4:4.28820509846002:0.00515201558824328:0.0239249157857065!JUNB#3726;3:18.3663795958927:0.000331631981170089:0.00337773673507148!TCF7L2#6934;3:6.46210593788241:0.00693010875568919:0.0293156315904015!TFAP2C#7022;3:6.48553716591613:0.00685895151794:0.029055813968611!ZZZ3#26009;3:143.64792746114:7.21371177912933e-07:3.21550509816683e-05
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}}
}}

Revision as of 11:34, 19 October 2012


Full id: C1682_schwannoma_Fibroblast_hepatoblastoma_Wilms_adrenal_Aortic_meningioma



Phase1 CAGE Peaks

Hg19::chr12:66218836..66218888,+p1@HMGA2
Hg19::chr12:66218904..66218913,+p11@HMGA2
Hg19::chr12:66218923..66218934,+p14@HMGA2
Hg19::chr12:66357214..66357233,+p13@HMGA2
Hg19::chr12:66358080..66358094,+p15@HMGA2


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
multilaminar epithelium3.75e-2383
somite1.98e-2071
presomitic mesoderm1.98e-2071
presumptive segmental plate1.98e-2071
dermomyotome1.98e-2071
trunk paraxial mesoderm1.98e-2071
dense mesenchyme tissue2.94e-2073
epithelial vesicle8.93e-2078
paraxial mesoderm9.26e-2072
presumptive paraxial mesoderm9.26e-2072
skeletal muscle tissue1.32e-1962
striated muscle tissue1.32e-1962
myotome1.32e-1962
unilaminar epithelium3.74e-19148
muscle tissue3.29e-1864
musculature3.29e-1864
musculature of body3.29e-1864
artery1.18e-1642
arterial blood vessel1.18e-1642
arterial system1.18e-1642
vasculature3.53e-1678
vascular system3.53e-1678
organism subdivision3.09e-15264
mesenchyme1.04e-14160
entire embryonic mesenchyme1.04e-14160
trunk mesenchyme4.38e-14122
epithelial tube4.70e-14117
epithelial tube open at both ends1.05e-1359
blood vessel1.05e-1359
blood vasculature1.05e-1359
vascular cord1.05e-1359
systemic artery2.32e-1333
systemic arterial system2.32e-1333
cell layer1.64e-12309
vessel2.29e-1268
epithelium5.30e-12306
splanchnic layer of lateral plate mesoderm7.65e-1283
cardiovascular system3.18e-11109
circulatory system2.99e-10112
trunk1.05e-09199
surface structure2.69e-0999
aorta1.20e-0821
aortic system1.20e-0821
head1.65e-0856
multi-tissue structure3.00e-08342
blood vessel smooth muscle5.00e-0810
arterial system smooth muscle5.00e-0810
artery smooth muscle tissue5.00e-0810
aorta smooth muscle tissue5.00e-0810
subdivision of head5.37e-0849
anatomical system1.47e-07624
anatomical group2.02e-07625
multi-cellular organism3.59e-07656
embryo4.91e-07592
anterior region of body8.85e-0762
craniocervical region8.85e-0762


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
CTCF#1066444.288205098460020.005152015588243280.0239249157857065
JUNB#3726318.36637959589270.0003316319811700890.00337773673507148
TCF7L2#693436.462105937882410.006930108755689190.0293156315904015
TFAP2C#702236.485537165916130.006858951517940.029055813968611
ZZZ3#260093143.647927461147.21371177912933e-073.21550509816683e-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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