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Coexpression cluster:C1417: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!1.63e-18!365;UBERON:0002100!4.49e-18!216;UBERON:0000481!6.00e-16!347;UBERON:0000119!5.44e-13!312;UBERON:0000483!5.02e-12!309;UBERON:0002049!5.99e-12!79;UBERON:0007798!5.99e-12!79;UBERON:0005256!6.77e-12!143;UBERON:0003104!1.20e-11!238;UBERON:0009142!1.20e-11!238;UBERON:0000468!1.20e-11!659;UBERON:0000490!1.42e-11!138;UBERON:0004872!1.41e-10!84;UBERON:0002385!1.74e-10!63;UBERON:0001015!1.74e-10!63;UBERON:0000383!1.74e-10!63;UBERON:0001134!3.55e-10!61;UBERON:0002036!3.55e-10!61;UBERON:0003082!3.55e-10!61;UBERON:0000486!9.50e-10!82;UBERON:0004111!1.97e-09!241;UBERON:0004290!2.04e-09!70;UBERON:0000477!2.30e-09!286;UBERON:0003914!3.33e-09!118;UBERON:0003886!3.36e-09!63;UBERON:0004923!5.01e-09!57;UBERON:0000467!9.20e-09!625;UBERON:0000914!9.70e-09!83;UBERON:0002329!9.70e-09!83;UBERON:0003077!9.70e-09!83;UBERON:0003059!9.70e-09!83;UBERON:0007282!9.70e-09!83;UBERON:0009618!9.70e-09!83;UBERON:0007285!9.70e-09!83;UBERON:0000464!1.03e-08!104;UBERON:0000055!1.13e-08!69;UBERON:0005156!1.32e-08!59;UBERON:0000990!1.32e-08!59;UBERON:0000480!1.50e-08!626;UBERON:0001981!1.76e-08!60;UBERON:0007500!1.76e-08!60;UBERON:0004537!1.76e-08!60;UBERON:0006965!1.76e-08!60;UBERON:0001637!9.07e-08!42;UBERON:0003509!9.07e-08!42;UBERON:0004572!9.07e-08!42;UBERON:0002323!9.30e-08!46;UBERON:0002553!1.86e-07!70;UBERON:0004573!2.28e-07!33;UBERON:0004571!2.28e-07!33;UBERON:0004458!2.46e-07!49;UBERON:0000466!2.50e-07!126;UBERON:0001008!4.59e-07!45;UBERON:0006554!5.70e-07!44;UBERON:0000064!5.94e-07!219;UBERON:0004535!7.43e-07!110;UBERON:0000947!8.33e-07!21;UBERON:0010191!8.33e-07!21;UBERON:0001009!8.47e-07!113
|ontology_enrichment_uberon=UBERON:0000475!1.63e-18!365;UBERON:0002100!4.49e-18!216;UBERON:0000481!6.00e-16!347;UBERON:0000119!5.44e-13!312;UBERON:0000483!5.02e-12!309;UBERON:0002049!5.99e-12!79;UBERON:0007798!5.99e-12!79;UBERON:0005256!6.77e-12!143;UBERON:0003104!1.20e-11!238;UBERON:0009142!1.20e-11!238;UBERON:0000468!1.20e-11!659;UBERON:0000490!1.42e-11!138;UBERON:0004872!1.41e-10!84;UBERON:0002385!1.74e-10!63;UBERON:0001015!1.74e-10!63;UBERON:0000383!1.74e-10!63;UBERON:0001134!3.55e-10!61;UBERON:0002036!3.55e-10!61;UBERON:0003082!3.55e-10!61;UBERON:0000486!9.50e-10!82;UBERON:0004111!1.97e-09!241;UBERON:0004290!2.04e-09!70;UBERON:0000477!2.30e-09!286;UBERON:0003914!3.33e-09!118;UBERON:0003886!3.36e-09!63;UBERON:0004923!5.01e-09!57;UBERON:0000467!9.20e-09!625;UBERON:0000914!9.70e-09!83;UBERON:0002329!9.70e-09!83;UBERON:0003077!9.70e-09!83;UBERON:0003059!9.70e-09!83;UBERON:0007282!9.70e-09!83;UBERON:0009618!9.70e-09!83;UBERON:0007285!9.70e-09!83;UBERON:0000464!1.03e-08!104;UBERON:0000055!1.13e-08!69;UBERON:0005156!1.32e-08!59;UBERON:0000990!1.32e-08!59;UBERON:0000480!1.50e-08!626;UBERON:0001981!1.76e-08!60;UBERON:0007500!1.76e-08!60;UBERON:0004537!1.76e-08!60;UBERON:0006965!1.76e-08!60;UBERON:0001637!9.07e-08!42;UBERON:0003509!9.07e-08!42;UBERON:0004572!9.07e-08!42;UBERON:0002323!9.30e-08!46;UBERON:0002553!1.86e-07!70;UBERON:0004573!2.28e-07!33;UBERON:0004571!2.28e-07!33;UBERON:0004458!2.46e-07!49;UBERON:0000466!2.50e-07!126;UBERON:0001008!4.59e-07!45;UBERON:0006554!5.70e-07!44;UBERON:0000064!5.94e-07!219;UBERON:0004535!7.43e-07!110;UBERON:0000947!8.33e-07!21;UBERON:0010191!8.33e-07!21;UBERON:0001009!8.47e-07!113
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}}
}}

Revision as of 13:33, 5 September 2012


Full id: C1417_Mesenchymal_leiomyoblastoma_chorionic_alveolar_uterus_extraskeletal_mesenchymal



Phase1 CAGE Peaks

Hg19::chr15:96869114..96869160,+p11@NR2F2
Hg19::chr15:96869165..96869183,+p20@NR2F2
Hg19::chr15:96869206..96869220,+p21@NR2F2
Hg19::chr15:96869222..96869251,+p18@NR2F2
Hg19::chr15:96869255..96869291,+p6@NR2F2
Hg19::chr15:96869292..96869320,+p15@NR2F2


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
organism subdivision1.63e-18365
trunk4.49e-18216
multi-tissue structure6.00e-16347
cell layer5.44e-13312
epithelium5.02e-12309
vasculature5.99e-1279
vascular system5.99e-1279
trunk mesenchyme6.77e-12143
mesenchyme1.20e-11238
entire embryonic mesenchyme1.20e-11238
multi-cellular organism1.20e-11659
unilaminar epithelium1.42e-11138
splanchnic layer of lateral plate mesoderm1.41e-1084
muscle tissue1.74e-1063
musculature1.74e-1063
musculature of body1.74e-1063
skeletal muscle tissue3.55e-1061
striated muscle tissue3.55e-1061
myotome3.55e-1061
multilaminar epithelium9.50e-1082
anatomical conduit1.97e-09241
dermomyotome2.04e-0970
anatomical cluster2.30e-09286
epithelial tube3.33e-09118
body cavity precursor3.36e-0963
organ component layer5.01e-0957
anatomical system9.20e-09625
somite9.70e-0983
paraxial mesoderm9.70e-0983
presomitic mesoderm9.70e-0983
presumptive segmental plate9.70e-0983
trunk paraxial mesoderm9.70e-0983
presumptive paraxial mesoderm9.70e-0983
anatomical space1.03e-08104
vessel1.13e-0869
reproductive structure1.32e-0859
reproductive system1.32e-0859
anatomical group1.50e-08626
blood vessel1.76e-0860
epithelial tube open at both ends1.76e-0860
blood vasculature1.76e-0860
vascular cord1.76e-0860
artery9.07e-0842
arterial blood vessel9.07e-0842
arterial system9.07e-0842
body cavity9.30e-0846
anatomical cavity1.86e-0770
systemic artery2.28e-0733
systemic arterial system2.28e-0733
body cavity or lining2.46e-0749
immaterial anatomical entity2.50e-07126
renal system4.59e-0745
urinary system structure5.70e-0744
organ part5.94e-07219
cardiovascular system7.43e-07110
aorta8.33e-0721
aortic system8.33e-0721
circulatory system8.47e-07113


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
E2F1#186964.907389214879327.15746523583771e-050.00112713888987584
EP300#203355.644951438519330.0003688138931814860.00366983176352717
GATA2#2624612.7449317335542.33109997620343e-071.22648740763078e-05
GATA3#2625418.15767757147072.56597141799789e-050.000554724671753843
HDAC2#306648.94374682441750.0004094079565307180.00390271609822121
POLR2A#543062.147453176558070.01019570676818780.03802283232147
SUZ12#23512650.11578091106296.2866744827465e-116.98482974791024e-09
TCF7L2#693447.180117708758230.0009553297120679730.0068747798386734
ZNF263#1012768.221841637010683.23542093046082e-060.000108720761440283



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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