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Coexpression cluster:C1417: Difference between revisions

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|full_id=C1417_Mesenchymal_leiomyoblastoma_chorionic_alveolar_uterus_extraskeletal_mesenchymal
|full_id=C1417_Mesenchymal_leiomyoblastoma_chorionic_alveolar_uterus_extraskeletal_mesenchymal
|id=C1417
|id=C1417
|ontology_enrichment_celltype=CL:0000183!2.25e-13!59;CL:0000222!3.10e-13!119;CL:0000187!1.99e-11!54;CL:0000055!2.37e-11!180;CL:0000192!9.29e-11!42;CL:0000514!9.29e-11!42;CL:0000680!1.93e-10!57;CL:0000056!1.93e-10!57;CL:0000355!1.93e-10!57;CL:0000359!2.68e-08!32;CL:0000393!3.74e-08!60;CL:0000211!3.74e-08!60;CL:0000057!5.45e-08!75;CL:0000220!1.78e-07!246;CL:0002321!3.94e-07!248
|ontology_enrichment_celltype=CL:0000222!1.38e-12!121;CL:0000183!2.08e-12!59;CL:0000187!1.12e-10!55;CL:0000192!1.51e-10!43;CL:0000514!1.51e-10!43;CL:0000680!1.50e-09!58;CL:0000056!1.50e-09!58;CL:0000355!1.50e-09!58;CL:0000057!1.63e-08!76;CL:0000359!5.11e-08!32;CL:0000393!1.23e-07!61;CL:0000211!1.23e-07!61;CL:0000349!9.98e-07!19
|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!5.64e-19!264;UBERON:0002100!7.90e-17!199;UBERON:0003104!5.00e-14!160;UBERON:0009142!5.00e-14!160;UBERON:0000481!1.54e-13!342;UBERON:0000477!8.10e-13!373;UBERON:0000119!4.71e-12!309;UBERON:0000468!7.90e-12!656;UBERON:0002049!3.90e-11!78;UBERON:0007798!3.90e-11!78;UBERON:0000483!4.03e-11!306;UBERON:0005256!2.10e-10!122;UBERON:0000490!4.32e-10!148;UBERON:0002385!9.72e-10!64;UBERON:0001015!9.72e-10!64;UBERON:0000383!9.72e-10!64;UBERON:0001134!1.97e-09!62;UBERON:0002036!1.97e-09!62;UBERON:0003082!1.97e-09!62;UBERON:0004872!2.63e-09!83;UBERON:0000467!3.00e-09!624;UBERON:0000480!4.93e-09!625;UBERON:0000486!5.57e-09!83;UBERON:0004111!7.46e-09!240;UBERON:0007503!8.43e-09!78;UBERON:0003886!9.04e-09!54;UBERON:0007524!1.56e-08!73;UBERON:0005156!1.62e-08!59;UBERON:0000990!1.62e-08!59;UBERON:0002329!1.85e-08!71;UBERON:0003059!1.85e-08!71;UBERON:0007282!1.85e-08!71;UBERON:0004290!1.85e-08!71;UBERON:0009618!1.85e-08!71;UBERON:0003077!2.71e-08!72;UBERON:0007285!2.71e-08!72;UBERON:0002323!3.73e-08!46;UBERON:0000464!4.24e-08!95;UBERON:0003914!5.37e-08!117;UBERON:0001008!7.27e-08!48;UBERON:0000055!7.49e-08!68;UBERON:0004458!9.98e-08!49;UBERON:0006554!1.05e-07!47;UBERON:0004923!1.12e-07!66;UBERON:0007500!1.55e-07!59;UBERON:0001981!1.55e-07!59;UBERON:0004537!1.55e-07!59;UBERON:0006965!1.55e-07!59;UBERON:0001637!3.00e-07!42;UBERON:0003509!3.00e-07!42;UBERON:0004572!3.00e-07!42;UBERON:0004573!7.16e-07!33;UBERON:0004571!7.16e-07!33;UBERON:0002553!7.51e-07!61
|tf_chipseq_enrich=E2F1#1869;6:4.90738921487932:7.15746523583771e-05:0.00112713888987584!EP300#2033;5:5.64495143851933:0.000368813893181486:0.00366983176352717!GATA2#2624;6:12.744931733554:2.33109997620343e-07:1.22648740763078e-05!GATA3#2625;4:18.1576775714707:2.56597141799789e-05:0.000554724671753843!HDAC2#3066;4:8.9437468244175:0.000409407956530718:0.00390271609822121!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.03802283232147!SUZ12#23512;6:50.1157809110629:6.2866744827465e-11:6.98482974791024e-09!TCF7L2#6934;4:7.18011770875823:0.000955329712067973:0.0068747798386734!ZNF263#10127;6:8.22184163701068:3.23542093046082e-06:0.000108720761440283
|tf_chipseq_enrich=E2F1#1869;6:4.90738921487932:7.15746523583771e-05:0.00112713888987584!EP300#2033;5:5.64495143851933:0.000368813893181486:0.00366983176352717!GATA2#2624;6:12.744931733554:2.33109997620343e-07:1.22648740763078e-05!GATA3#2625;4:18.1576775714707:2.56597141799789e-05:0.000554724671753843!HDAC2#3066;4:8.9437468244175:0.000409407956530718:0.00390271609822121!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.03802283232147!SUZ12#23512;6:50.1157809110629:6.2866744827465e-11:6.98482974791024e-09!TCF7L2#6934;4:7.18011770875823:0.000955329712067973:0.0068747798386734!ZNF263#10127;6:8.22184163701068:3.23542093046082e-06:0.000108720761440283
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}}
}}

Revision as of 11:15, 19 October 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 subdivision5.64e-19264
trunk7.90e-17199
mesenchyme5.00e-14160
entire embryonic mesenchyme5.00e-14160
multi-tissue structure1.54e-13342
anatomical cluster8.10e-13373
cell layer4.71e-12309
multi-cellular organism7.90e-12656
vasculature3.90e-1178
vascular system3.90e-1178
epithelium4.03e-11306
trunk mesenchyme2.10e-10122
unilaminar epithelium4.32e-10148
muscle tissue9.72e-1064
musculature9.72e-1064
musculature of body9.72e-1064
skeletal muscle tissue1.97e-0962
striated muscle tissue1.97e-0962
myotome1.97e-0962
splanchnic layer of lateral plate mesoderm2.63e-0983
anatomical system3.00e-09624
anatomical group4.93e-09625
multilaminar epithelium5.57e-0983
anatomical conduit7.46e-09240
epithelial vesicle8.43e-0978
body cavity precursor9.04e-0954
dense mesenchyme tissue1.56e-0873
reproductive structure1.62e-0859
reproductive system1.62e-0859
somite1.85e-0871
presomitic mesoderm1.85e-0871
presumptive segmental plate1.85e-0871
dermomyotome1.85e-0871
trunk paraxial mesoderm1.85e-0871
paraxial mesoderm2.71e-0872
presumptive paraxial mesoderm2.71e-0872
body cavity3.73e-0846
anatomical space4.24e-0895
epithelial tube5.37e-08117
renal system7.27e-0848
vessel7.49e-0868
body cavity or lining9.98e-0849
urinary system structure1.05e-0747
organ component layer1.12e-0766
epithelial tube open at both ends1.55e-0759
blood vessel1.55e-0759
blood vasculature1.55e-0759
vascular cord1.55e-0759
artery3.00e-0742
arterial blood vessel3.00e-0742
arterial system3.00e-0742
systemic artery7.16e-0733
systemic arterial system7.16e-0733
anatomical cavity7.51e-0761


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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