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Coexpression cluster:C2820: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!5.31e-37!94;UBERON:0001016!5.31e-37!94;UBERON:0005743!4.29e-36!86;UBERON:0001017!1.01e-34!82;UBERON:0002346!5.77e-33!90;UBERON:0001049!5.92e-33!57;UBERON:0005068!5.92e-33!57;UBERON:0006241!5.92e-33!57;UBERON:0007135!5.92e-33!57;UBERON:0003075!6.42e-31!86;UBERON:0007284!6.42e-31!86;UBERON:0000955!2.49e-29!69;UBERON:0006238!2.49e-29!69;UBERON:0000924!6.98e-29!173;UBERON:0006601!6.98e-29!173;UBERON:0002780!3.31e-28!41;UBERON:0001890!3.31e-28!41;UBERON:0006240!3.31e-28!41;UBERON:0002616!8.93e-28!59;UBERON:0004121!4.77e-27!169;UBERON:0003080!5.75e-27!42;UBERON:0003056!4.91e-25!61;UBERON:0002020!5.39e-24!34;UBERON:0003528!5.39e-24!34;UBERON:0001893!6.92e-24!34;UBERON:0002791!3.72e-23!33;UBERON:0001869!7.14e-23!32;UBERON:0000033!4.99e-21!123;UBERON:0000153!5.14e-20!129;UBERON:0007811!5.14e-20!129;UBERON:0000956!1.57e-18!25;UBERON:0000203!1.57e-18!25;UBERON:0000475!2.96e-18!365;UBERON:0007023!4.43e-18!115;UBERON:0002619!1.61e-17!22;UBERON:0001950!3.20e-16!20;UBERON:0000025!1.69e-13!194;UBERON:0000468!6.67e-13!659;UBERON:0000064!1.25e-12!219;UBERON:0000483!5.48e-12!309;UBERON:0000119!2.20e-11!312;UBERON:0004111!2.66e-11!241;UBERON:0000467!5.61e-11!625;UBERON:0000480!8.25e-11!626;UBERON:0000477!3.82e-09!286;UBERON:0000922!4.11e-09!612;UBERON:0000481!5.05e-09!347;UBERON:0000062!8.05e-09!511;UBERON:0002050!5.78e-08!605;UBERON:0005423!5.78e-08!605;UBERON:0000923!1.04e-07!604;UBERON:0005291!1.04e-07!604;UBERON:0006598!1.04e-07!604;UBERON:0002532!1.04e-07!604;UBERON:0003076!2.70e-07!15;UBERON:0003057!2.70e-07!15;UBERON:0001871!5.47e-07!7;UBERON:0002420!6.45e-07!9;UBERON:0007245!6.45e-07!9;UBERON:0010009!6.45e-07!9;UBERON:0010011!6.45e-07!9;UBERON:0000454!6.45e-07!9;UBERON:0002308!6.54e-07!9;UBERON:0000125!6.54e-07!9
|ontology_enrichment_uberon=UBERON:0001049!9.32e-42!56;UBERON:0005068!9.32e-42!56;UBERON:0006241!9.32e-42!56;UBERON:0007135!9.32e-42!56;UBERON:0001017!5.18e-41!81;UBERON:0001016!1.06e-39!89;UBERON:0000073!2.77e-39!53;UBERON:0002616!2.77e-39!53;UBERON:0002346!4.39e-36!86;UBERON:0000955!2.15e-35!68;UBERON:0006238!2.15e-35!68;UBERON:0003075!6.03e-35!82;UBERON:0007284!6.03e-35!82;UBERON:0002780!8.30e-34!41;UBERON:0001890!8.30e-34!41;UBERON:0003080!8.30e-34!41;UBERON:0006240!8.30e-34!41;UBERON:0003056!4.25e-30!61;UBERON:0003528!1.24e-28!34;UBERON:0002020!1.24e-28!34;UBERON:0001893!1.68e-28!34;UBERON:0001869!2.69e-27!32;UBERON:0002791!5.57e-27!32;UBERON:0004121!9.20e-27!171;UBERON:0000924!9.20e-27!171;UBERON:0006601!9.20e-27!171;UBERON:0010371!4.49e-26!104;UBERON:0010314!3.12e-22!132;UBERON:0000956!5.21e-22!25;UBERON:0000203!5.21e-22!25;UBERON:0002619!7.07e-21!22;UBERON:0001950!2.30e-19!20;UBERON:0007023!2.88e-19!114;UBERON:0011216!6.00e-15!223;UBERON:0000025!5.98e-12!192;UBERON:0000477!2.04e-11!373;UBERON:0000064!3.55e-10!218;UBERON:0000468!7.51e-10!656;UBERON:0003076!3.73e-09!15;UBERON:0003057!3.73e-09!15;UBERON:0004111!6.27e-09!240;UBERON:0000467!6.44e-09!624;UBERON:0000480!8.28e-09!625;UBERON:0000483!3.75e-08!306;UBERON:0000125!4.86e-08!9;UBERON:0002308!4.86e-08!9;UBERON:0002420!4.94e-08!9;UBERON:0007245!4.94e-08!9;UBERON:0010009!4.94e-08!9;UBERON:0010011!4.94e-08!9;UBERON:0000454!4.94e-08!9;UBERON:0000062!8.71e-08!503;UBERON:0000119!8.71e-08!309;UBERON:0001871!3.70e-07!6;UBERON:0000481!4.06e-07!342;UBERON:0000922!5.40e-07!592;UBERON:0004733!6.02e-07!12;UBERON:0002028!6.02e-07!12;UBERON:0007277!6.02e-07!12;UBERON:0005631!7.09e-07!14;UBERON:0000158!7.09e-07!14;UBERON:0000200!8.17e-07!6
|tf_chipseq_enrich=JUND#3727;3:5.24599795640327:0.0104343275174842:0.0387150323859078!NANOG#79923;3:21.9335838607595:0.000155753581638277:0.00196553266224263!RAD21#5885;3:7.76627542159225:0.003341119385872:0.0172761247421074!RXRA#6256;3:15.05596285435:0.000475830799730358:0.00434020025266715!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.032311935243295!TCF12#6938;3:7.97584867663982:0.00309092039601307:0.0162880385104803
|tf_chipseq_enrich=JUND#3727;3:5.24599795640327:0.0104343275174842:0.0387150323859078!NANOG#79923;3:21.9335838607595:0.000155753581638277:0.00196553266224263!RAD21#5885;3:7.76627542159225:0.003341119385872:0.0172761247421074!RXRA#6256;3:15.05596285435:0.000475830799730358:0.00434020025266715!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.032311935243295!TCF12#6938;3:7.97584867663982:0.00309092039601307:0.0162880385104803
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}}
}}

Revision as of 14:27, 19 October 2012


Full id: C2820_pineal_epithelioid_cerebellum_occipital_temporal_parietal_myxofibrosarcoma



Phase1 CAGE Peaks

Hg19::chr5:24644931..24644947,-p4@CDH10
Hg19::chr5:24645032..24645068,-p1@CDH10
Hg19::chr5:24645078..24645096,-p2@CDH10
Hg19::chr8:12809475..12809502,+p7@KIAA1456


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
neural tube9.32e-4256
neural rod9.32e-4256
future spinal cord9.32e-4256
neural keel9.32e-4256
central nervous system5.18e-4181
nervous system1.06e-3989
regional part of nervous system2.77e-3953
regional part of brain2.77e-3953
neurectoderm4.39e-3686
brain2.15e-3568
future brain2.15e-3568
neural plate6.03e-3582
presumptive neural plate6.03e-3582
regional part of forebrain8.30e-3441
forebrain8.30e-3441
anterior neural tube8.30e-3441
future forebrain8.30e-3441
pre-chordal neural plate4.25e-3061
brain grey matter1.24e-2834
gray matter1.24e-2834
telencephalon1.68e-2834
cerebral hemisphere2.69e-2732
regional part of telencephalon5.57e-2732
ectoderm-derived structure9.20e-27171
ectoderm9.20e-27171
presumptive ectoderm9.20e-27171
ecto-epithelium4.49e-26104
structure with developmental contribution from neural crest3.12e-22132
cerebral cortex5.21e-2225
pallium5.21e-2225
regional part of cerebral cortex7.07e-2122
neocortex2.30e-1920
adult organism2.88e-19114
organ system subdivision6.00e-15223
tube5.98e-12192
anatomical cluster2.04e-11373
organ part3.55e-10218
multi-cellular organism7.51e-10656
posterior neural tube3.73e-0915
chordal neural plate3.73e-0915
anatomical conduit6.27e-09240
anatomical system6.44e-09624
anatomical group8.28e-09625
epithelium3.75e-08306
neural nucleus4.86e-089
nucleus of brain4.86e-089
basal ganglion4.94e-089
nuclear complex of neuraxis4.94e-089
aggregate regional part of brain4.94e-089
collection of basal ganglia4.94e-089
cerebral subcortex4.94e-089
organ8.71e-08503
cell layer8.71e-08309
temporal lobe3.70e-076
multi-tissue structure4.06e-07342
embryo5.40e-07592
segmental subdivision of hindbrain6.02e-0712
hindbrain6.02e-0712
presumptive hindbrain6.02e-0712
extraembryonic membrane7.09e-0714
membranous layer7.09e-0714
gyrus8.17e-076


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
JUND#372735.245997956403270.01043432751748420.0387150323859078
NANOG#79923321.93358386075950.0001557535816382770.00196553266224263
RAD21#588537.766275421592250.0033411193858720.0172761247421074
RXRA#6256315.055962854350.0004758307997303580.00434020025266715
TAF1#687243.343046285745290.008005664898701650.032311935243295
TCF12#693837.975848676639820.003090920396013070.0162880385104803



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.