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Coexpression cluster:C2951: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!8.55e-34!115;UBERON:0001049!2.07e-32!57;UBERON:0005068!2.07e-32!57;UBERON:0006241!2.07e-32!57;UBERON:0007135!2.07e-32!57;UBERON:0001017!4.58e-32!82;UBERON:0005743!5.20e-32!86;UBERON:0000073!2.02e-30!94;UBERON:0001016!2.02e-30!94;UBERON:0000955!3.11e-28!69;UBERON:0006238!3.11e-28!69;UBERON:0002616!4.86e-28!59;UBERON:0000924!5.07e-28!173;UBERON:0006601!5.07e-28!173;UBERON:0002346!7.88e-28!90;UBERON:0003075!1.78e-27!86;UBERON:0007284!1.78e-27!86;UBERON:0004121!2.01e-27!169;UBERON:0003080!1.49e-24!42;UBERON:0002780!2.91e-24!41;UBERON:0001890!2.91e-24!41;UBERON:0006240!2.91e-24!41;UBERON:0000153!4.51e-22!129;UBERON:0007811!4.51e-22!129;UBERON:0000033!2.04e-21!123;UBERON:0002020!5.69e-21!34;UBERON:0003528!5.69e-21!34;UBERON:0001893!6.76e-21!34;UBERON:0003056!1.20e-20!61;UBERON:0002791!2.49e-20!33;UBERON:0001869!1.15e-19!32;UBERON:0000956!1.84e-15!25;UBERON:0000203!1.84e-15!25;UBERON:0002619!5.45e-14!22;UBERON:0001950!8.69e-13!20;UBERON:0000064!1.61e-12!219;UBERON:0000475!2.73e-12!365;UBERON:0000062!5.02e-11!511;UBERON:0000468!1.13e-09!659;UBERON:0000481!4.09e-09!347;UBERON:0003076!6.33e-09!15;UBERON:0003057!6.33e-09!15;UBERON:0000025!6.85e-09!194;UBERON:0000477!1.80e-08!286;UBERON:0005631!2.66e-08!14;UBERON:0000158!2.66e-08!14;UBERON:0000483!3.52e-08!309;UBERON:0000119!3.86e-08!312;UBERON:0004111!4.16e-08!241;UBERON:0004732!1.12e-07!13;UBERON:0000480!2.56e-07!626;UBERON:0000467!2.97e-07!625;UBERON:0004733!3.20e-07!12;UBERON:0002028!3.20e-07!12;UBERON:0007277!3.20e-07!12;UBERON:0002308!5.56e-07!9;UBERON:0000125!5.56e-07!9;UBERON:0002420!7.06e-07!9;UBERON:0007245!7.06e-07!9;UBERON:0010009!7.06e-07!9;UBERON:0010011!7.06e-07!9;UBERON:0000454!7.06e-07!9
|ontology_enrichment_uberon=UBERON:0001017!4.30e-37!81;UBERON:0001049!2.56e-36!56;UBERON:0005068!2.56e-36!56;UBERON:0006241!2.56e-36!56;UBERON:0007135!2.56e-36!56;UBERON:0001016!1.25e-35!89;UBERON:0000073!2.57e-34!53;UBERON:0002616!2.57e-34!53;UBERON:0000955!2.59e-32!68;UBERON:0006238!2.59e-32!68;UBERON:0004121!4.43e-31!171;UBERON:0000924!4.43e-31!171;UBERON:0006601!4.43e-31!171;UBERON:0007023!3.91e-30!114;UBERON:0002346!6.92e-30!86;UBERON:0003075!9.19e-30!82;UBERON:0007284!9.19e-30!82;UBERON:0002780!1.53e-27!41;UBERON:0001890!1.53e-27!41;UBERON:0003080!1.53e-27!41;UBERON:0006240!1.53e-27!41;UBERON:0003528!3.78e-24!34;UBERON:0002020!3.78e-24!34;UBERON:0001893!4.79e-24!34;UBERON:0001869!1.17e-22!32;UBERON:0002791!1.19e-22!32;UBERON:0010371!1.39e-22!104;UBERON:0003056!7.75e-22!61;UBERON:0010314!1.62e-19!132;UBERON:0011216!6.30e-19!223;UBERON:0000956!1.01e-17!25;UBERON:0000203!1.01e-17!25;UBERON:0002619!7.34e-16!22;UBERON:0000477!8.62e-16!373;UBERON:0001950!1.63e-14!20;UBERON:0000064!3.41e-12!218;UBERON:0000481!2.28e-10!342;UBERON:0003076!8.57e-10!15;UBERON:0003057!8.57e-10!15;UBERON:0005631!1.48e-09!14;UBERON:0000158!1.48e-09!14;UBERON:0000468!3.35e-09!656;UBERON:0000062!1.29e-08!503;UBERON:0004732!1.84e-08!13;UBERON:0000025!4.14e-08!192;UBERON:0004111!4.91e-08!240;UBERON:0004733!6.06e-08!12;UBERON:0002028!6.06e-08!12;UBERON:0007277!6.06e-08!12;UBERON:0000125!6.99e-08!9;UBERON:0002308!6.99e-08!9;UBERON:0002420!1.02e-07!9;UBERON:0007245!1.02e-07!9;UBERON:0010009!1.02e-07!9;UBERON:0010011!1.02e-07!9;UBERON:0000454!1.02e-07!9
|tf_chipseq_enrich=CTBP2#1488;4:62.7170003393281:6.45042639894877e-08:3.97214671391398e-06!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00250272812999021
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}}
}}

Revision as of 14:37, 19 October 2012


Full id: C2951_epididymis_ductus_embryonic_seminal_Amniotic_locus_diaphragm



Phase1 CAGE Peaks

Hg19::chrX:112083964..112083975,-p6@AMOT
Hg19::chrX:112084001..112084012,-p4@AMOT
Hg19::chrX:112084017..112084031,-p3@AMOT
Hg19::chrX:112084045..112084071,-p1@AMOT


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
central nervous system4.30e-3781
neural tube2.56e-3656
neural rod2.56e-3656
future spinal cord2.56e-3656
neural keel2.56e-3656
nervous system1.25e-3589
regional part of nervous system2.57e-3453
regional part of brain2.57e-3453
brain2.59e-3268
future brain2.59e-3268
ectoderm-derived structure4.43e-31171
ectoderm4.43e-31171
presumptive ectoderm4.43e-31171
adult organism3.91e-30114
neurectoderm6.92e-3086
neural plate9.19e-3082
presumptive neural plate9.19e-3082
regional part of forebrain1.53e-2741
forebrain1.53e-2741
anterior neural tube1.53e-2741
future forebrain1.53e-2741
brain grey matter3.78e-2434
gray matter3.78e-2434
telencephalon4.79e-2434
cerebral hemisphere1.17e-2232
regional part of telencephalon1.19e-2232
ecto-epithelium1.39e-22104
pre-chordal neural plate7.75e-2261
structure with developmental contribution from neural crest1.62e-19132
organ system subdivision6.30e-19223
cerebral cortex1.01e-1725
pallium1.01e-1725
regional part of cerebral cortex7.34e-1622
anatomical cluster8.62e-16373
neocortex1.63e-1420
organ part3.41e-12218
multi-tissue structure2.28e-10342
posterior neural tube8.57e-1015
chordal neural plate8.57e-1015
extraembryonic membrane1.48e-0914
membranous layer1.48e-0914
multi-cellular organism3.35e-09656
organ1.29e-08503
segmental subdivision of nervous system1.84e-0813
tube4.14e-08192
anatomical conduit4.91e-08240
segmental subdivision of hindbrain6.06e-0812
hindbrain6.06e-0812
presumptive hindbrain6.06e-0812
neural nucleus6.99e-089
nucleus of brain6.99e-089
basal ganglion1.02e-079
nuclear complex of neuraxis1.02e-079
aggregate regional part of brain1.02e-079
collection of basal ganglia1.02e-079
cerebral subcortex1.02e-079


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
CTBP2#1488462.71700033932816.45042639894877e-083.97214671391398e-06
ZNF263#1012748.221841637010680.0002187871180958320.00250272812999021



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.