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Coexpression cluster:C4050: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!3.11e-37!115;UBERON:0005743!5.90e-37!86;UBERON:0000073!3.51e-35!94;UBERON:0001016!3.51e-35!94;UBERON:0001017!1.48e-34!82;UBERON:0001049!1.38e-30!57;UBERON:0005068!1.38e-30!57;UBERON:0006241!1.38e-30!57;UBERON:0007135!1.38e-30!57;UBERON:0002346!4.66e-30!90;UBERON:0003075!7.09e-29!86;UBERON:0007284!7.09e-29!86;UBERON:0000955!6.88e-28!69;UBERON:0006238!6.88e-28!69;UBERON:0000924!1.73e-26!173;UBERON:0006601!1.73e-26!173;UBERON:0004121!2.71e-25!169;UBERON:0002616!3.59e-25!59;UBERON:0002780!3.43e-24!41;UBERON:0001890!3.43e-24!41;UBERON:0006240!3.43e-24!41;UBERON:0003080!3.25e-23!42;UBERON:0000153!3.55e-23!129;UBERON:0007811!3.55e-23!129;UBERON:0000033!3.31e-22!123;UBERON:0003056!4.16e-21!61;UBERON:0002020!5.71e-21!34;UBERON:0003528!5.71e-21!34;UBERON:0001893!6.67e-21!34;UBERON:0002791!2.47e-20!33;UBERON:0001869!2.39e-19!32;UBERON:0000064!2.63e-16!219;UBERON:0000956!4.33e-15!25;UBERON:0000203!4.33e-15!25;UBERON:0002619!8.20e-14!22;UBERON:0000062!1.38e-13!511;UBERON:0001950!2.16e-12!20;UBERON:0000468!3.19e-12!659;UBERON:0000922!5.81e-12!612;UBERON:0000475!5.81e-12!365;UBERON:0000481!1.11e-11!347;UBERON:0002050!2.05e-09!605;UBERON:0005423!2.05e-09!605;UBERON:0000923!4.51e-09!604;UBERON:0005291!4.51e-09!604;UBERON:0006598!4.51e-09!604;UBERON:0002532!4.51e-09!604;UBERON:0000480!7.75e-09!626;UBERON:0000467!1.40e-08!625;UBERON:0003076!1.79e-08!15;UBERON:0003057!1.79e-08!15;UBERON:0005409!3.03e-08!35;UBERON:0004111!2.04e-07!241;UBERON:0002308!2.19e-07!9;UBERON:0000125!2.19e-07!9;UBERON:0004732!3.22e-07!13;UBERON:0002420!4.86e-07!9;UBERON:0007245!4.86e-07!9;UBERON:0010009!4.86e-07!9;UBERON:0010011!4.86e-07!9;UBERON:0000454!4.86e-07!9;UBERON:0000489!5.62e-07!32;UBERON:0000160!5.79e-07!27
|ontology_enrichment_uberon=UBERON:0007023!2.11e-39!114;UBERON:0001017!2.21e-39!81;UBERON:0001016!3.88e-37!89;UBERON:0001049!8.93e-37!56;UBERON:0005068!8.93e-37!56;UBERON:0006241!8.93e-37!56;UBERON:0007135!8.93e-37!56;UBERON:0000073!4.80e-34!53;UBERON:0002616!4.80e-34!53;UBERON:0002346!5.87e-33!86;UBERON:0000955!8.11e-33!68;UBERON:0006238!8.11e-33!68;UBERON:0003075!2.20e-31!82;UBERON:0007284!2.20e-31!82;UBERON:0002780!4.21e-28!41;UBERON:0001890!4.21e-28!41;UBERON:0003080!4.21e-28!41;UBERON:0006240!4.21e-28!41;UBERON:0004121!7.84e-26!171;UBERON:0000924!7.84e-26!171;UBERON:0006601!7.84e-26!171;UBERON:0003056!1.55e-24!61;UBERON:0001893!2.34e-24!34;UBERON:0003528!2.78e-24!34;UBERON:0002020!2.78e-24!34;UBERON:0010371!6.12e-24!104;UBERON:0011216!2.22e-23!223;UBERON:0002791!9.45e-23!32;UBERON:0001869!1.58e-22!32;UBERON:0010314!2.24e-21!132;UBERON:0000477!1.41e-17!373;UBERON:0000956!2.31e-17!25;UBERON:0000203!2.31e-17!25;UBERON:0002619!9.38e-16!22;UBERON:0000064!1.24e-14!218;UBERON:0001950!5.43e-14!20;UBERON:0000062!5.57e-12!503;UBERON:0000468!1.60e-11!656;UBERON:0000481!2.56e-11!342;UBERON:0000922!1.55e-10!592;UBERON:0003076!1.07e-09!15;UBERON:0003057!1.07e-09!15;UBERON:0000125!2.04e-08!9;UBERON:0002308!2.04e-08!9;UBERON:0004732!4.17e-08!13;UBERON:0002420!4.84e-08!9;UBERON:0007245!4.84e-08!9;UBERON:0010009!4.84e-08!9;UBERON:0010011!4.84e-08!9;UBERON:0000454!4.84e-08!9;UBERON:0005423!4.97e-08!581;UBERON:0004111!8.80e-08!240;UBERON:0000480!1.53e-07!625;UBERON:0000025!2.52e-07!192;UBERON:0000467!2.65e-07!624;UBERON:0004733!3.37e-07!12;UBERON:0002028!3.37e-07!12;UBERON:0007277!3.37e-07!12;UBERON:0009663!6.39e-07!7;UBERON:0005409!9.23e-07!25
|tf_chipseq_enrich=ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109589004690682
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}}
}}

Revision as of 15:38, 19 October 2012


Full id: C4050_MCF7_Burkitt_keratoacanthoma_colon_small_synovial_peripheral



Phase1 CAGE Peaks

Hg19::chr20:55841403..55841458,-p2@BMP7
Hg19::chr20:55841618..55841629,-p6@BMP7
Hg19::chr20:55841662..55841736,-p1@BMP7


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
adult organism2.11e-39114
central nervous system2.21e-3981
nervous system3.88e-3789
neural tube8.93e-3756
neural rod8.93e-3756
future spinal cord8.93e-3756
neural keel8.93e-3756
regional part of nervous system4.80e-3453
regional part of brain4.80e-3453
neurectoderm5.87e-3386
brain8.11e-3368
future brain8.11e-3368
neural plate2.20e-3182
presumptive neural plate2.20e-3182
regional part of forebrain4.21e-2841
forebrain4.21e-2841
anterior neural tube4.21e-2841
future forebrain4.21e-2841
ectoderm-derived structure7.84e-26171
ectoderm7.84e-26171
presumptive ectoderm7.84e-26171
pre-chordal neural plate1.55e-2461
telencephalon2.34e-2434
brain grey matter2.78e-2434
gray matter2.78e-2434
ecto-epithelium6.12e-24104
organ system subdivision2.22e-23223
regional part of telencephalon9.45e-2332
cerebral hemisphere1.58e-2232
structure with developmental contribution from neural crest2.24e-21132
anatomical cluster1.41e-17373
cerebral cortex2.31e-1725
pallium2.31e-1725
regional part of cerebral cortex9.38e-1622
organ part1.24e-14218
neocortex5.43e-1420
organ5.57e-12503
multi-cellular organism1.60e-11656
multi-tissue structure2.56e-11342
embryo1.55e-10592
posterior neural tube1.07e-0915
chordal neural plate1.07e-0915
neural nucleus2.04e-089
nucleus of brain2.04e-089
segmental subdivision of nervous system4.17e-0813
basal ganglion4.84e-089
nuclear complex of neuraxis4.84e-089
aggregate regional part of brain4.84e-089
collection of basal ganglia4.84e-089
cerebral subcortex4.84e-089
developing anatomical structure4.97e-08581
anatomical conduit8.80e-08240
anatomical group1.53e-07625
tube2.52e-07192
anatomical system2.65e-07624
segmental subdivision of hindbrain3.37e-0712
hindbrain3.37e-0712
presumptive hindbrain3.37e-0712
telencephalic nucleus6.39e-077
gastrointestinal system9.23e-0725


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
ZNF263#1012738.221841637010680.001799043925565870.0109589004690682



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.