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Coexpression cluster:C2657: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005743!2.04e-43!86;UBERON:0001017!2.72e-42!82;UBERON:0000073!1.09e-39!94;UBERON:0001016!1.09e-39!94;UBERON:0001049!4.07e-39!57;UBERON:0005068!4.07e-39!57;UBERON:0006241!4.07e-39!57;UBERON:0007135!4.07e-39!57;UBERON:0003075!3.52e-33!86;UBERON:0007284!3.52e-33!86;UBERON:0001893!5.15e-33!34;UBERON:0002020!5.85e-33!34;UBERON:0003528!5.85e-33!34;UBERON:0002780!2.44e-32!41;UBERON:0001890!2.44e-32!41;UBERON:0006240!2.44e-32!41;UBERON:0002616!5.11e-32!59;UBERON:0000955!5.40e-32!69;UBERON:0006238!5.40e-32!69;UBERON:0002791!5.84e-32!33;UBERON:0002346!7.74e-32!90;UBERON:0001869!1.33e-31!32;UBERON:0003080!3.21e-31!42;UBERON:0007023!4.27e-30!115;UBERON:0000956!1.22e-25!25;UBERON:0000203!1.22e-25!25;UBERON:0003056!3.96e-25!61;UBERON:0002619!2.50e-24!22;UBERON:0001950!1.30e-22!20;UBERON:0004121!5.08e-20!169;UBERON:0000924!1.23e-19!173;UBERON:0006601!1.23e-19!173;UBERON:0000153!2.51e-18!129;UBERON:0007811!2.51e-18!129;UBERON:0000033!3.18e-17!123;UBERON:0000025!3.49e-10!194;UBERON:0001871!2.49e-09!7;UBERON:0002420!3.96e-09!9;UBERON:0007245!3.96e-09!9;UBERON:0010009!3.96e-09!9;UBERON:0010011!3.96e-09!9;UBERON:0000454!3.96e-09!9;UBERON:0003076!5.16e-09!15;UBERON:0003057!5.16e-09!15;UBERON:0002308!1.00e-08!9;UBERON:0000125!1.00e-08!9;UBERON:0000200!9.81e-08!6;UBERON:0000064!1.05e-07!219;UBERON:0004732!1.81e-07!13;UBERON:0009663!4.70e-07!7;UBERON:0004733!7.97e-07!12;UBERON:0002028!7.97e-07!12;UBERON:0007277!7.97e-07!12
|ontology_enrichment_uberon=UBERON:0005743!2.04e-43!86;UBERON:0001017!2.72e-42!82;UBERON:0000073!1.09e-39!94;UBERON:0001016!1.09e-39!94;UBERON:0001049!4.07e-39!57;UBERON:0005068!4.07e-39!57;UBERON:0006241!4.07e-39!57;UBERON:0007135!4.07e-39!57;UBERON:0003075!3.52e-33!86;UBERON:0007284!3.52e-33!86;UBERON:0001893!5.15e-33!34;UBERON:0002020!5.85e-33!34;UBERON:0003528!5.85e-33!34;UBERON:0002780!2.44e-32!41;UBERON:0001890!2.44e-32!41;UBERON:0006240!2.44e-32!41;UBERON:0002616!5.11e-32!59;UBERON:0000955!5.40e-32!69;UBERON:0006238!5.40e-32!69;UBERON:0002791!5.84e-32!33;UBERON:0002346!7.74e-32!90;UBERON:0001869!1.33e-31!32;UBERON:0003080!3.21e-31!42;UBERON:0007023!4.27e-30!115;UBERON:0000956!1.22e-25!25;UBERON:0000203!1.22e-25!25;UBERON:0003056!3.96e-25!61;UBERON:0002619!2.50e-24!22;UBERON:0001950!1.30e-22!20;UBERON:0004121!5.08e-20!169;UBERON:0000924!1.23e-19!173;UBERON:0006601!1.23e-19!173;UBERON:0000153!2.51e-18!129;UBERON:0007811!2.51e-18!129;UBERON:0000033!3.18e-17!123;UBERON:0000025!3.49e-10!194;UBERON:0001871!2.49e-09!7;UBERON:0002420!3.96e-09!9;UBERON:0007245!3.96e-09!9;UBERON:0010009!3.96e-09!9;UBERON:0010011!3.96e-09!9;UBERON:0000454!3.96e-09!9;UBERON:0003076!5.16e-09!15;UBERON:0003057!5.16e-09!15;UBERON:0002308!1.00e-08!9;UBERON:0000125!1.00e-08!9;UBERON:0000200!9.81e-08!6;UBERON:0000064!1.05e-07!219;UBERON:0004732!1.81e-07!13;UBERON:0009663!4.70e-07!7;UBERON:0004733!7.97e-07!12;UBERON:0002028!7.97e-07!12;UBERON:0007277!7.97e-07!12
|tf_chipseq_enrich=JUND#3727;3:5.24599795640327:0.0104343275174842:0.0387040322346403
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}}
}}

Revision as of 13:57, 5 September 2012


Full id: C2657_retinoblastoma_nonsmall_acute_myelodysplastic_large_hepatoblastoma_brain



Phase1 CAGE Peaks

Hg19::chr2:115897297..115897302,-p@chr2:115897297..115897302
-
Hg19::chr2:115918904..115918922,-p1@LOC389023
Hg19::chr2:115918927..115918946,-p2@LOC389023
Hg19::chr2:115919049..115919088,+p2@DPP10


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


GO IDGO nameFDR corrected p-value
GO:0004274dipeptidyl-peptidase IV activity0.0041014168530947
GO:0016806dipeptidyl-peptidase and tripeptidyl-peptidase activity0.0041014168530947
GO:0008239dipeptidyl-peptidase activity0.0041014168530947
GO:0008238exopeptidase activity0.0302749322971859
GO:0008236serine-type peptidase activity0.0406903724635975
GO:0017171serine hydrolase activity0.0406903724635975



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>


Cell Type
Ontology termp-valuen
neuronal stem cell7.76e-088
neural cell8.21e-0725
Uber Anatomy
Ontology termp-valuen
central nervous system2.72e-4282
regional part of nervous system1.09e-3994
nervous system1.09e-3994
neural tube4.07e-3957
neural rod4.07e-3957
future spinal cord4.07e-3957
neural keel4.07e-3957
neural plate3.52e-3386
presumptive neural plate3.52e-3386
telencephalon5.15e-3334
gray matter5.85e-3334
brain grey matter5.85e-3334
regional part of forebrain2.44e-3241
forebrain2.44e-3241
future forebrain2.44e-3241
regional part of brain5.11e-3259
brain5.40e-3269
future brain5.40e-3269
regional part of telencephalon5.84e-3233
neurectoderm7.74e-3290
cerebral hemisphere1.33e-3132
anterior neural tube3.21e-3142
adult organism4.27e-30115
cerebral cortex1.22e-2525
pallium1.22e-2525
pre-chordal neural plate3.96e-2561
regional part of cerebral cortex2.50e-2422
neocortex1.30e-2220
ectoderm-derived structure5.08e-20169
ectoderm1.23e-19173
presumptive ectoderm1.23e-19173
anterior region of body2.51e-18129
craniocervical region2.51e-18129
head3.18e-17123
tube3.49e-10194
temporal lobe2.49e-097
basal ganglion3.96e-099
nuclear complex of neuraxis3.96e-099
aggregate regional part of brain3.96e-099
collection of basal ganglia3.96e-099
cerebral subcortex3.96e-099
posterior neural tube5.16e-0915
chordal neural plate5.16e-0915
nucleus of brain1.00e-089
neural nucleus1.00e-089
gyrus9.81e-086
organ part1.05e-07219
segmental subdivision of nervous system1.81e-0713
telencephalic nucleus4.70e-077
segmental subdivision of hindbrain7.97e-0712
hindbrain7.97e-0712
presumptive hindbrain7.97e-0712


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#372735.245997956403270.01043432751748420.0387040322346403



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.