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Coexpression cluster:C2528: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007023!6.52e-75!114;UBERON:0001049!4.86e-39!56;UBERON:0005068!4.86e-39!56;UBERON:0006241!4.86e-39!56;UBERON:0007135!4.86e-39!56;UBERON:0000073!3.44e-36!53;UBERON:0002616!3.44e-36!53;UBERON:0000955!1.75e-31!68;UBERON:0006238!1.75e-31!68;UBERON:0003075!9.16e-31!82;UBERON:0007284!9.16e-31!82;UBERON:0001017!2.81e-30!81;UBERON:0002780!3.85e-29!41;UBERON:0001890!3.85e-29!41;UBERON:0003080!3.85e-29!41;UBERON:0006240!3.85e-29!41;UBERON:0002346!2.38e-28!86;UBERON:0001016!1.96e-27!89;UBERON:0010371!4.17e-23!104;UBERON:0001893!6.80e-23!34;UBERON:0003528!9.01e-23!34;UBERON:0002020!9.01e-23!34;UBERON:0001869!6.67e-21!32;UBERON:0002791!7.46e-21!32;UBERON:0003056!1.68e-20!61;UBERON:0010314!2.65e-20!132;UBERON:0002619!5.15e-16!22;UBERON:0011216!1.74e-14!223;UBERON:0000956!1.83e-14!25;UBERON:0000203!1.83e-14!25;UBERON:0004121!1.84e-14!171;UBERON:0000924!1.84e-14!171;UBERON:0006601!1.84e-14!171;UBERON:0001950!3.54e-14!20;UBERON:0003076!7.70e-11!15;UBERON:0003057!7.70e-11!15;UBERON:0000125!2.85e-10!9;UBERON:0002308!2.85e-10!9;UBERON:0000025!3.75e-10!192;UBERON:0002420!3.79e-10!9;UBERON:0007245!3.79e-10!9;UBERON:0010009!3.79e-10!9;UBERON:0010011!3.79e-10!9;UBERON:0000454!3.79e-10!9;UBERON:0004732!4.41e-09!13;UBERON:0004111!5.15e-09!240;UBERON:0000481!1.20e-08!342;UBERON:0009663!2.64e-08!7;UBERON:0004733!3.36e-08!12;UBERON:0002028!3.36e-08!12;UBERON:0007277!3.36e-08!12;UBERON:0000200!5.23e-08!6;UBERON:0001894!8.60e-08!7;UBERON:0006222!8.60e-08!7;UBERON:0000477!1.98e-07!373;UBERON:0002298!2.10e-07!6;UBERON:0000062!3.95e-07!503
|ontology_enrichment_uberon=UBERON:0007023!6.52e-75!114;UBERON:0001049!4.86e-39!56;UBERON:0005068!4.86e-39!56;UBERON:0006241!4.86e-39!56;UBERON:0007135!4.86e-39!56;UBERON:0000073!3.44e-36!53;UBERON:0002616!3.44e-36!53;UBERON:0000955!1.75e-31!68;UBERON:0006238!1.75e-31!68;UBERON:0003075!9.16e-31!82;UBERON:0007284!9.16e-31!82;UBERON:0001017!2.81e-30!81;UBERON:0002780!3.85e-29!41;UBERON:0001890!3.85e-29!41;UBERON:0003080!3.85e-29!41;UBERON:0006240!3.85e-29!41;UBERON:0002346!2.38e-28!86;UBERON:0001016!1.96e-27!89;UBERON:0010371!4.17e-23!104;UBERON:0001893!6.80e-23!34;UBERON:0003528!9.01e-23!34;UBERON:0002020!9.01e-23!34;UBERON:0001869!6.67e-21!32;UBERON:0002791!7.46e-21!32;UBERON:0003056!1.68e-20!61;UBERON:0010314!2.65e-20!132;UBERON:0002619!5.15e-16!22;UBERON:0011216!1.74e-14!223;UBERON:0000956!1.83e-14!25;UBERON:0000203!1.83e-14!25;UBERON:0004121!1.84e-14!171;UBERON:0000924!1.84e-14!171;UBERON:0006601!1.84e-14!171;UBERON:0001950!3.54e-14!20;UBERON:0003076!7.70e-11!15;UBERON:0003057!7.70e-11!15;UBERON:0000125!2.85e-10!9;UBERON:0002308!2.85e-10!9;UBERON:0000025!3.75e-10!192;UBERON:0002420!3.79e-10!9;UBERON:0007245!3.79e-10!9;UBERON:0010009!3.79e-10!9;UBERON:0010011!3.79e-10!9;UBERON:0000454!3.79e-10!9;UBERON:0004732!4.41e-09!13;UBERON:0004111!5.15e-09!240;UBERON:0000481!1.20e-08!342;UBERON:0009663!2.64e-08!7;UBERON:0004733!3.36e-08!12;UBERON:0002028!3.36e-08!12;UBERON:0007277!3.36e-08!12;UBERON:0000200!5.23e-08!6;UBERON:0001894!8.60e-08!7;UBERON:0006222!8.60e-08!7;UBERON:0000477!1.98e-07!373;UBERON:0002298!2.10e-07!6;UBERON:0000062!3.95e-07!503
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}}
}}

Revision as of 15:33, 26 November 2012


Full id: C2528_left_heart_skeletal_salivary_parotid_melanoma_tongue



Phase1 CAGE Peaks

Hg19::chr1:153600869..153600926,+p1@S100A1
Hg19::chr1:153603063..153603085,+p2@S100A1
Hg19::chr3:42744146..42744193,-p1@HHATL
Hg19::chr3:48057890..48057923,-p6@MAP4


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:0048155S100 alpha binding0.00953642375842857
GO:0051117ATPase binding0.00953642375842857
GO:0048154S100 beta binding0.00953642375842857
GO:0007026negative regulation of microtubule depolymerization0.0198552699367001
GO:0031114regulation of microtubule depolymerization0.0198552699367001
GO:0007019microtubule depolymerization0.0198552699367001
GO:0031111negative regulation of microtubule polymerization or depolymerization0.0198552699367001
GO:0016528sarcoplasm0.0198552699367001
GO:0016529sarcoplasmic reticulum0.0198552699367001
GO:0031110regulation of microtubule polymerization or depolymerization0.0207264605348736
GO:0031109microtubule polymerization or depolymerization0.0207895971926477
GO:0008016regulation of heart contraction0.0223822396814111
GO:0051261protein depolymerization0.0223822396814111
GO:0060047heart contraction0.0223822396814111
GO:0003015heart process0.0223822396814111
GO:0051129negative regulation of cellular component organization and biogenesis0.0232122025618016
GO:0051128regulation of cellular component organization and biogenesis0.039034393714147
GO:0000226microtubule cytoskeleton organization and biogenesis0.039034393714147
GO:0051248negative regulation of protein metabolic process0.039034393714147



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 organism6.52e-75114
neural tube4.86e-3956
neural rod4.86e-3956
future spinal cord4.86e-3956
neural keel4.86e-3956
regional part of nervous system3.44e-3653
regional part of brain3.44e-3653
brain1.75e-3168
future brain1.75e-3168
neural plate9.16e-3182
presumptive neural plate9.16e-3182
central nervous system2.81e-3081
regional part of forebrain3.85e-2941
forebrain3.85e-2941
anterior neural tube3.85e-2941
future forebrain3.85e-2941
neurectoderm2.38e-2886
nervous system1.96e-2789
ecto-epithelium4.17e-23104
telencephalon6.80e-2334
brain grey matter9.01e-2334
gray matter9.01e-2334
cerebral hemisphere6.67e-2132
regional part of telencephalon7.46e-2132
pre-chordal neural plate1.68e-2061
structure with developmental contribution from neural crest2.65e-20132
regional part of cerebral cortex5.15e-1622
organ system subdivision1.74e-14223
cerebral cortex1.83e-1425
pallium1.83e-1425
ectoderm-derived structure1.84e-14171
ectoderm1.84e-14171
presumptive ectoderm1.84e-14171
neocortex3.54e-1420
posterior neural tube7.70e-1115
chordal neural plate7.70e-1115
neural nucleus2.85e-109
nucleus of brain2.85e-109
tube3.75e-10192
basal ganglion3.79e-109
nuclear complex of neuraxis3.79e-109
aggregate regional part of brain3.79e-109
collection of basal ganglia3.79e-109
cerebral subcortex3.79e-109
segmental subdivision of nervous system4.41e-0913
anatomical conduit5.15e-09240
multi-tissue structure1.20e-08342
telencephalic nucleus2.64e-087
segmental subdivision of hindbrain3.36e-0812
hindbrain3.36e-0812
presumptive hindbrain3.36e-0812
gyrus5.23e-086
diencephalon8.60e-087
future diencephalon8.60e-087
anatomical cluster1.98e-07373
brainstem2.10e-076
organ3.95e-07503


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


No analysis results for this cluster

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.