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Coexpression cluster:C4434: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001016!2.13e-30!89;UBERON:0001017!1.71e-29!81;UBERON:0001049!1.73e-29!56;UBERON:0005068!1.73e-29!56;UBERON:0006241!1.73e-29!56;UBERON:0007135!1.73e-29!56;UBERON:0000955!1.33e-27!68;UBERON:0006238!1.33e-27!68;UBERON:0000073!3.63e-27!53;UBERON:0002616!3.63e-27!53;UBERON:0002780!3.11e-25!41;UBERON:0001890!3.11e-25!41;UBERON:0003080!3.11e-25!41;UBERON:0006240!3.11e-25!41;UBERON:0007023!9.28e-25!114;UBERON:0003075!6.05e-22!82;UBERON:0007284!6.05e-22!82;UBERON:0001893!9.60e-22!34;UBERON:0003528!1.26e-21!34;UBERON:0002020!1.26e-21!34;UBERON:0002619!1.58e-21!22;UBERON:0002346!3.16e-21!86;UBERON:0001869!3.39e-20!32;UBERON:0002791!4.66e-20!32;UBERON:0001950!1.88e-19!20;UBERON:0000956!3.59e-18!25;UBERON:0000203!3.59e-18!25;UBERON:0010314!3.86e-18!132;UBERON:0010371!4.87e-18!104;UBERON:0003056!1.04e-16!61;UBERON:0004121!6.90e-15!171;UBERON:0000924!6.90e-15!171;UBERON:0006601!6.90e-15!171;UBERON:0011216!2.00e-13!223;UBERON:0001871!1.07e-09!6;UBERON:0000119!1.01e-07!309;UBERON:0000483!1.53e-07!306;UBERON:0002021!3.18e-07!5;UBERON:0000025!3.80e-07!192;UBERON:0002298!6.14e-07!6;UBERON:0000349!6.31e-07!5;UBERON:0000481!6.50e-07!342
|ontology_enrichment_uberon=UBERON:0001016!2.13e-30!89;UBERON:0001017!1.71e-29!81;UBERON:0001049!1.73e-29!56;UBERON:0005068!1.73e-29!56;UBERON:0006241!1.73e-29!56;UBERON:0007135!1.73e-29!56;UBERON:0000955!1.33e-27!68;UBERON:0006238!1.33e-27!68;UBERON:0000073!3.63e-27!53;UBERON:0002616!3.63e-27!53;UBERON:0002780!3.11e-25!41;UBERON:0001890!3.11e-25!41;UBERON:0003080!3.11e-25!41;UBERON:0006240!3.11e-25!41;UBERON:0007023!9.28e-25!114;UBERON:0003075!6.05e-22!82;UBERON:0007284!6.05e-22!82;UBERON:0001893!9.60e-22!34;UBERON:0003528!1.26e-21!34;UBERON:0002020!1.26e-21!34;UBERON:0002619!1.58e-21!22;UBERON:0002346!3.16e-21!86;UBERON:0001869!3.39e-20!32;UBERON:0002791!4.66e-20!32;UBERON:0001950!1.88e-19!20;UBERON:0000956!3.59e-18!25;UBERON:0000203!3.59e-18!25;UBERON:0010314!3.86e-18!132;UBERON:0010371!4.87e-18!104;UBERON:0003056!1.04e-16!61;UBERON:0004121!6.90e-15!171;UBERON:0000924!6.90e-15!171;UBERON:0006601!6.90e-15!171;UBERON:0011216!2.00e-13!223;UBERON:0001871!1.07e-09!6;UBERON:0000119!1.01e-07!309;UBERON:0000483!1.53e-07!306;UBERON:0002021!3.18e-07!5;UBERON:0000025!3.80e-07!192;UBERON:0002298!6.14e-07!6;UBERON:0000349!6.31e-07!5;UBERON:0000481!6.50e-07!342
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}}
}}

Revision as of 16:44, 26 November 2012


Full id: C4434_Mast_acute_small_pineal_CD34_CD133_anaplastic



Phase1 CAGE Peaks

Hg19::chr4:82136284..82136295,-p3@PRKG2
Hg19::chr4:82136311..82136326,-p2@PRKG2
Hg19::chr4:82136339..82136392,-p1@PRKG2


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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
skin fibroblast1.19e-0723
Uber Anatomy
Ontology termp-valuen
nervous system2.13e-3089
central nervous system1.71e-2981
neural tube1.73e-2956
neural rod1.73e-2956
future spinal cord1.73e-2956
neural keel1.73e-2956
brain1.33e-2768
future brain1.33e-2768
regional part of nervous system3.63e-2753
regional part of brain3.63e-2753
regional part of forebrain3.11e-2541
forebrain3.11e-2541
anterior neural tube3.11e-2541
future forebrain3.11e-2541
adult organism9.28e-25114
neural plate6.05e-2282
presumptive neural plate6.05e-2282
telencephalon9.60e-2234
brain grey matter1.26e-2134
gray matter1.26e-2134
regional part of cerebral cortex1.58e-2122
neurectoderm3.16e-2186
cerebral hemisphere3.39e-2032
regional part of telencephalon4.66e-2032
neocortex1.88e-1920
cerebral cortex3.59e-1825
pallium3.59e-1825
structure with developmental contribution from neural crest3.86e-18132
ecto-epithelium4.87e-18104
pre-chordal neural plate1.04e-1661
ectoderm-derived structure6.90e-15171
ectoderm6.90e-15171
presumptive ectoderm6.90e-15171
organ system subdivision2.00e-13223
temporal lobe1.07e-096
cell layer1.01e-07309
epithelium1.53e-07306
occipital lobe3.18e-075
tube3.80e-07192
brainstem6.14e-076
limbic system6.31e-075
multi-tissue structure6.50e-07342


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)

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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.

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