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Coexpression cluster:C2517: Difference between revisions

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|id=C2517
|id=C2517
|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=DOID:0050687!5.95e-07!143
|ontology_enrichment_uberon=UBERON:0007023!2.15e-37!115;UBERON:0001049!2.80e-24!57;UBERON:0005068!2.80e-24!57;UBERON:0006241!2.80e-24!57;UBERON:0007135!2.80e-24!57;UBERON:0002780!6.77e-22!41;UBERON:0001890!6.77e-22!41;UBERON:0006240!6.77e-22!41;UBERON:0003080!2.70e-21!42;UBERON:0001017!6.35e-21!82;UBERON:0000955!5.98e-20!69;UBERON:0006238!5.98e-20!69;UBERON:0002616!2.35e-19!59;UBERON:0005743!5.96e-19!86;UBERON:0002020!6.50e-18!34;UBERON:0003528!6.50e-18!34;UBERON:0001893!8.24e-18!34;UBERON:0000073!1.65e-17!94;UBERON:0001016!1.65e-17!94;UBERON:0002791!2.92e-17!33;UBERON:0001869!7.31e-17!32;UBERON:0002619!5.88e-15!22;UBERON:0001950!7.67e-14!20;UBERON:0000956!1.03e-12!25;UBERON:0000203!1.03e-12!25;UBERON:0002346!1.28e-12!90;UBERON:0003075!5.20e-12!86;UBERON:0007284!5.20e-12!86;UBERON:0003056!4.83e-09!61;UBERON:0000924!2.95e-07!173;UBERON:0006601!2.95e-07!173;UBERON:0000153!4.69e-07!129;UBERON:0007811!4.69e-07!129;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:0000033!8.34e-07!123;UBERON:0004121!8.65e-07!169;UBERON:0002308!9.55e-07!9;UBERON:0000125!9.55e-07!9
|ontology_enrichment_uberon=UBERON:0007023!4.35e-36!114;UBERON:0001049!7.05e-25!56;UBERON:0005068!7.05e-25!56;UBERON:0006241!7.05e-25!56;UBERON:0007135!7.05e-25!56;UBERON:0000073!5.39e-24!53;UBERON:0002616!5.39e-24!53;UBERON:0002780!1.68e-21!41;UBERON:0001890!1.68e-21!41;UBERON:0003080!1.68e-21!41;UBERON:0006240!1.68e-21!41;UBERON:0001017!2.73e-21!81;UBERON:0000955!8.55e-21!68;UBERON:0006238!8.55e-21!68;UBERON:0001016!4.20e-19!89;UBERON:0003528!1.68e-17!34;UBERON:0002020!1.68e-17!34;UBERON:0001893!2.24e-17!34;UBERON:0002791!1.45e-16!32;UBERON:0001869!1.62e-16!32;UBERON:0002619!8.92e-15!22;UBERON:0001950!1.22e-13!20;UBERON:0000956!2.22e-12!25;UBERON:0000203!2.22e-12!25;UBERON:0002346!5.84e-12!86;UBERON:0003075!2.33e-11!82;UBERON:0007284!2.33e-11!82;UBERON:0011216!7.13e-10!223;UBERON:0003056!1.46e-08!61;UBERON:0002420!4.62e-07!9;UBERON:0007245!4.62e-07!9;UBERON:0010009!4.62e-07!9;UBERON:0010011!4.62e-07!9;UBERON:0000454!4.62e-07!9;UBERON:0004121!4.70e-07!171;UBERON:0000924!4.70e-07!171;UBERON:0006601!4.70e-07!171
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}}
}}

Revision as of 14:07, 19 October 2012


Full id: C2517_testis_putamen_brain_Whole_caudate_parietal_middle



Phase1 CAGE Peaks

Hg19::chr1:117944801..117944860,+p@chr1:117944801..117944860
+
Hg19::chr1:117948207..117948222,+p@chr1:117948207..117948222
+
Hg19::chr1:117957343..117957358,+p@chr1:117957343..117957358
+
Hg19::chr1:117963209..117963245,+p2@MAN1A2


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
adult organism4.35e-36114
neural tube7.05e-2556
neural rod7.05e-2556
future spinal cord7.05e-2556
neural keel7.05e-2556
regional part of nervous system5.39e-2453
regional part of brain5.39e-2453
regional part of forebrain1.68e-2141
forebrain1.68e-2141
anterior neural tube1.68e-2141
future forebrain1.68e-2141
central nervous system2.73e-2181
brain8.55e-2168
future brain8.55e-2168
nervous system4.20e-1989
brain grey matter1.68e-1734
gray matter1.68e-1734
telencephalon2.24e-1734
regional part of telencephalon1.45e-1632
cerebral hemisphere1.62e-1632
regional part of cerebral cortex8.92e-1522
neocortex1.22e-1320
cerebral cortex2.22e-1225
pallium2.22e-1225
neurectoderm5.84e-1286
neural plate2.33e-1182
presumptive neural plate2.33e-1182
organ system subdivision7.13e-10223
pre-chordal neural plate1.46e-0861
basal ganglion4.62e-079
nuclear complex of neuraxis4.62e-079
aggregate regional part of brain4.62e-079
collection of basal ganglia4.62e-079
cerebral subcortex4.62e-079
ectoderm-derived structure4.70e-07171
ectoderm4.70e-07171
presumptive ectoderm4.70e-07171
Disease
Ontology termp-valuen
cell type cancer5.95e-07143


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.

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