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Coexpression cluster:C1316: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.47e-52!115;UBERON:0001049!6.69e-31!57;UBERON:0005068!6.69e-31!57;UBERON:0006241!6.69e-31!57;UBERON:0007135!6.69e-31!57;UBERON:0003080!1.22e-25!42;UBERON:0001017!1.52e-25!82;UBERON:0002616!2.91e-25!59;UBERON:0002780!3.22e-25!41;UBERON:0001890!3.22e-25!41;UBERON:0006240!3.22e-25!41;UBERON:0005743!2.42e-24!86;UBERON:0000073!2.93e-24!94;UBERON:0001016!2.93e-24!94;UBERON:0000955!8.71e-23!69;UBERON:0006238!8.71e-23!69;UBERON:0002020!3.85e-21!34;UBERON:0003528!3.85e-21!34;UBERON:0001893!5.03e-21!34;UBERON:0002791!1.92e-20!33;UBERON:0001869!1.03e-19!32;UBERON:0002346!5.24e-19!90;UBERON:0003075!2.97e-18!86;UBERON:0007284!2.97e-18!86;UBERON:0000956!2.43e-15!25;UBERON:0000203!2.43e-15!25;UBERON:0002619!5.13e-15!22;UBERON:0003056!7.95e-14!61;UBERON:0001950!1.01e-13!20;UBERON:0000153!2.97e-09!129;UBERON:0007811!2.97e-09!129;UBERON:0000924!1.21e-08!173;UBERON:0006601!1.21e-08!173;UBERON:0000033!2.49e-08!123;UBERON:0004121!4.50e-08!169;UBERON:0002308!2.73e-07!9;UBERON:0000125!2.73e-07!9;UBERON:0002420!3.52e-07!9;UBERON:0007245!3.52e-07!9;UBERON:0010009!3.52e-07!9;UBERON:0010011!3.52e-07!9;UBERON:0000454!3.52e-07!9
|ontology_enrichment_uberon=UBERON:0007023!1.85e-51!114;UBERON:0001049!2.85e-30!56;UBERON:0005068!2.85e-30!56;UBERON:0006241!2.85e-30!56;UBERON:0007135!2.85e-30!56;UBERON:0000073!1.96e-28!53;UBERON:0002616!1.96e-28!53;UBERON:0001016!1.04e-26!89;UBERON:0001017!1.85e-26!81;UBERON:0002780!3.02e-25!41;UBERON:0001890!3.02e-25!41;UBERON:0003080!3.02e-25!41;UBERON:0006240!3.02e-25!41;UBERON:0000955!8.60e-24!68;UBERON:0006238!8.60e-24!68;UBERON:0003528!4.58e-21!34;UBERON:0002020!4.58e-21!34;UBERON:0001893!5.94e-21!34;UBERON:0002791!9.22e-20!32;UBERON:0001869!1.16e-19!32;UBERON:0002346!1.51e-18!86;UBERON:0003075!1.07e-17!82;UBERON:0007284!1.07e-17!82;UBERON:0000956!2.83e-15!25;UBERON:0000203!2.83e-15!25;UBERON:0002619!4.45e-15!22;UBERON:0001950!8.88e-14!20;UBERON:0011216!1.40e-13!223;UBERON:0003056!5.53e-13!61;UBERON:0010371!6.10e-11!104;UBERON:0004121!1.95e-10!171;UBERON:0000924!1.95e-10!171;UBERON:0006601!1.95e-10!171;UBERON:0010314!1.72e-07!132;UBERON:0000125!2.77e-07!9;UBERON:0002308!2.77e-07!9;UBERON:0002420!3.58e-07!9;UBERON:0007245!3.58e-07!9;UBERON:0010009!3.58e-07!9;UBERON:0010011!3.58e-07!9;UBERON:0000454!3.58e-07!9
|tf_chipseq_enrich=MAX#4149;4:4.30170367267141:0.00664492391067637:0.0282926009338795
|tf_chipseq_enrich=MAX#4149;4:4.30170367267141:0.00664492391067637:0.0282926009338795
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}}
}}

Revision as of 11:07, 19 October 2012


Full id: C1316_cerebellum_thalamus_globus_substantia_occipital_hippocampus_middle



Phase1 CAGE Peaks

Hg19::chr10:594847..594852,-p@chr10:594847..594852
-
Hg19::chr10:94000428..94000487,-p4@CPEB3
Hg19::chr19:21603457..21603460,+p@chr19:21603457..21603460
+
Hg19::chr1:65533390..65533443,-p1@ENST00000448344
Hg19::chr2:70313393..70313424,-p1@PCBP1-AS1
Hg19::chr9:14314946..14314983,-p8@NFIB


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 organism1.85e-51114
neural tube2.85e-3056
neural rod2.85e-3056
future spinal cord2.85e-3056
neural keel2.85e-3056
regional part of nervous system1.96e-2853
regional part of brain1.96e-2853
nervous system1.04e-2689
central nervous system1.85e-2681
regional part of forebrain3.02e-2541
forebrain3.02e-2541
anterior neural tube3.02e-2541
future forebrain3.02e-2541
brain8.60e-2468
future brain8.60e-2468
brain grey matter4.58e-2134
gray matter4.58e-2134
telencephalon5.94e-2134
regional part of telencephalon9.22e-2032
cerebral hemisphere1.16e-1932
neurectoderm1.51e-1886
neural plate1.07e-1782
presumptive neural plate1.07e-1782
cerebral cortex2.83e-1525
pallium2.83e-1525
regional part of cerebral cortex4.45e-1522
neocortex8.88e-1420
organ system subdivision1.40e-13223
pre-chordal neural plate5.53e-1361
ecto-epithelium6.10e-11104
ectoderm-derived structure1.95e-10171
ectoderm1.95e-10171
presumptive ectoderm1.95e-10171
structure with developmental contribution from neural crest1.72e-07132
neural nucleus2.77e-079
nucleus of brain2.77e-079
basal ganglion3.58e-079
nuclear complex of neuraxis3.58e-079
aggregate regional part of brain3.58e-079
collection of basal ganglia3.58e-079
cerebral subcortex3.58e-079


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
MAX#414944.301703672671410.006644923910676370.0282926009338795



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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