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Coexpression cluster:C2262: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!4.76e-37!115;UBERON:0002616!8.71e-26!59;UBERON:0000073!9.29e-25!94;UBERON:0001016!9.29e-25!94;UBERON:0001049!1.49e-24!57;UBERON:0005068!1.49e-24!57;UBERON:0006241!1.49e-24!57;UBERON:0007135!1.49e-24!57;UBERON:0000955!4.27e-24!69;UBERON:0006238!4.27e-24!69;UBERON:0001017!3.04e-23!82;UBERON:0000153!1.44e-22!129;UBERON:0007811!1.44e-22!129;UBERON:0000033!1.86e-22!123;UBERON:0003080!3.24e-22!42;UBERON:0002780!5.90e-22!41;UBERON:0001890!5.90e-22!41;UBERON:0006240!5.90e-22!41;UBERON:0005743!6.43e-22!86;UBERON:0002346!7.80e-22!90;UBERON:0000924!2.68e-21!173;UBERON:0006601!2.68e-21!173;UBERON:0002020!4.83e-20!34;UBERON:0003528!4.83e-20!34;UBERON:0001893!6.97e-20!34;UBERON:0001869!1.86e-19!32;UBERON:0003075!2.25e-19!86;UBERON:0007284!2.25e-19!86;UBERON:0004121!3.26e-19!169;UBERON:0002791!3.73e-19!33;UBERON:0002619!7.66e-16!22;UBERON:0000956!1.97e-15!25;UBERON:0000203!1.97e-15!25;UBERON:0003056!3.22e-15!61;UBERON:0001950!8.49e-15!20;UBERON:0000481!7.20e-10!347;UBERON:0000477!1.80e-09!286;UBERON:0000475!1.53e-08!365;UBERON:0004111!6.41e-08!241;UBERON:0000062!3.50e-07!511;UBERON:0001871!9.17e-07!7
|ontology_enrichment_uberon=UBERON:0007023!4.76e-37!115;UBERON:0002616!8.71e-26!59;UBERON:0000073!9.29e-25!94;UBERON:0001016!9.29e-25!94;UBERON:0001049!1.49e-24!57;UBERON:0005068!1.49e-24!57;UBERON:0006241!1.49e-24!57;UBERON:0007135!1.49e-24!57;UBERON:0000955!4.27e-24!69;UBERON:0006238!4.27e-24!69;UBERON:0001017!3.04e-23!82;UBERON:0000153!1.44e-22!129;UBERON:0007811!1.44e-22!129;UBERON:0000033!1.86e-22!123;UBERON:0003080!3.24e-22!42;UBERON:0002780!5.90e-22!41;UBERON:0001890!5.90e-22!41;UBERON:0006240!5.90e-22!41;UBERON:0005743!6.43e-22!86;UBERON:0002346!7.80e-22!90;UBERON:0000924!2.68e-21!173;UBERON:0006601!2.68e-21!173;UBERON:0002020!4.83e-20!34;UBERON:0003528!4.83e-20!34;UBERON:0001893!6.97e-20!34;UBERON:0001869!1.86e-19!32;UBERON:0003075!2.25e-19!86;UBERON:0007284!2.25e-19!86;UBERON:0004121!3.26e-19!169;UBERON:0002791!3.73e-19!33;UBERON:0002619!7.66e-16!22;UBERON:0000956!1.97e-15!25;UBERON:0000203!1.97e-15!25;UBERON:0003056!3.22e-15!61;UBERON:0001950!8.49e-15!20;UBERON:0000481!7.20e-10!347;UBERON:0000477!1.80e-09!286;UBERON:0000475!1.53e-08!365;UBERON:0004111!6.41e-08!241;UBERON:0000062!3.50e-07!511;UBERON:0001871!9.17e-07!7
|tf_chipseq_enrich=EP300#2033;4:6.7739417262232:0.000474845982144264:0.00433651972098328!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00767110625783102!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321541220765105!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0243709918755017
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}}
}}

Revision as of 12:24, 5 September 2012


Full id: C2262_neuroectodermal_extraskeletal_neuroblastoma_B_carcinoid_plasma_choriocarcinoma



Phase1 CAGE Peaks

Hg19::chr13:33780076..33780094,-p5@STARD13
Hg19::chr13:33780107..33780116,-p9@STARD13
Hg19::chr13:33780118..33780132,-p7@STARD13
Hg19::chr13:33780133..33780168,-p2@STARD13


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 organism4.76e-37115
regional part of brain8.71e-2659
regional part of nervous system9.29e-2594
nervous system9.29e-2594
neural tube1.49e-2457
neural rod1.49e-2457
future spinal cord1.49e-2457
neural keel1.49e-2457
brain4.27e-2469
future brain4.27e-2469
central nervous system3.04e-2382
anterior region of body1.44e-22129
craniocervical region1.44e-22129
head1.86e-22123
anterior neural tube3.24e-2242
regional part of forebrain5.90e-2241
forebrain5.90e-2241
future forebrain5.90e-2241
neurectoderm7.80e-2290
ectoderm2.68e-21173
presumptive ectoderm2.68e-21173
gray matter4.83e-2034
brain grey matter4.83e-2034
telencephalon6.97e-2034
cerebral hemisphere1.86e-1932
neural plate2.25e-1986
presumptive neural plate2.25e-1986
ectoderm-derived structure3.26e-19169
regional part of telencephalon3.73e-1933
regional part of cerebral cortex7.66e-1622
cerebral cortex1.97e-1525
pallium1.97e-1525
pre-chordal neural plate3.22e-1561
neocortex8.49e-1520
multi-tissue structure7.20e-10347
anatomical cluster1.80e-09286
organism subdivision1.53e-08365
anatomical conduit6.41e-08241
organ3.50e-07511
temporal lobe9.17e-077


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
EP300#203346.77394172622320.0004748459821442640.00433651972098328
NFKB1#479045.488063424193840.001102199566301980.00767110625783102
TAF1#687243.343046285745290.008005664898701650.0321541220765105
TBP#690843.706770687096390.005296377814784350.0243709918755017



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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