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Coexpression cluster:C1788: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.22e-49!115;UBERON:0001049!9.59e-22!57;UBERON:0005068!9.59e-22!57;UBERON:0006241!9.59e-22!57;UBERON:0007135!9.59e-22!57;UBERON:0003075!6.84e-21!86;UBERON:0007284!6.84e-21!86;UBERON:0002346!4.30e-19!90;UBERON:0002616!7.94e-18!59;UBERON:0003080!1.76e-17!42;UBERON:0000073!1.78e-17!94;UBERON:0001016!1.78e-17!94;UBERON:0002780!9.13e-17!41;UBERON:0001890!9.13e-17!41;UBERON:0006240!9.13e-17!41;UBERON:0000153!7.67e-16!129;UBERON:0007811!7.67e-16!129;UBERON:0000033!2.45e-15!123;UBERON:0005743!2.59e-15!86;UBERON:0003056!3.58e-15!61;UBERON:0001017!5.18e-15!82;UBERON:0002020!6.44e-15!34;UBERON:0003528!6.44e-15!34;UBERON:0001893!7.02e-15!34;UBERON:0004121!1.04e-14!169;UBERON:0000955!1.61e-14!69;UBERON:0006238!1.61e-14!69;UBERON:0002791!3.00e-14!33;UBERON:0000475!6.78e-14!365;UBERON:0000924!8.15e-14!173;UBERON:0006601!8.15e-14!173;UBERON:0001869!2.26e-13!32;UBERON:0000481!2.31e-12!347;UBERON:0002619!3.19e-11!22;UBERON:0001950!9.33e-10!20;UBERON:0000956!3.38e-09!25;UBERON:0000203!3.38e-09!25;UBERON:0002298!8.97e-08!8;UBERON:0002420!9.13e-08!9;UBERON:0007245!9.13e-08!9;UBERON:0010009!9.13e-08!9;UBERON:0010011!9.13e-08!9;UBERON:0000454!9.13e-08!9;UBERON:0002308!9.21e-08!9;UBERON:0000125!9.21e-08!9;UBERON:0000483!1.04e-07!309;UBERON:0000477!1.10e-07!286;UBERON:0000119!1.19e-07!312;UBERON:0000064!5.06e-07!219;UBERON:0000468!8.22e-07!659;UBERON:0000062!8.58e-07!511
|ontology_enrichment_uberon=UBERON:0007023!3.65e-38!114;UBERON:0001049!4.61e-12!56;UBERON:0005068!4.61e-12!56;UBERON:0006241!4.61e-12!56;UBERON:0007135!4.61e-12!56;UBERON:0000073!9.38e-12!53;UBERON:0002616!9.38e-12!53;UBERON:0003075!1.03e-11!82;UBERON:0007284!1.03e-11!82;UBERON:0000481!6.17e-11!342;UBERON:0002346!8.19e-11!86;UBERON:0000477!9.79e-11!373;UBERON:0011216!1.01e-10!223;UBERON:0010314!1.23e-10!132;UBERON:0001893!6.06e-10!34;UBERON:0001016!6.10e-10!89;UBERON:0003528!7.32e-10!34;UBERON:0002020!7.32e-10!34;UBERON:0001017!8.61e-09!81;UBERON:0002780!1.18e-08!41;UBERON:0001890!1.18e-08!41;UBERON:0003080!1.18e-08!41;UBERON:0006240!1.18e-08!41;UBERON:0000955!1.53e-08!68;UBERON:0006238!1.53e-08!68;UBERON:0002791!4.25e-08!32;UBERON:0004121!4.53e-08!171;UBERON:0000924!4.53e-08!171;UBERON:0006601!4.53e-08!171;UBERON:0001869!5.49e-08!32;UBERON:0003056!9.79e-08!61;UBERON:0010371!1.13e-07!104;UBERON:0006947!1.17e-07!3;UBERON:0004054!1.17e-07!3;UBERON:0002298!4.11e-07!6;UBERON:0000062!8.15e-07!503
|tf_chipseq_enrich=SUZ12#23512;5:50.1157809110629:3.15480790456198e-09:2.62328807917635e-07
|tf_chipseq_enrich=SUZ12#23512;5:50.1157809110629:3.15480790456198e-09:2.62328807917635e-07
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}}
}}

Revision as of 11:41, 19 October 2012


Full id: C1788_seminal_rhabdomyosarcoma_ductus_lung_epididymis_skeletal_tridermal



Phase1 CAGE Peaks

Hg19::chr17:59475321..59475327,+p@chr17:59475321..59475327
+
Hg19::chr17:59475638..59475661,+p@chr17:59475638..59475661
+
Hg19::chr17:59475669..59475689,+p@chr17:59475669..59475689
+
Hg19::chr17:59475721..59475732,+p@chr17:59475721..59475732
+
Hg19::chr17:59475868..59475879,+p@chr17:59475868..59475879
+


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 organism3.65e-38114
neural tube4.61e-1256
neural rod4.61e-1256
future spinal cord4.61e-1256
neural keel4.61e-1256
regional part of nervous system9.38e-1253
regional part of brain9.38e-1253
neural plate1.03e-1182
presumptive neural plate1.03e-1182
multi-tissue structure6.17e-11342
neurectoderm8.19e-1186
anatomical cluster9.79e-11373
organ system subdivision1.01e-10223
structure with developmental contribution from neural crest1.23e-10132
telencephalon6.06e-1034
nervous system6.10e-1089
brain grey matter7.32e-1034
gray matter7.32e-1034
central nervous system8.61e-0981
regional part of forebrain1.18e-0841
forebrain1.18e-0841
anterior neural tube1.18e-0841
future forebrain1.18e-0841
brain1.53e-0868
future brain1.53e-0868
regional part of telencephalon4.25e-0832
ectoderm-derived structure4.53e-08171
ectoderm4.53e-08171
presumptive ectoderm4.53e-08171
cerebral hemisphere5.49e-0832
pre-chordal neural plate9.79e-0861
ecto-epithelium1.13e-07104
male genital duct1.17e-073
internal male genitalia1.17e-073
brainstem4.11e-076
organ8.15e-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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
SUZ12#23512550.11578091106293.15480790456198e-092.62328807917635e-07



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.