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Coexpression cluster:C4555: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!4.55e-33!94;UBERON:0001016!4.55e-33!94;UBERON:0001017!1.97e-32!82;UBERON:0005743!1.85e-30!86;UBERON:0000955!1.97e-24!69;UBERON:0006238!1.97e-24!69;UBERON:0001049!5.59e-23!57;UBERON:0005068!5.59e-23!57;UBERON:0006241!5.59e-23!57;UBERON:0007135!5.59e-23!57;UBERON:0002616!1.02e-21!59;UBERON:0003075!1.05e-21!86;UBERON:0007284!1.05e-21!86;UBERON:0002346!2.61e-21!90;UBERON:0004121!3.70e-21!169;UBERON:0000924!4.09e-21!173;UBERON:0006601!4.09e-21!173;UBERON:0000033!2.16e-18!123;UBERON:0003056!2.08e-17!61;UBERON:0000475!2.43e-17!365;UBERON:0000153!2.94e-16!129;UBERON:0007811!2.94e-16!129;UBERON:0000119!9.31e-16!312;UBERON:0002780!9.74e-16!41;UBERON:0001890!9.74e-16!41;UBERON:0006240!9.74e-16!41;UBERON:0003080!4.85e-15!42;UBERON:0000483!6.16e-15!309;UBERON:0000025!1.23e-13!194;UBERON:0002020!1.67e-13!34;UBERON:0003528!1.67e-13!34;UBERON:0001893!5.08e-13!34;UBERON:0002791!1.31e-12!33;UBERON:0001869!1.51e-12!32;UBERON:0000481!4.55e-12!347;UBERON:0000956!1.14e-11!25;UBERON:0000203!1.14e-11!25;UBERON:0000914!7.03e-10!83;UBERON:0002329!7.03e-10!83;UBERON:0003077!7.03e-10!83;UBERON:0003059!7.03e-10!83;UBERON:0007282!7.03e-10!83;UBERON:0009618!7.03e-10!83;UBERON:0007285!7.03e-10!83;UBERON:0002619!1.45e-09!22;UBERON:0003076!1.90e-09!15;UBERON:0003057!1.90e-09!15;UBERON:0004290!2.97e-09!70;UBERON:0001950!4.40e-09!20;UBERON:0004732!8.17e-09!13;UBERON:0004733!2.13e-08!12;UBERON:0002028!2.13e-08!12;UBERON:0007277!2.13e-08!12;UBERON:0004111!3.35e-08!241;UBERON:0000477!6.78e-08!286;UBERON:0001134!1.78e-07!61;UBERON:0002036!1.78e-07!61;UBERON:0003082!1.78e-07!61;UBERON:0002385!2.74e-07!63;UBERON:0001015!2.74e-07!63;UBERON:0000383!2.74e-07!63;UBERON:0002680!6.19e-07!9;UBERON:0001895!6.19e-07!9;UBERON:0010092!6.19e-07!9;UBERON:0000064!7.79e-07!219
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}}
}}

Revision as of 20:07, 8 August 2012


Full id: C4555_neuroblastoma_occipital_parietal_carcinoid_brain_Neural_mesothelioma



Phase1 CAGE Peaks

Hg19::chr6:127840021..127840047,-p4@C6orf174
Hg19::chr6:127840048..127840074,-p5@C6orf174
Hg19::chr6:127840089..127840099,-p16@C6orf174


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>


Uber Anatomy
Ontology termp-valuen
regional part of nervous system4.55e-3394
nervous system4.55e-3394
central nervous system1.97e-3282
brain1.97e-2469
future brain1.97e-2469
neural tube5.59e-2357
neural rod5.59e-2357
future spinal cord5.59e-2357
neural keel5.59e-2357
regional part of brain1.02e-2159
neural plate1.05e-2186
presumptive neural plate1.05e-2186
neurectoderm2.61e-2190
ectoderm-derived structure3.70e-21169
ectoderm4.09e-21173
presumptive ectoderm4.09e-21173
head2.16e-18123
pre-chordal neural plate2.08e-1761
organism subdivision2.43e-17365
anterior region of body2.94e-16129
craniocervical region2.94e-16129
cell layer9.31e-16312
regional part of forebrain9.74e-1641
forebrain9.74e-1641
future forebrain9.74e-1641
anterior neural tube4.85e-1542
epithelium6.16e-15309
tube1.23e-13194
gray matter1.67e-1334
brain grey matter1.67e-1334
telencephalon5.08e-1334
regional part of telencephalon1.31e-1233
cerebral hemisphere1.51e-1232
multi-tissue structure4.55e-12347
cerebral cortex1.14e-1125
pallium1.14e-1125
somite7.03e-1083
paraxial mesoderm7.03e-1083
presomitic mesoderm7.03e-1083
presumptive segmental plate7.03e-1083
trunk paraxial mesoderm7.03e-1083
presumptive paraxial mesoderm7.03e-1083
regional part of cerebral cortex1.45e-0922
posterior neural tube1.90e-0915
chordal neural plate1.90e-0915
dermomyotome2.97e-0970
neocortex4.40e-0920
segmental subdivision of nervous system8.17e-0913
segmental subdivision of hindbrain2.13e-0812
hindbrain2.13e-0812
presumptive hindbrain2.13e-0812
anatomical conduit3.35e-08241
anatomical cluster6.78e-08286
skeletal muscle tissue1.78e-0761
striated muscle tissue1.78e-0761
myotome1.78e-0761
muscle tissue2.74e-0763
musculature2.74e-0763
musculature of body2.74e-0763
regional part of metencephalon6.19e-079
metencephalon6.19e-079
future metencephalon6.19e-079
organ part7.79e-07219


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.