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Coexpression cluster:C4389: Difference between revisions

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|id=C4389
|id=C4389
|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=DOID:169!2.35e-07!6
|ontology_enrichment_uberon=UBERON:0000073!6.37e-48!94;UBERON:0001016!6.37e-48!94;UBERON:0005743!1.68e-44!86;UBERON:0001017!4.44e-43!82;UBERON:0001049!1.43e-42!57;UBERON:0005068!1.43e-42!57;UBERON:0006241!1.43e-42!57;UBERON:0007135!1.43e-42!57;UBERON:0000955!4.33e-39!69;UBERON:0006238!4.33e-39!69;UBERON:0002616!3.60e-38!59;UBERON:0002780!1.26e-33!41;UBERON:0001890!1.26e-33!41;UBERON:0006240!1.26e-33!41;UBERON:0003075!6.46e-33!86;UBERON:0007284!6.46e-33!86;UBERON:0003080!1.22e-32!42;UBERON:0002346!1.38e-32!90;UBERON:0002020!8.86e-30!34;UBERON:0003528!8.86e-30!34;UBERON:0001893!1.31e-29!34;UBERON:0001869!2.67e-29!32;UBERON:0002791!7.45e-28!33;UBERON:0002619!2.63e-27!22;UBERON:0001950!4.01e-27!20;UBERON:0003056!6.23e-27!61;UBERON:0007023!6.21e-26!115;UBERON:0000033!1.88e-25!123;UBERON:0000924!5.12e-25!173;UBERON:0006601!5.12e-25!173;UBERON:0004121!7.90e-25!169;UBERON:0000153!1.14e-23!129;UBERON:0007811!1.14e-23!129;UBERON:0000956!1.57e-23!25;UBERON:0000203!1.57e-23!25;UBERON:0001871!7.28e-13!7;UBERON:0004732!1.03e-12!13;UBERON:0004733!5.05e-11!12;UBERON:0002028!5.05e-11!12;UBERON:0007277!5.05e-11!12;UBERON:0003076!7.77e-11!15;UBERON:0003057!7.77e-11!15;UBERON:0000200!1.32e-09!6;UBERON:0000025!3.23e-09!194;UBERON:0002680!7.27e-09!9;UBERON:0001895!7.27e-09!9;UBERON:0010092!7.27e-09!9;UBERON:0002021!9.62e-08!5;UBERON:0002420!1.02e-07!9;UBERON:0007245!1.02e-07!9;UBERON:0010009!1.02e-07!9;UBERON:0010011!1.02e-07!9;UBERON:0000454!1.02e-07!9;UBERON:0002308!1.06e-07!9;UBERON:0000125!1.06e-07!9;UBERON:0002771!1.49e-07!3;UBERON:0001872!2.07e-07!5;UBERON:0000064!2.71e-07!219;UBERON:0000988!2.86e-07!3;UBERON:0000349!4.08e-07!5
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}}
}}

Revision as of 15:55, 19 October 2012


Full id: C4389_small_neuroblastoma_nonsmall_heart_cerebellum_medulloblastoma_temporal



Phase1 CAGE Peaks

Hg19::chr4:163084988..163084999,-p5@FSTL5
Hg19::chr5:16179713..16179724,-p4@MARCH11
Hg19::chr5:16179727..16179759,-p2@MARCH11


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
neural tube7.98e-4356
neural rod7.98e-4356
future spinal cord7.98e-4356
neural keel7.98e-4356
regional part of nervous system1.01e-4153
regional part of brain1.01e-4153
nervous system1.03e-4189
central nervous system1.10e-3781
brain2.49e-3668
future brain2.49e-3668
neural plate8.50e-3582
presumptive neural plate8.50e-3582
neurectoderm7.08e-3386
ecto-epithelium3.30e-28104
regional part of cerebral cortex3.16e-2722
regional part of forebrain3.18e-2741
forebrain3.18e-2741
anterior neural tube3.18e-2741
future forebrain3.18e-2741
brain grey matter3.93e-2634
gray matter3.93e-2634
neocortex1.37e-2520
cerebral hemisphere3.13e-2432
pre-chordal neural plate8.72e-2461
cerebral cortex9.44e-2425
pallium9.44e-2425
ectoderm-derived structure8.25e-23171
ectoderm8.25e-23171
presumptive ectoderm8.25e-23171
telencephalon1.20e-2234
structure with developmental contribution from neural crest1.64e-22132
regional part of telencephalon5.28e-2132
adult organism1.28e-19114
brainstem2.34e-176
posterior neural tube5.41e-1715
chordal neural plate5.41e-1715
gyrus5.89e-176
organ system subdivision6.38e-17223
segmental subdivision of hindbrain1.80e-1612
hindbrain1.80e-1612
presumptive hindbrain1.80e-1612
segmental subdivision of nervous system3.97e-1513
occipital lobe8.48e-145
pons1.88e-133
tube2.35e-12192
regional part of metencephalon8.00e-129
metencephalon8.00e-129
future metencephalon8.00e-129
locus ceruleus1.81e-092
brainstem nucleus1.81e-092
hindbrain nucleus1.81e-092
middle temporal gyrus2.43e-092
organ part4.98e-09218
anatomical cluster5.15e-09373
sympathetic nervous system9.32e-095
autonomic nervous system9.32e-095
anatomical conduit1.52e-08240
epithelium7.06e-08306
cell layer9.92e-08309
Disease
Ontology termp-valuen
neuroendocrine tumor2.35e-076


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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