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Coexpression cluster:C2588: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!1.70e-59!57;UBERON:0005068!1.70e-59!57;UBERON:0006241!1.70e-59!57;UBERON:0007135!1.70e-59!57;UBERON:0001017!1.77e-54!82;UBERON:0000073!3.02e-53!94;UBERON:0001016!3.02e-53!94;UBERON:0005743!1.16e-52!86;UBERON:0002616!1.38e-49!59;UBERON:0007023!7.41e-48!115;UBERON:0002780!4.81e-46!41;UBERON:0001890!4.81e-46!41;UBERON:0006240!4.81e-46!41;UBERON:0000955!8.91e-45!69;UBERON:0006238!8.91e-45!69;UBERON:0003080!1.36e-44!42;UBERON:0003075!1.59e-41!86;UBERON:0007284!1.59e-41!86;UBERON:0002020!1.47e-39!34;UBERON:0003528!1.47e-39!34;UBERON:0001893!3.63e-39!34;UBERON:0002346!1.03e-38!90;UBERON:0002791!7.48e-38!33;UBERON:0001869!3.05e-37!32;UBERON:0002619!4.91e-30!22;UBERON:0000956!7.99e-30!25;UBERON:0000203!7.99e-30!25;UBERON:0003056!7.11e-29!61;UBERON:0001950!1.07e-27!20;UBERON:0004121!4.49e-27!169;UBERON:0000924!7.31e-26!173;UBERON:0006601!7.31e-26!173;UBERON:0000153!4.99e-22!129;UBERON:0007811!4.99e-22!129;UBERON:0000033!2.14e-21!123;UBERON:0003076!2.04e-15!15;UBERON:0003057!2.04e-15!15;UBERON:0000025!1.13e-13!194;UBERON:0004732!4.94e-13!13;UBERON:0004733!3.58e-12!12;UBERON:0002028!3.58e-12!12;UBERON:0007277!3.58e-12!12;UBERON:0001871!3.23e-11!7;UBERON:0002308!4.77e-11!9;UBERON:0000125!4.77e-11!9;UBERON:0002420!8.89e-11!9;UBERON:0007245!8.89e-11!9;UBERON:0010009!8.89e-11!9;UBERON:0010011!8.89e-11!9;UBERON:0000454!8.89e-11!9;UBERON:0004111!2.53e-10!241;UBERON:0000064!1.46e-09!219;UBERON:0000200!1.93e-09!6;UBERON:0002680!9.76e-09!9;UBERON:0001895!9.76e-09!9;UBERON:0010092!9.76e-09!9;UBERON:0002298!1.59e-08!8;UBERON:0009663!1.80e-08!7;UBERON:0000477!3.20e-08!286;UBERON:0001894!3.62e-08!7;UBERON:0006222!3.62e-08!7;UBERON:0001872!5.07e-08!5;UBERON:0000062!5.71e-08!511;UBERON:0002021!8.14e-08!5;UBERON:0000922!1.04e-07!612;UBERON:0000349!2.00e-07!5
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}}
}}

Revision as of 18:25, 8 August 2012


Full id: C2588_occipital_neuroblastoma_medial_parietal_pons_locus_middle



Phase1 CAGE Peaks

Hg19::chr1:50571340..50571365,+p10@ELAVL4
Hg19::chr1:50571897..50571910,+p9@ELAVL4
Hg19::chr1:50571949..50571958,+p15@ELAVL4
Hg19::chr1:50574585..50574627,+p1@ELAVL4


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
neural tube1.70e-5957
neural rod1.70e-5957
future spinal cord1.70e-5957
neural keel1.70e-5957
central nervous system1.77e-5482
regional part of nervous system3.02e-5394
nervous system3.02e-5394
regional part of brain1.38e-4959
adult organism7.41e-48115
regional part of forebrain4.81e-4641
forebrain4.81e-4641
future forebrain4.81e-4641
brain8.91e-4569
future brain8.91e-4569
anterior neural tube1.36e-4442
neural plate1.59e-4186
presumptive neural plate1.59e-4186
gray matter1.47e-3934
brain grey matter1.47e-3934
telencephalon3.63e-3934
neurectoderm1.03e-3890
regional part of telencephalon7.48e-3833
cerebral hemisphere3.05e-3732
regional part of cerebral cortex4.91e-3022
cerebral cortex7.99e-3025
pallium7.99e-3025
pre-chordal neural plate7.11e-2961
neocortex1.07e-2720
ectoderm-derived structure4.49e-27169
ectoderm7.31e-26173
presumptive ectoderm7.31e-26173
anterior region of body4.99e-22129
craniocervical region4.99e-22129
head2.14e-21123
posterior neural tube2.04e-1515
chordal neural plate2.04e-1515
tube1.13e-13194
segmental subdivision of nervous system4.94e-1313
segmental subdivision of hindbrain3.58e-1212
hindbrain3.58e-1212
presumptive hindbrain3.58e-1212
temporal lobe3.23e-117
nucleus of brain4.77e-119
neural nucleus4.77e-119
basal ganglion8.89e-119
nuclear complex of neuraxis8.89e-119
aggregate regional part of brain8.89e-119
collection of basal ganglia8.89e-119
cerebral subcortex8.89e-119
anatomical conduit2.53e-10241
organ part1.46e-09219
gyrus1.93e-096
regional part of metencephalon9.76e-099
metencephalon9.76e-099
future metencephalon9.76e-099
brainstem1.59e-088
telencephalic nucleus1.80e-087
anatomical cluster3.20e-08286
diencephalon3.62e-087
future diencephalon3.62e-087
parietal lobe5.07e-085
organ5.71e-08511
occipital lobe8.14e-085
embryo1.04e-07612
limbic system2.00e-075


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.