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Coexpression cluster:C1559: Difference between revisions

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|id=C1559
|id=C1559
|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=DOID:305!1.95e-07!106
|ontology_enrichment_disease=DOID:1749!6.02e-07!14
|ontology_enrichment_uberon=UBERON:0001049!8.62e-36!57;UBERON:0005068!8.62e-36!57;UBERON:0006241!8.62e-36!57;UBERON:0007135!8.62e-36!57;UBERON:0007023!2.96e-34!115;UBERON:0002780!2.57e-31!41;UBERON:0001890!2.57e-31!41;UBERON:0006240!2.57e-31!41;UBERON:0001017!4.31e-31!82;UBERON:0003080!3.71e-30!42;UBERON:0005743!1.07e-29!86;UBERON:0002616!3.48e-29!59;UBERON:0000955!7.48e-28!69;UBERON:0006238!7.48e-28!69;UBERON:0000073!1.53e-27!94;UBERON:0001016!1.53e-27!94;UBERON:0003075!1.84e-26!86;UBERON:0007284!1.84e-26!86;UBERON:0001893!7.43e-26!34;UBERON:0002020!8.53e-26!34;UBERON:0003528!8.53e-26!34;UBERON:0002346!4.80e-25!90;UBERON:0001869!5.91e-25!32;UBERON:0002791!6.26e-25!33;UBERON:0002619!9.69e-23!22;UBERON:0003056!6.51e-21!61;UBERON:0001950!6.60e-21!20;UBERON:0000956!7.48e-19!25;UBERON:0000203!7.48e-19!25;UBERON:0004121!1.23e-15!169;UBERON:0000924!3.93e-15!173;UBERON:0006601!3.93e-15!173;UBERON:0000033!9.07e-15!123;UBERON:0000153!1.38e-14!129;UBERON:0007811!1.38e-14!129;UBERON:0000064!3.09e-13!219;UBERON:0001871!5.65e-09!7;UBERON:0002420!6.46e-09!9;UBERON:0007245!6.46e-09!9;UBERON:0010009!6.46e-09!9;UBERON:0010011!6.46e-09!9;UBERON:0000454!6.46e-09!9;UBERON:0002308!2.16e-08!9;UBERON:0000125!2.16e-08!9;UBERON:0000062!5.55e-08!511;UBERON:0000025!3.00e-07!194;UBERON:0000200!3.40e-07!6;UBERON:0003076!4.06e-07!15;UBERON:0003057!4.06e-07!15;UBERON:0009663!6.02e-07!7;UBERON:0001894!7.61e-07!7;UBERON:0006222!7.61e-07!7
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}}
}}

Revision as of 11:26, 19 October 2012


Full id: C1559_large_amygdala_pineal_temporal_medial_olfactory_cerebellum



Phase1 CAGE Peaks

Hg19::chr10:105253535..105253604,+p5@NEURL
Hg19::chr10:105253611..105253627,+p10@NEURL
Hg19::chr10:105253790..105253822,+p19@NEURL
Hg19::chr10:105254031..105254098,+p2@NEURL
Hg19::chr10:105254104..105254135,+p6@NEURL


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 tube5.69e-5456
neural rod5.69e-5456
future spinal cord5.69e-5456
neural keel5.69e-5456
regional part of nervous system4.85e-5153
regional part of brain4.85e-5153
regional part of forebrain3.64e-4541
forebrain3.64e-4541
anterior neural tube3.64e-4541
future forebrain3.64e-4541
central nervous system4.76e-4581
brain2.82e-4368
future brain2.82e-4368
nervous system1.65e-4189
cerebral hemisphere2.19e-3732
telencephalon7.63e-3734
brain grey matter1.01e-3634
gray matter1.01e-3634
adult organism1.93e-35114
regional part of telencephalon1.57e-3432
neural plate7.83e-3382
presumptive neural plate7.83e-3382
regional part of cerebral cortex8.63e-3322
neurectoderm1.68e-3086
neocortex3.67e-3020
cerebral cortex5.49e-2825
pallium5.49e-2825
pre-chordal neural plate1.60e-2761
ecto-epithelium9.66e-25104
structure with developmental contribution from neural crest2.96e-20132
organ system subdivision4.09e-20223
ectoderm-derived structure3.86e-19171
ectoderm3.86e-19171
presumptive ectoderm3.86e-19171
tube5.59e-13192
organ part6.10e-12218
anatomical conduit2.44e-11240
temporal lobe3.70e-116
basal ganglion9.86e-119
nuclear complex of neuraxis9.86e-119
aggregate regional part of brain9.86e-119
collection of basal ganglia9.86e-119
cerebral subcortex9.86e-119
posterior neural tube3.14e-1015
chordal neural plate3.14e-1015
neural nucleus4.40e-109
nucleus of brain4.40e-109
gyrus7.52e-106
anatomical cluster8.64e-10373
organ1.07e-09503
diencephalon1.31e-097
future diencephalon1.31e-097
limbic system1.60e-085
occipital lobe1.73e-085
embryo2.91e-08592
parietal lobe3.60e-085
telencephalic nucleus5.62e-087
multi-tissue structure9.03e-08342
segmental subdivision of hindbrain1.17e-0712
hindbrain1.17e-0712
presumptive hindbrain1.17e-0712
brainstem1.40e-076
epithelium2.07e-07306
corpus striatum2.37e-074
striatum2.37e-074
ventral part of telencephalon2.37e-074
future corpus striatum2.37e-074
cell layer3.66e-07309
segmental subdivision of nervous system6.48e-0713
multi-cellular organism7.22e-07656
Disease
Ontology termp-valuen
squamous cell carcinoma6.02e-0714


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.