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Coexpression cluster:C4486: Difference between revisions

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}}
}}

Revision as of 16:46, 26 November 2012


Full id: C4486_maxillary_somatostatinoma_small_testicular_H9_hippocampus_temporal



Phase1 CAGE Peaks

Hg19::chr5:16738265..16738289,-p4@MYO10
Hg19::chr5:16738290..16738320,-p2@MYO10
Hg19::chr5:16738328..16738363,-p5@MYO10


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>

Cell Type
Ontology termp-valuen
neuronal stem cell1.66e-088
embryonic stem cell4.89e-075
Uber Anatomy
Ontology termp-valuen
central nervous system1.97e-4981
neural tube2.64e-4656
neural rod2.64e-4656
future spinal cord2.64e-4656
neural keel2.64e-4656
regional part of nervous system1.91e-4353
regional part of brain1.91e-4353
nervous system6.59e-4289
brain4.47e-3868
future brain4.47e-3868
regional part of forebrain2.26e-3741
forebrain2.26e-3741
anterior neural tube2.26e-3741
future forebrain2.26e-3741
neural plate1.12e-3382
presumptive neural plate1.12e-3382
neurectoderm4.33e-3286
telencephalon9.25e-3234
brain grey matter1.21e-3134
gray matter1.21e-3134
adult organism1.75e-31114
organ system subdivision7.83e-31223
cerebral hemisphere5.76e-3032
regional part of telencephalon8.73e-3032
pre-chordal neural plate6.31e-2961
ectoderm-derived structure6.17e-25171
ectoderm6.17e-25171
presumptive ectoderm6.17e-25171
ecto-epithelium6.54e-25104
regional part of cerebral cortex4.46e-2322
cerebral cortex5.82e-2325
pallium5.82e-2325
neocortex4.42e-2120
structure with developmental contribution from neural crest3.62e-19132
anatomical cluster9.07e-18373
tube2.72e-12192
anatomical conduit8.17e-12240
multi-tissue structure1.08e-10342
basal ganglion3.96e-109
nuclear complex of neuraxis3.96e-109
aggregate regional part of brain3.96e-109
collection of basal ganglia3.96e-109
cerebral subcortex3.96e-109
neural nucleus4.32e-109
nucleus of brain4.32e-109
posterior neural tube4.52e-1015
chordal neural plate4.52e-1015
embryo2.87e-09592
telencephalic nucleus2.67e-087
temporal lobe6.60e-086
segmental subdivision of hindbrain1.57e-0712
hindbrain1.57e-0712
presumptive hindbrain1.57e-0712
gyrus2.13e-076
organ part2.39e-07218
multi-cellular organism2.96e-07656
developing anatomical structure5.14e-07581
diencephalon5.86e-077
future diencephalon5.86e-077
epithelium7.86e-07306
organ8.04e-07503
brainstem8.52e-076
segmental subdivision of nervous system9.70e-0713


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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