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Coexpression cluster:C4771: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 20:19, 8 August 2012


Full id: C4771_medulloblastoma_parietal_gastrointestinal_temporal_duodenum_occipital_neuroblastoma



Phase1 CAGE Peaks

Hg19::chr8:73449511..73449521,+p5@KCNB2
Hg19::chr8:73449535..73449575,+p3@KCNB2
Hg19::chr8:73560820..73560822,+p@chr8:73560820..73560822
+


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 plate3.28e-4286
presumptive neural plate3.28e-4286
neural tube3.44e-4157
neural rod3.44e-4157
future spinal cord3.44e-4157
neural keel3.44e-4157
central nervous system7.26e-4082
neurectoderm1.32e-3990
regional part of nervous system1.88e-3794
nervous system1.88e-3794
regional part of forebrain3.97e-3641
forebrain3.97e-3641
future forebrain3.97e-3641
anterior neural tube4.94e-3542
pre-chordal neural plate5.46e-3561
brain1.13e-3369
future brain1.13e-3369
regional part of brain5.54e-3359
adult organism3.45e-32115
regional part of cerebral cortex6.74e-3222
gray matter8.27e-3234
brain grey matter8.27e-3234
cerebral hemisphere1.53e-3132
telencephalon1.92e-3134
regional part of telencephalon5.69e-3033
neocortex8.14e-2920
cerebral cortex2.20e-2725
pallium2.20e-2725
anterior region of body5.72e-24129
craniocervical region5.72e-24129
ectoderm-derived structure5.74e-24169
ectoderm5.35e-23173
presumptive ectoderm5.35e-23173
head1.91e-22123
gyrus2.35e-116
temporal lobe3.22e-117
organ part4.57e-11219
tube9.32e-10194
occipital lobe1.11e-095
limbic system3.58e-095
epithelium7.86e-09309
cell layer1.38e-08312
embryo1.49e-08612
posterior neural tube1.02e-0715
chordal neural plate1.02e-0715
brainstem3.00e-078
multi-tissue structure3.05e-07347
anatomical cluster3.10e-07286


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)

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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.