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Coexpression cluster:C4611: Difference between revisions

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|tf_chipseq_enrich=SUZ12#23512;3:50.1157809110629:7.93834897779404e-06:0.000223289315618592
|tf_chipseq_enrich=SUZ12#23512;3:50.1157809110629:7.93834897779404e-06:0.000223289315618592
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}}
}}

Revision as of 16:51, 26 November 2012


Full id: C4611_smallcell_neuroblastoma_colon_occipital_acute_mesothelioma_maxillary



Phase1 CAGE Peaks

Hg19::chr6:48036363..48036404,-p4@C6orf138
Hg19::chr6:48036553..48036578,-p3@C6orf138
Hg19::chr6:48036820..48036832,-p6@C6orf138


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 tube2.10e-4756
neural rod2.10e-4756
future spinal cord2.10e-4756
neural keel2.10e-4756
nervous system5.59e-4589
regional part of nervous system1.07e-4453
regional part of brain1.07e-4453
brain grey matter7.95e-4334
gray matter7.95e-4334
telencephalon1.01e-4234
cerebral hemisphere1.74e-4232
central nervous system1.86e-4181
neocortex4.10e-4120
regional part of cerebral cortex8.05e-4122
regional part of telencephalon6.44e-3932
brain8.90e-3968
future brain8.90e-3968
regional part of forebrain2.98e-3741
forebrain2.98e-3741
anterior neural tube2.98e-3741
future forebrain2.98e-3741
neural plate3.60e-3782
presumptive neural plate3.60e-3782
cerebral cortex2.08e-3525
pallium2.08e-3525
neurectoderm6.25e-3586
pre-chordal neural plate1.04e-3061
ecto-epithelium1.48e-28104
ectoderm-derived structure4.86e-26171
ectoderm4.86e-26171
presumptive ectoderm4.86e-26171
structure with developmental contribution from neural crest1.08e-25132
adult organism1.48e-19114
organ system subdivision5.24e-17223
gyrus1.75e-156
organ part1.29e-13218
parietal lobe3.22e-135
temporal lobe4.29e-136
posterior neural tube4.15e-1115
chordal neural plate4.15e-1115
basal ganglion2.12e-099
nuclear complex of neuraxis2.12e-099
aggregate regional part of brain2.12e-099
collection of basal ganglia2.12e-099
cerebral subcortex2.12e-099
brainstem2.27e-096
anatomical cluster3.21e-09373
tube3.22e-09192
neural nucleus4.69e-099
nucleus of brain4.69e-099
occipital lobe5.76e-095
segmental subdivision of hindbrain1.19e-0812
hindbrain1.19e-0812
presumptive hindbrain1.19e-0812
frontal cortex1.25e-083
limbic system3.17e-085
segmental subdivision of nervous system6.62e-0813
pons1.73e-073
epithelium2.76e-07306
cell layer4.17e-07309


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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
SUZ12#23512350.11578091106297.93834897779404e-060.000223289315618592



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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