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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4056_retina_anaplastic_pituitary_small_salivary_submaxillary_thyroid
|full_id=C4056_retina_anaplastic_pituitary_small_salivary_submaxillary_thyroid
|id=C4056
|id=C4056

Revision as of 17:05, 12 September 2012


Full id: C4056_retina_anaplastic_pituitary_small_salivary_submaxillary_thyroid



Phase1 CAGE Peaks

Hg19::chr20:57875631..57875638,+p6@EDN3
Hg19::chr20:57875644..57875657,+p3@EDN3
Hg19::chr20:57875658..57875673,+p1@EDN3


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
adult organism1.78e-62115
neural tube9.94e-4657
neural rod9.94e-4657
future spinal cord9.94e-4657
neural keel9.94e-4657
regional part of brain1.97e-3759
anterior neural tube2.43e-3742
central nervous system1.80e-3682
regional part of forebrain2.60e-3641
forebrain2.60e-3641
future forebrain2.60e-3641
neural plate7.27e-3486
presumptive neural plate7.27e-3486
regional part of nervous system2.07e-3394
nervous system2.07e-3394
brain2.10e-3269
future brain2.10e-3269
neurectoderm1.36e-3190
pre-chordal neural plate1.56e-2861
telencephalon4.09e-2834
gray matter1.10e-2734
brain grey matter1.10e-2734
regional part of telencephalon6.72e-2733
anterior region of body9.03e-27129
craniocervical region9.03e-27129
cerebral hemisphere6.25e-2632
head3.22e-25123
ectoderm-derived structure8.01e-24169
ectoderm8.64e-23173
presumptive ectoderm8.64e-23173
regional part of cerebral cortex1.21e-2122
neocortex1.28e-1920
cerebral cortex2.22e-1825
pallium2.22e-1825
organ part2.40e-12219
multi-tissue structure2.57e-12347
organ4.68e-12511
nucleus of brain4.84e-119
neural nucleus4.84e-119
basal ganglion5.17e-119
nuclear complex of neuraxis5.17e-119
aggregate regional part of brain5.17e-119
collection of basal ganglia5.17e-119
cerebral subcortex5.17e-119
brainstem1.22e-108
organism subdivision2.86e-10365
embryo3.23e-10612
temporal lobe5.84e-107
diencephalon8.66e-107
future diencephalon8.66e-107
posterior neural tube1.42e-0915
chordal neural plate1.42e-0915
embryonic structure3.83e-09605
developing anatomical structure3.83e-09605
telencephalic nucleus4.44e-097
multi-cellular organism7.18e-09659
germ layer1.12e-08604
embryonic tissue1.12e-08604
presumptive structure1.12e-08604
epiblast (generic)1.12e-08604
anatomical system1.57e-08625
anatomical group1.83e-08626
anatomical cluster2.06e-08286
anatomical conduit2.96e-08241
tube6.15e-08194
epithelium7.97e-08309
cell layer1.41e-07312
parietal lobe5.61e-075
limbic system8.84e-075
gastrointestinal system9.36e-0735


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-060.000222989034129056



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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