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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3238_Small_salivary_duodenum_temporal_Wilms_Neurons_Neural
|full_id=C3238_Small_salivary_duodenum_temporal_Wilms_Neurons_Neural
|id=C3238
|id=C3238

Revision as of 16:07, 12 September 2012


Full id: C3238_Small_salivary_duodenum_temporal_Wilms_Neurons_Neural



Phase1 CAGE Peaks

Hg19::chr12:111472591..111472630,+p@chr12:111472591..111472630
+
Hg19::chr12:111472632..111472643,+p@chr12:111472632..111472643
+
Hg19::chr12:111473432..111473437,+p@chr12:111473432..111473437
+


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
respiratory epithelial cell8.30e-0913
neuron1.02e-076
neuroblast1.02e-076
electrically signaling cell1.02e-076
neuronal stem cell1.22e-078
Uber Anatomy
Ontology termp-valuen
regional part of nervous system2.11e-4494
nervous system2.11e-4494
central nervous system6.90e-4482
neural tube7.51e-4057
neural rod7.51e-4057
future spinal cord7.51e-4057
neural keel7.51e-4057
adult organism1.06e-34115
brain2.14e-3369
future brain2.14e-3369
regional part of brain4.23e-3359
regional part of forebrain2.44e-3141
forebrain2.44e-3141
future forebrain2.44e-3141
neurectoderm3.12e-3190
anterior neural tube2.71e-3042
neural plate2.59e-2986
presumptive neural plate2.59e-2986
telencephalon2.94e-2434
regional part of cerebral cortex3.45e-2422
gray matter3.60e-2434
brain grey matter3.60e-2434
ectoderm8.68e-24173
presumptive ectoderm8.68e-24173
regional part of telencephalon3.51e-2333
cerebral hemisphere8.24e-2332
neocortex1.75e-2220
ectoderm-derived structure3.67e-22169
pre-chordal neural plate6.95e-2261
cerebral cortex1.91e-2025
pallium1.91e-2025
anterior region of body8.17e-20129
craniocervical region8.17e-20129
head8.73e-20123
embryo1.44e-10612
posterior neural tube1.71e-1015
chordal neural plate1.71e-1015
segmental subdivision of nervous system2.69e-0913
diencephalon1.08e-087
future diencephalon1.08e-087
segmental subdivision of hindbrain1.76e-0812
hindbrain1.76e-0812
presumptive hindbrain1.76e-0812
multi-cellular organism1.93e-08659
gyrus3.46e-086
embryonic structure5.41e-08605
developing anatomical structure5.41e-08605
temporal lobe1.02e-077
germ layer1.20e-07604
embryonic tissue1.20e-07604
presumptive structure1.20e-07604
epiblast (generic)1.20e-07604
parietal lobe1.72e-075
occipital lobe1.93e-075
male reproductive organ4.39e-0711


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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