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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1458_cerebellum_small_temporal_parietal_occipital_somatostatinoma_neuroectodermal
|full_id=C1458_cerebellum_small_temporal_parietal_occipital_somatostatinoma_neuroectodermal
|id=C1458
|id=C1458

Revision as of 14:01, 12 September 2012


Full id: C1458_cerebellum_small_temporal_parietal_occipital_somatostatinoma_neuroectodermal



Phase1 CAGE Peaks

Hg19::chr19:7939079..7939096,-p@chr19:7939079..7939096
-
Hg19::chr7:29233853..29233864,+p15@CHN2
Hg19::chr7:29234032..29234043,+p16@CHN2
Hg19::chr7:29234101..29234130,+p6@CHN2
Hg19::chr7:29234147..29234156,+p24@CHN2
Hg19::chr7:29323567..29323571,+p@chr7:29323567..29323571
+


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
granulocyte monocyte progenitor cell4.06e-0771
Uber Anatomy
Ontology termp-valuen
adult organism3.71e-33115
neural tube1.82e-2857
neural rod1.82e-2857
future spinal cord1.82e-2857
neural keel1.82e-2857
regional part of nervous system2.60e-2794
nervous system2.60e-2794
central nervous system1.14e-2682
anterior neural tube9.63e-2442
regional part of forebrain1.06e-2341
forebrain1.06e-2341
future forebrain1.06e-2341
regional part of brain1.21e-2259
brain1.50e-2169
future brain1.50e-2169
neurectoderm1.15e-2090
telencephalon8.89e-2034
gray matter1.08e-1934
brain grey matter1.08e-1934
regional part of telencephalon4.48e-1933
neural plate7.99e-1986
presumptive neural plate7.99e-1986
cerebral hemisphere1.92e-1832
regional part of cerebral cortex4.05e-1622
neocortex8.15e-1520
cerebral cortex5.01e-1425
pallium5.01e-1425
pre-chordal neural plate6.14e-1461
ectoderm5.06e-11173
presumptive ectoderm5.06e-11173
ectoderm-derived structure8.12e-10169
organ1.47e-09511
anterior region of body2.94e-07129
craniocervical region2.94e-07129
nucleus of brain3.35e-079
neural nucleus3.35e-079
basal ganglion6.13e-079
nuclear complex of neuraxis6.13e-079
aggregate regional part of brain6.13e-079
collection of basal ganglia6.13e-079
cerebral subcortex6.13e-079
head6.46e-07123


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#23512433.41052060737532.29902183370319e-068.18920672885836e-05



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.