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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C466_cerebellum_retinoblastoma_pineal_small_pituitary_parietal_pons
|full_id=C466_cerebellum_retinoblastoma_pineal_small_pituitary_parietal_pons
|id=C466
|id=C466

Revision as of 17:47, 12 September 2012


Full id: C466_cerebellum_retinoblastoma_pineal_small_pituitary_parietal_pons



Phase1 CAGE Peaks

Hg19::chr11:17785684..17785695,+p@chr11:17785684..17785695
+
Hg19::chr18:35128158..35128201,-p@chr18:35128158..35128201
-
Hg19::chr18:35145981..35146017,-p3@CELF4
Hg19::chr20:24945160..24945169,-p@chr20:24945160..24945169
-
Hg19::chr7:149700383..149700403,-p@chr7:149700383..149700403
-
Hg19::chr7:149700477..149700562,-p@chr7:149700477..149700562
-
Hg19::chr7:149700569..149700636,-p@chr7:149700569..149700636
-
Hg19::chr7:149700639..149700651,-p@chr7:149700639..149700651
-
Hg19::chr7:149700652..149700676,-p@chr7:149700652..149700676
-
Hg19::chr7:149700678..149700703,-p@chr7:149700678..149700703
-
Hg19::chr7:149700712..149700747,-p@chr7:149700712..149700747
-
Hg19::chr7:149700748..149700770,-p@chr7:149700748..149700770
-
Hg19::chr7:149700790..149700823,-p@chr7:149700790..149700823
-
Hg19::chr7:149700827..149700889,-p@chr7:149700827..149700889
-
Hg19::chr7:149700989..149701027,-p@chr7:149700989..149701027
-
Hg19::chr7:149701365..149701397,-p@chr7:149701365..149701397
-
Hg19::chr7:149701457..149701484,-p@chr7:149701457..149701484
-
Hg19::chr7:149745353..149745375,-p@chr7:149745353..149745375
-
Hg19::chr7:153790013..153790040,+p@chr7:153790013..153790040
+
Hg19::chr7:153790151..153790200,+p@chr7:153790151..153790200
+
Hg19::chr7:153931630..153931643,+p@chr7:153931630..153931643
+


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 organism1.27e-38115
neural tube2.64e-3157
neural rod2.64e-3157
future spinal cord2.64e-3157
neural keel2.64e-3157
central nervous system6.85e-2882
regional part of nervous system1.55e-2794
nervous system1.55e-2794
regional part of forebrain8.18e-2641
forebrain8.18e-2641
future forebrain8.18e-2641
anterior neural tube1.11e-2542
regional part of brain5.97e-2559
neurectoderm3.10e-2490
brain2.42e-2369
future brain2.42e-2369
neural plate5.97e-2386
presumptive neural plate5.97e-2386
gray matter4.08e-2134
brain grey matter4.08e-2134
telencephalon5.52e-2134
regional part of telencephalon2.29e-2033
cerebral hemisphere9.56e-2032
pre-chordal neural plate1.24e-1661
regional part of cerebral cortex8.57e-1622
cerebral cortex2.40e-1525
pallium2.40e-1525
neocortex1.90e-1420
ectoderm5.45e-13173
presumptive ectoderm5.45e-13173
ectoderm-derived structure5.02e-12169
anterior region of body5.47e-11129
craniocervical region5.47e-11129
head1.09e-09123
nucleus of brain2.94e-079
neural nucleus2.94e-079
basal ganglion3.27e-079
nuclear complex of neuraxis3.27e-079
aggregate regional part of brain3.27e-079
collection of basal ganglia3.27e-079
cerebral subcortex3.27e-079
posterior neural tube5.88e-0715
chordal neural plate5.88e-0715


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
MYC#4609102.486800891242570.002914290739054180.0157473929271564
NR2C2#71821015.53076709773371.88496708895321e-101.96079758768112e-08



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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