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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4284_neuroblastoma_occipital_duodenum_temporal_brain_parietal_Neural
|full_id=C4284_neuroblastoma_occipital_duodenum_temporal_brain_parietal_Neural
|id=C4284
|id=C4284

Revision as of 17:20, 12 September 2012


Full id: C4284_neuroblastoma_occipital_duodenum_temporal_brain_parietal_Neural



Phase1 CAGE Peaks

Hg19::chr3:132757184..132757209,+p2@TMEM108
Hg19::chr3:132757215..132757247,+p1@TMEM108
Hg19::chr8:1012255..1012307,+p@chr8:1012255..1012307
+


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
neural cell4.43e-0725
neuronal stem cell7.87e-078
neurectodermal cell9.61e-0759
Uber Anatomy
Ontology termp-valuen
regional part of nervous system3.25e-4394
nervous system3.25e-4394
central nervous system5.45e-4382
adult organism1.88e-40115
neural tube1.75e-3757
neural rod1.75e-3757
future spinal cord1.75e-3757
neural keel1.75e-3757
neural plate2.12e-3686
presumptive neural plate2.12e-3686
regional part of brain5.63e-3559
neurectoderm1.45e-3490
brain3.00e-3469
future brain3.00e-3469
regional part of forebrain7.19e-3041
forebrain7.19e-3041
future forebrain7.19e-3041
anterior neural tube1.28e-2842
ectoderm-derived structure1.78e-27169
ectoderm1.03e-26173
presumptive ectoderm1.03e-26173
pre-chordal neural plate1.15e-2661
telencephalon2.73e-2534
gray matter3.55e-2534
brain grey matter3.55e-2534
anterior region of body4.11e-25129
craniocervical region4.11e-25129
head9.60e-25123
regional part of telencephalon1.66e-2433
cerebral hemisphere2.04e-2432
cerebral cortex5.69e-2025
pallium5.69e-2025
regional part of cerebral cortex2.41e-1822
neocortex5.88e-1720
multi-tissue structure4.14e-14347
cell layer5.17e-14312
tube1.68e-13194
epithelium3.21e-13309
embryo4.81e-13612
organ part3.08e-11219
anatomical cluster4.45e-11286
embryonic structure1.26e-10605
developing anatomical structure1.26e-10605
multi-cellular organism1.60e-10659
germ layer2.49e-10604
embryonic tissue2.49e-10604
presumptive structure2.49e-10604
epiblast (generic)2.49e-10604
posterior neural tube7.47e-1015
chordal neural plate7.47e-1015
anatomical conduit8.97e-10241
organism subdivision9.51e-10365
segmental subdivision of nervous system1.44e-0813
anatomical system2.08e-08625
anatomical group2.84e-08626
segmental subdivision of hindbrain3.27e-0812
hindbrain3.27e-0812
presumptive hindbrain3.27e-0812
organ8.12e-08511
temporal lobe4.05e-077
basal ganglion6.33e-079
nuclear complex of neuraxis6.33e-079
aggregate regional part of brain6.33e-079
collection of basal ganglia6.33e-079
cerebral subcortex6.33e-079


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
ATF3#467214.97544968400580.005768294540793880.0259636647651585
NFYA#4800212.28372046655370.008516011403724430.0324860733068002
NFYB#4801211.17319550235760.01025467135054530.0381460187056417
SP1#666735.69838137814090.005403962701712170.0247244254875418



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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