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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1954_occipital_parietal_temporal_duodenum_brain_Neurons_medulloblastoma
|full_id=C1954_occipital_parietal_temporal_duodenum_brain_Neurons_medulloblastoma
|id=C1954
|id=C1954

Revision as of 14:35, 12 September 2012


Full id: C1954_occipital_parietal_temporal_duodenum_brain_Neurons_medulloblastoma



Phase1 CAGE Peaks

Hg19::chr5:146833190..146833201,-p10@DPYSL3
Hg19::chr5:146833206..146833217,-p9@DPYSL3
Hg19::chr5:146833222..146833261,-p1@DPYSL3
Hg19::chr5:146833451..146833484,-p5@DPYSL3
Hg19::chr5:146833803..146833825,-p14@DPYSL3


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>

Uber Anatomy
Ontology termp-valuen
central nervous system3.92e-2882
regional part of nervous system1.71e-2794
nervous system1.71e-2794
multi-cellular organism5.97e-26659
tube1.07e-24194
neural plate3.38e-2486
presumptive neural plate3.38e-2486
ectoderm-derived structure5.72e-24169
anatomical conduit3.35e-23241
ectoderm1.95e-22173
presumptive ectoderm1.95e-22173
embryo3.78e-22612
neurectoderm7.96e-2290
anatomical cluster9.46e-22286
brain9.35e-2169
future brain9.35e-2169
epithelium1.11e-20309
anatomical group1.73e-20626
cell layer2.64e-20312
anatomical system3.66e-20625
neural tube4.01e-2057
neural rod4.01e-2057
future spinal cord4.01e-2057
neural keel4.01e-2057
embryonic structure1.17e-18605
developing anatomical structure1.17e-18605
germ layer3.06e-18604
embryonic tissue3.06e-18604
presumptive structure3.06e-18604
epiblast (generic)3.06e-18604
adult organism3.57e-18115
regional part of brain4.14e-1859
head2.11e-17123
anterior region of body2.11e-16129
craniocervical region2.11e-16129
organism subdivision9.64e-16365
splanchnic layer of lateral plate mesoderm1.10e-1584
pre-chordal neural plate1.21e-1561
multi-tissue structure4.52e-15347
anterior neural tube2.30e-1442
regional part of forebrain2.89e-1441
forebrain2.89e-1441
future forebrain2.89e-1441
gray matter2.44e-1334
brain grey matter2.44e-1334
telencephalon4.89e-1334
regional part of telencephalon8.64e-1333
cerebral hemisphere3.18e-1232
blood vessel3.85e-1260
epithelial tube open at both ends3.85e-1260
blood vasculature3.85e-1260
vascular cord3.85e-1260
vasculature5.17e-1279
vascular system5.17e-1279
artery5.85e-1242
arterial blood vessel5.85e-1242
arterial system5.85e-1242
organ9.30e-11511
epithelial tube1.00e-10118
organ part1.05e-10219
vessel1.69e-1069
cerebral cortex9.35e-1025
pallium9.35e-1025
systemic artery2.46e-0933
systemic arterial system2.46e-0933
circulatory system7.49e-09113
cardiovascular system9.56e-09110
regional part of cerebral cortex3.35e-0822
heart1.92e-0724
primitive heart tube1.92e-0724
primary heart field1.92e-0724
anterior lateral plate mesoderm1.92e-0724
heart tube1.92e-0724
heart primordium1.92e-0724
cardiac mesoderm1.92e-0724
cardiogenic plate1.92e-0724
heart rudiment1.92e-0724
muscle tissue2.27e-0763
musculature2.27e-0763
musculature of body2.27e-0763
neocortex2.61e-0720
primary circulatory organ2.84e-0727
posterior neural tube4.62e-0715
chordal neural plate4.62e-0715
skeletal muscle tissue6.98e-0761
striated muscle tissue6.98e-0761
myotome6.98e-0761


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
CTCF#1066455.360256373075030.0002259278299937090.00250192732867277
EGR1#195843.990543275848110.0067800983001440.0287754667737621
RAD21#5885510.35503389545638.39503550283973e-060.000229881781038563
SMC3#9126515.04493284493281.29633924985553e-065.16749522578862e-05
YY1#752854.911170749853860.00034993140821360.00353106148235943
ZNF143#770238.100525931336740.003624870512090980.0183366197526044



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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