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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1056_small_Neural_Astrocyte_teratocarcinoma_H9_hippocampus_testicular
|full_id=C1056_small_Neural_Astrocyte_teratocarcinoma_H9_hippocampus_testicular
|id=C1056
|id=C1056

Revision as of 13:29, 12 September 2012


Full id: C1056_small_Neural_Astrocyte_teratocarcinoma_H9_hippocampus_testicular



Phase1 CAGE Peaks

Hg19::chr18:53019208..53019223,-p@chr18:53019208..53019223
-
Hg19::chr3:181429641..181429650,+p3@SOX2
Hg19::chr3:181429704..181429722,+p1@SOX2
Hg19::chr3:181429741..181429767,+p2@SOX2
Hg19::chr3:181431050..181431079,+p@chr3:181431050..181431079
+
Hg19::chr3:181431124..181431130,+p@chr3:181431124..181431130
+
Hg19::chr3:181431210..181431225,-p@chr3:181431210..181431225
-
Hg19::chr3:181431401..181431408,+p@chr3:181431401..181431408
+


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 cell4.62e-1225
neurectodermal cell8.05e-0959
neuronal stem cell2.77e-088
ectodermal cell4.14e-0871
endo-epithelial cell4.69e-0743
Uber Anatomy
Ontology termp-valuen
central nervous system8.32e-4882
regional part of nervous system2.89e-4694
nervous system2.89e-4694
neural tube6.80e-4157
neural rod6.80e-4157
future spinal cord6.80e-4157
neural keel6.80e-4157
ectoderm6.99e-40173
presumptive ectoderm6.99e-40173
ectoderm-derived structure1.43e-38169
brain2.79e-3769
future brain2.79e-3769
regional part of brain3.68e-3759
neurectoderm7.49e-3590
neural plate9.95e-3486
presumptive neural plate9.95e-3486
adult organism1.63e-33115
anterior region of body6.28e-32129
craniocervical region6.28e-32129
regional part of forebrain7.93e-3141
forebrain7.93e-3141
future forebrain7.93e-3141
head8.06e-31123
anterior neural tube1.23e-2942
telencephalon2.80e-2634
gray matter2.82e-2634
brain grey matter2.82e-2634
regional part of telencephalon1.36e-2533
cerebral hemisphere1.33e-2432
pre-chordal neural plate4.44e-2461
cerebral cortex1.88e-1925
pallium1.88e-1925
regional part of cerebral cortex8.49e-1722
organ part1.39e-15219
neocortex3.66e-1520
organism subdivision9.03e-13365
embryo2.57e-12612
posterior neural tube3.81e-1215
chordal neural plate3.81e-1215
multi-cellular organism1.30e-11659
segmental subdivision of nervous system3.38e-1013
anatomical conduit7.85e-10241
segmental subdivision of hindbrain8.75e-1012
hindbrain8.75e-1012
presumptive hindbrain8.75e-1012
embryonic structure1.31e-09605
developing anatomical structure1.31e-09605
germ layer2.26e-09604
embryonic tissue2.26e-09604
presumptive structure2.26e-09604
epiblast (generic)2.26e-09604
multi-tissue structure4.37e-09347
anatomical cluster4.85e-09286
tube8.25e-09194
organ9.14e-09511
basal ganglion2.26e-089
nuclear complex of neuraxis2.26e-089
aggregate regional part of brain2.26e-089
collection of basal ganglia2.26e-089
cerebral subcortex2.26e-089
nucleus of brain2.95e-089
neural nucleus2.95e-089
anatomical group3.15e-08626
epithelium3.84e-08309
anatomical system5.01e-08625
cell layer9.33e-08312
regional part of metencephalon1.49e-079
metencephalon1.49e-079
future metencephalon1.49e-079
telencephalic nucleus8.94e-077


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
NANOG#79923414.62238924050638.55931368384764e-050.00128345464727547



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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