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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3374_caudate_putamen_amygdala_Mallassezderived_mesenchymal_astrocytoma_hippocampus
|full_id=C3374_caudate_putamen_amygdala_Mallassezderived_mesenchymal_astrocytoma_hippocampus
|id=C3374
|id=C3374

Revision as of 16:17, 12 September 2012


Full id: C3374_caudate_putamen_amygdala_Mallassezderived_mesenchymal_astrocytoma_hippocampus



Phase1 CAGE Peaks

Hg19::chr13:45768800..45768816,-p1@KCTD4
Hg19::chr13:45768841..45768855,-p3@KCTD4
Hg19::chr13:45768859..45768871,-p4@KCTD4


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
neural tube7.37e-5057
neural rod7.37e-5057
future spinal cord7.37e-5057
neural keel7.37e-5057
central nervous system1.23e-4182
regional part of brain5.22e-4159
regional part of forebrain2.36e-4041
forebrain2.36e-4041
future forebrain2.36e-4041
brain1.49e-3969
future brain1.49e-3969
anterior neural tube5.29e-3942
regional part of nervous system1.58e-3894
nervous system1.58e-3894
ectoderm-derived structure3.09e-38169
ectoderm1.48e-36173
presumptive ectoderm1.48e-36173
neural plate8.06e-3586
presumptive neural plate8.06e-3586
gray matter6.33e-3434
brain grey matter6.33e-3434
telencephalon1.07e-3334
regional part of telencephalon8.80e-3333
neurectoderm3.11e-3290
cerebral hemisphere1.16e-3132
adult organism2.15e-31115
head2.24e-31123
anterior region of body1.47e-29129
craniocervical region1.47e-29129
cerebral cortex3.28e-2425
pallium3.28e-2425
regional part of cerebral cortex6.23e-2422
pre-chordal neural plate2.20e-2361
neocortex1.12e-2120
organism subdivision2.47e-19365
tube1.01e-16194
anatomical conduit2.14e-15241
anatomical cluster3.74e-12286
epithelium3.92e-12309
cell layer9.93e-12312
posterior neural tube1.02e-1115
chordal neural plate1.02e-1115
multi-tissue structure1.17e-11347
organ1.80e-11511
basal ganglion2.02e-119
nuclear complex of neuraxis2.02e-119
aggregate regional part of brain2.02e-119
collection of basal ganglia2.02e-119
cerebral subcortex2.02e-119
nucleus of brain3.89e-119
neural nucleus3.89e-119
anatomical system9.27e-11625
anatomical group1.16e-10626
segmental subdivision of nervous system7.53e-1013
temporal lobe1.54e-097
multi-cellular organism2.87e-09659
telencephalic nucleus4.26e-097
segmental subdivision of hindbrain6.97e-0912
hindbrain6.97e-0912
presumptive hindbrain6.97e-0912
organ part7.20e-09219
diencephalon5.75e-087
future diencephalon5.75e-087
gyrus9.93e-086
embryo2.45e-07612
germ layer2.51e-07604
embryonic tissue2.51e-07604
presumptive structure2.51e-07604
epiblast (generic)2.51e-07604
limbic system2.58e-075
embryonic structure3.02e-07605
developing anatomical structure3.02e-07605
subdivision of skeletal system3.14e-0713
skeleton3.14e-0713
sclerotome3.14e-0713
brainstem5.36e-078


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#1066435.360256373075030.0064925092527670.0278743391371263
RAD21#5885310.35503389545630.0009004912073565420.00662625246284153



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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