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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1093_neuroblastoma_thyroid_cerebellum_pons_peripheral_testis_thalamus
|full_id=C1093_neuroblastoma_thyroid_cerebellum_pons_peripheral_testis_thalamus
|id=C1093
|id=C1093

Revision as of 13:32, 12 September 2012


Full id: C1093_neuroblastoma_thyroid_cerebellum_pons_peripheral_testis_thalamus



Phase1 CAGE Peaks

Hg19::chr7:153584120..153584136,+p13@DPP6
Hg19::chr7:153584146..153584162,+p19@DPP6
Hg19::chr7:153584166..153584196,+p8@DPP6
Hg19::chr7:153584214..153584226,+p21@DPP6
Hg19::chr7:153584257..153584277,+p20@DPP6
Hg19::chr7:153584378..153584393,+p5@DPP6
Hg19::chr7:153584403..153584435,+p2@DPP6
Hg19::chr7:153585814..153585818,+p@chr7:153585814..153585818
+


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 organism1.41e-64115
neural tube4.62e-5557
neural rod4.62e-5557
future spinal cord4.62e-5557
neural keel4.62e-5557
central nervous system5.69e-4982
regional part of nervous system1.62e-4894
nervous system1.62e-4894
regional part of brain4.83e-4759
brain2.75e-4269
future brain2.75e-4269
neurectoderm3.66e-4290
regional part of forebrain3.67e-4141
forebrain3.67e-4141
future forebrain3.67e-4141
neural plate3.13e-4086
presumptive neural plate3.13e-4086
anterior neural tube7.89e-4042
gray matter1.09e-3334
brain grey matter1.09e-3334
telencephalon1.51e-3334
regional part of telencephalon2.03e-3233
cerebral hemisphere2.77e-3132
pre-chordal neural plate2.05e-2961
ectoderm8.81e-28173
presumptive ectoderm8.81e-28173
ectoderm-derived structure4.23e-26169
anterior region of body5.63e-26129
craniocervical region5.63e-26129
regional part of cerebral cortex8.20e-2622
head5.21e-24123
neocortex9.62e-2420
cerebral cortex1.49e-2325
pallium1.49e-2325
posterior neural tube8.12e-1615
chordal neural plate8.12e-1615
segmental subdivision of nervous system2.36e-1313
tube2.82e-13194
segmental subdivision of hindbrain2.00e-1212
hindbrain2.00e-1212
presumptive hindbrain2.00e-1212
nucleus of brain1.28e-119
neural nucleus1.28e-119
basal ganglion2.12e-119
nuclear complex of neuraxis2.12e-119
aggregate regional part of brain2.12e-119
collection of basal ganglia2.12e-119
cerebral subcortex2.12e-119
organ8.70e-11511
embryo1.93e-10612
anatomical conduit2.73e-10241
organ part3.40e-10219
embryonic structure5.14e-10605
developing anatomical structure5.14e-10605
temporal lobe9.06e-107
germ layer1.29e-09604
embryonic tissue1.29e-09604
presumptive structure1.29e-09604
epiblast (generic)1.29e-09604
anatomical cluster1.49e-09286
telencephalic nucleus3.42e-097
multi-tissue structure3.87e-09347
diencephalon6.12e-097
future diencephalon6.12e-097
regional part of metencephalon7.55e-099
metencephalon7.55e-099
future metencephalon7.55e-099
multi-cellular organism1.02e-08659
brainstem1.50e-088
epithelium1.88e-08309
anatomical system3.46e-08625
cell layer3.73e-08312
anatomical group4.14e-08626
organism subdivision5.21e-08365
gyrus5.37e-086
limbic system5.47e-075
parietal lobe6.58e-075
occipital lobe6.99e-075


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#1066474.690224326440655.26249365325459e-050.00089411025647024



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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