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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C798_cerebellum_small_carcinosarcoma_argyrophil_Neural_gastric_Ciliary
|full_id=C798_cerebellum_small_carcinosarcoma_argyrophil_Neural_gastric_Ciliary
|id=C798
|id=C798

Revision as of 18:31, 12 September 2012


Full id: C798_cerebellum_small_carcinosarcoma_argyrophil_Neural_gastric_Ciliary



Phase1 CAGE Peaks

Hg19::chr11:31816236..31816261,-p@chr11:31816236..31816261
-
Hg19::chr11:31816304..31816311,-p@chr11:31816304..31816311
-
Hg19::chr11:31819053..31819055,-p@chr11:31819053..31819055
-
Hg19::chr11:31832581..31832601,-p7@PAX6
Hg19::chr11:31832610..31832639,-p5@PAX6
Hg19::chr11:31832658..31832681,-p1@PAX6
Hg19::chr11:31832687..31832704,-p6@PAX6
Hg19::chr11:31832807..31832823,-p4@PAX6
Hg19::chr11:31832862..31832884,-p2@PAX6
Hg19::chr11:31833011..31833025,+p@chr11:31833011..31833025
+


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>disease_data<br>

Cell Type
Ontology termp-valuen
neural cell2.73e-0925
neuron associated cell2.02e-0717
neuron associated cell (sensu Vertebrata)2.02e-0717
Uber Anatomy
Ontology termp-valuen
regional part of nervous system3.13e-4594
nervous system3.13e-4594
neurectoderm9.90e-4290
central nervous system1.72e-4082
neural plate3.12e-4086
presumptive neural plate3.12e-4086
neural tube7.53e-3857
neural rod7.53e-3857
future spinal cord7.53e-3857
neural keel7.53e-3857
brain1.96e-3569
future brain1.96e-3569
regional part of brain6.22e-3459
pre-chordal neural plate4.63e-3361
ectoderm3.57e-29173
presumptive ectoderm3.57e-29173
regional part of forebrain1.75e-2841
forebrain1.75e-2841
future forebrain1.75e-2841
head4.12e-28123
anterior region of body8.24e-28129
craniocervical region8.24e-28129
ectoderm-derived structure1.00e-27169
anterior neural tube2.60e-2742
gray matter3.42e-2434
brain grey matter3.42e-2434
telencephalon3.64e-2434
regional part of telencephalon1.25e-2333
cerebral hemisphere5.38e-2332
cerebral cortex1.98e-1825
pallium1.98e-1825
regional part of cerebral cortex5.06e-1622
neocortex1.55e-1420
posterior neural tube1.71e-1115
chordal neural plate1.71e-1115
adult organism2.75e-11115
segmental subdivision of nervous system1.68e-0913
pigment epithelium of eye1.82e-0911
segmental subdivision of hindbrain2.22e-0912
hindbrain2.22e-0912
presumptive hindbrain2.22e-0912
visual system2.94e-0821
eye4.85e-0820
organ part6.53e-08219
sensory system1.16e-0724
entire sense organ system1.16e-0724
sense organ1.95e-0723
basal ganglion2.02e-079
nuclear complex of neuraxis2.02e-079
aggregate regional part of brain2.02e-079
collection of basal ganglia2.02e-079
cerebral subcortex2.02e-079
regional part of metencephalon2.27e-079
metencephalon2.27e-079
future metencephalon2.27e-079
camera-type eye2.47e-0719
simple eye2.47e-0719
ocular region2.47e-0719
optic cup2.47e-0719
eye primordium2.47e-0719
optic vesicle2.47e-0719
nucleus of brain3.35e-079
neural nucleus3.35e-079
temporal lobe9.70e-077
Disease
Ontology termp-valuen
cell type cancer1.43e-12143
cancer4.66e-10235
disease of cellular proliferation5.66e-10239
carcinoma9.28e-09106


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
CCNT2#90574.435341103873840.0001875292697571890.00226735001205963
CEBPB#105175.579803338077374.14051761029175e-050.000751532010255926
CTBP2#1488743.90190023752972.99349477998484e-113.4698956862024e-09
E2F4#187478.867642220699111.84731179412716e-066.85369081587377e-05
E2F6#187673.512009012188170.0008453950419482970.00637258843637951
ELF1#199772.980668571165280.002378202870469130.0134731288087294
FOS#235376.298568716226081.848304348188e-050.00041991528784078
HDAC2#306668.049372141975762.76518202234458e-050.000584600901278635
JUND#372774.896264759309729.81446965345405e-050.00139173577208023
MAX#414974.516788856304990.0001665254509713970.00204152501162128
NANOG#79923720.47134493670895.96944508093541e-094.74101045481227e-07
NFYA#4800712.89790648988141.4357468212053e-078.1272608270927e-06
NFYB#4801711.73185527747552.74641977103244e-071.40950041507055e-05
POU2F2#545276.374286840419771.70647444265859e-050.000390838781396536
SPI1#668875.743026455965913.41922598863134e-050.00067825364297563
SUZ12#23512735.0810466377441.42572395471382e-101.51322341571501e-08
TAF1#687272.34013240002170.01040839844348330.0386352973073269
TBP#690872.594739480967470.00558866901773640.0252727864708107
TRIM28#10155713.01336753168381.35067750650695e-077.68737918812423e-06
ZNF263#1012775.755289145907473.37110736015453e-050.000669217033999579



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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