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Coexpression cluster:C2939: Difference between revisions

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|ontology_enrichment_disease=DOID:3095!5.63e-08!22;DOID:2994!5.63e-08!22;DOID:171!1.14e-07!10
|ontology_enrichment_disease=DOID:3095!5.63e-08!22;DOID:2994!5.63e-08!22;DOID:171!1.14e-07!10
|ontology_enrichment_uberon=UBERON:0001049!3.55e-57!57;UBERON:0005068!3.55e-57!57;UBERON:0006241!3.55e-57!57;UBERON:0007135!3.55e-57!57;UBERON:0001017!2.19e-55!82;UBERON:0000073!8.99e-53!94;UBERON:0001016!8.99e-53!94;UBERON:0005743!3.45e-52!86;UBERON:0001893!1.90e-50!34;UBERON:0001869!2.32e-50!32;UBERON:0002020!3.10e-50!34;UBERON:0003528!3.10e-50!34;UBERON:0002780!7.02e-50!41;UBERON:0001890!7.02e-50!41;UBERON:0006240!7.02e-50!41;UBERON:0000955!1.10e-49!69;UBERON:0006238!1.10e-49!69;UBERON:0002616!3.18e-49!59;UBERON:0003080!1.76e-48!42;UBERON:0002791!2.60e-48!33;UBERON:0002619!1.34e-46!22;UBERON:0002346!1.15e-45!90;UBERON:0001950!3.07e-42!20;UBERON:0003075!1.30e-41!86;UBERON:0007284!1.30e-41!86;UBERON:0000956!2.14e-40!25;UBERON:0000203!2.14e-40!25;UBERON:0003056!1.03e-32!61;UBERON:0007023!2.39e-32!115;UBERON:0000924!1.92e-28!173;UBERON:0006601!1.92e-28!173;UBERON:0004121!1.61e-25!169;UBERON:0000153!7.02e-25!129;UBERON:0007811!7.02e-25!129;UBERON:0000033!4.00e-24!123;UBERON:0000025!5.60e-15!194;UBERON:0000200!1.56e-14!6;UBERON:0001871!1.75e-14!7;UBERON:0001872!2.21e-12!5;UBERON:0000349!3.19e-12!5;UBERON:0002021!3.42e-12!5;UBERON:0002420!1.17e-11!9;UBERON:0007245!1.17e-11!9;UBERON:0010009!1.17e-11!9;UBERON:0010011!1.17e-11!9;UBERON:0000454!1.17e-11!9;UBERON:0002308!2.80e-11!9;UBERON:0000125!2.80e-11!9;UBERON:0003076!3.25e-10!15;UBERON:0003057!3.25e-10!15;UBERON:0004111!1.26e-09!241;UBERON:0000369!2.51e-09!4;UBERON:0002435!2.51e-09!4;UBERON:0000204!2.51e-09!4;UBERON:0010082!2.51e-09!4;UBERON:0002771!2.98e-08!3;UBERON:0004733!4.53e-08!12;UBERON:0002028!4.53e-08!12;UBERON:0007277!4.53e-08!12;UBERON:0009663!7.67e-08!7;UBERON:0004732!2.31e-07!13;UBERON:0000477!2.57e-07!286;UBERON:0000483!2.81e-07!309;UBERON:0005383!2.93e-07!3;UBERON:0005382!2.93e-07!3;UBERON:0000064!3.24e-07!219;UBERON:0000988!3.96e-07!3;UBERON:0000119!4.32e-07!312
|ontology_enrichment_uberon=UBERON:0001049!3.55e-57!57;UBERON:0005068!3.55e-57!57;UBERON:0006241!3.55e-57!57;UBERON:0007135!3.55e-57!57;UBERON:0001017!2.19e-55!82;UBERON:0000073!8.99e-53!94;UBERON:0001016!8.99e-53!94;UBERON:0005743!3.45e-52!86;UBERON:0001893!1.90e-50!34;UBERON:0001869!2.32e-50!32;UBERON:0002020!3.10e-50!34;UBERON:0003528!3.10e-50!34;UBERON:0002780!7.02e-50!41;UBERON:0001890!7.02e-50!41;UBERON:0006240!7.02e-50!41;UBERON:0000955!1.10e-49!69;UBERON:0006238!1.10e-49!69;UBERON:0002616!3.18e-49!59;UBERON:0003080!1.76e-48!42;UBERON:0002791!2.60e-48!33;UBERON:0002619!1.34e-46!22;UBERON:0002346!1.15e-45!90;UBERON:0001950!3.07e-42!20;UBERON:0003075!1.30e-41!86;UBERON:0007284!1.30e-41!86;UBERON:0000956!2.14e-40!25;UBERON:0000203!2.14e-40!25;UBERON:0003056!1.03e-32!61;UBERON:0007023!2.39e-32!115;UBERON:0000924!1.92e-28!173;UBERON:0006601!1.92e-28!173;UBERON:0004121!1.61e-25!169;UBERON:0000153!7.02e-25!129;UBERON:0007811!7.02e-25!129;UBERON:0000033!4.00e-24!123;UBERON:0000025!5.60e-15!194;UBERON:0000200!1.56e-14!6;UBERON:0001871!1.75e-14!7;UBERON:0001872!2.21e-12!5;UBERON:0000349!3.19e-12!5;UBERON:0002021!3.42e-12!5;UBERON:0002420!1.17e-11!9;UBERON:0007245!1.17e-11!9;UBERON:0010009!1.17e-11!9;UBERON:0010011!1.17e-11!9;UBERON:0000454!1.17e-11!9;UBERON:0002308!2.80e-11!9;UBERON:0000125!2.80e-11!9;UBERON:0003076!3.25e-10!15;UBERON:0003057!3.25e-10!15;UBERON:0004111!1.26e-09!241;UBERON:0000369!2.51e-09!4;UBERON:0002435!2.51e-09!4;UBERON:0000204!2.51e-09!4;UBERON:0010082!2.51e-09!4;UBERON:0002771!2.98e-08!3;UBERON:0004733!4.53e-08!12;UBERON:0002028!4.53e-08!12;UBERON:0007277!4.53e-08!12;UBERON:0009663!7.67e-08!7;UBERON:0004732!2.31e-07!13;UBERON:0000477!2.57e-07!286;UBERON:0000483!2.81e-07!309;UBERON:0005383!2.93e-07!3;UBERON:0005382!2.93e-07!3;UBERON:0000064!3.24e-07!219;UBERON:0000988!3.96e-07!3;UBERON:0000119!4.32e-07!312
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}}
}}

Revision as of 13:47, 5 September 2012


Full id: C2939_neuroblastoma_middle_occipital_parietal_medial_olfactory_smallcell



Phase1 CAGE Peaks

Hg19::chr9:136465122..136465132,-p2@AK124587
Hg19::chr9:136465213..136465223,-p@chr9:136465213..136465223
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Hg19::chr9:136465441..136465483,-p@chr9:136465441..136465483
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Hg19::chr9:136465528..136465544,-p@chr9:136465528..136465544
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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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
neural tube3.55e-5757
neural rod3.55e-5757
future spinal cord3.55e-5757
neural keel3.55e-5757
central nervous system2.19e-5582
regional part of nervous system8.99e-5394
nervous system8.99e-5394
telencephalon1.90e-5034
cerebral hemisphere2.32e-5032
gray matter3.10e-5034
brain grey matter3.10e-5034
regional part of forebrain7.02e-5041
forebrain7.02e-5041
future forebrain7.02e-5041
brain1.10e-4969
future brain1.10e-4969
regional part of brain3.18e-4959
anterior neural tube1.76e-4842
regional part of telencephalon2.60e-4833
regional part of cerebral cortex1.34e-4622
neurectoderm1.15e-4590
neocortex3.07e-4220
neural plate1.30e-4186
presumptive neural plate1.30e-4186
cerebral cortex2.14e-4025
pallium2.14e-4025
pre-chordal neural plate1.03e-3261
adult organism2.39e-32115
ectoderm1.92e-28173
presumptive ectoderm1.92e-28173
ectoderm-derived structure1.61e-25169
anterior region of body7.02e-25129
craniocervical region7.02e-25129
head4.00e-24123
tube5.60e-15194
gyrus1.56e-146
temporal lobe1.75e-147
parietal lobe2.21e-125
limbic system3.19e-125
occipital lobe3.42e-125
basal ganglion1.17e-119
nuclear complex of neuraxis1.17e-119
aggregate regional part of brain1.17e-119
collection of basal ganglia1.17e-119
cerebral subcortex1.17e-119
nucleus of brain2.80e-119
neural nucleus2.80e-119
posterior neural tube3.25e-1015
chordal neural plate3.25e-1015
anatomical conduit1.26e-09241
corpus striatum2.51e-094
striatum2.51e-094
ventral part of telencephalon2.51e-094
future corpus striatum2.51e-094
middle temporal gyrus2.98e-083
segmental subdivision of hindbrain4.53e-0812
hindbrain4.53e-0812
presumptive hindbrain4.53e-0812
telencephalic nucleus7.67e-087
segmental subdivision of nervous system2.31e-0713
anatomical cluster2.57e-07286
epithelium2.81e-07309
caudate-putamen2.93e-073
dorsal striatum2.93e-073
organ part3.24e-07219
pons3.96e-073
cell layer4.32e-07312
Disease
Ontology termp-valuen
germ cell and embryonal cancer5.63e-0822
germ cell cancer5.63e-0822
neuroectodermal tumor1.14e-0710


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
SUZ12#23512225.05789045553150.002325256716520610.0131881984477406



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.