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Coexpression cluster:C3006: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!1.56e-66!57;UBERON:0005068!1.56e-66!57;UBERON:0006241!1.56e-66!57;UBERON:0007135!1.56e-66!57;UBERON:0007023!8.10e-62!115;UBERON:0002616!1.10e-55!59;UBERON:0002780!2.13e-55!41;UBERON:0001890!2.13e-55!41;UBERON:0006240!2.13e-55!41;UBERON:0001017!1.69e-54!82;UBERON:0003080!8.77e-54!42;UBERON:0000955!1.29e-53!69;UBERON:0006238!1.29e-53!69;UBERON:0005743!2.11e-53!86;UBERON:0000073!7.74e-53!94;UBERON:0001016!7.74e-53!94;UBERON:0002346!8.00e-49!90;UBERON:0002020!3.40e-46!34;UBERON:0003528!3.40e-46!34;UBERON:0001893!6.72e-46!34;UBERON:0003075!7.50e-46!86;UBERON:0007284!7.50e-46!86;UBERON:0002791!3.73e-44!33;UBERON:0001869!8.97e-44!32;UBERON:0002619!9.54e-39!22;UBERON:0003056!5.35e-37!61;UBERON:0001950!1.41e-35!20;UBERON:0000956!2.61e-33!25;UBERON:0000203!2.61e-33!25;UBERON:0000153!4.96e-33!129;UBERON:0007811!4.96e-33!129;UBERON:0000033!2.41e-30!123;UBERON:0000924!2.90e-28!173;UBERON:0006601!2.90e-28!173;UBERON:0004121!5.33e-26!169;UBERON:0002420!3.24e-14!9;UBERON:0007245!3.24e-14!9;UBERON:0010009!3.24e-14!9;UBERON:0010011!3.24e-14!9;UBERON:0000454!3.24e-14!9;UBERON:0002308!3.68e-14!9;UBERON:0000125!3.68e-14!9;UBERON:0001871!5.83e-14!7;UBERON:0003076!1.29e-13!15;UBERON:0003057!1.29e-13!15;UBERON:0000025!4.44e-13!194;UBERON:0000200!1.07e-11!6;UBERON:0009663!3.22e-11!7;UBERON:0004111!8.64e-11!241;UBERON:0001894!1.13e-10!7;UBERON:0006222!1.13e-10!7;UBERON:0000064!4.54e-10!219;UBERON:0000477!5.58e-10!286;UBERON:0002298!5.80e-10!8;UBERON:0002021!6.41e-10!5;UBERON:0004733!6.81e-10!12;UBERON:0002028!6.81e-10!12;UBERON:0007277!6.81e-10!12;UBERON:0001872!7.25e-10!5;UBERON:0000349!2.43e-09!5;UBERON:0004732!5.67e-09!13;UBERON:0000475!2.50e-08!365;UBERON:0000922!6.78e-08!612;UBERON:0000481!1.32e-07!347;UBERON:0000369!1.69e-07!4;UBERON:0002435!1.69e-07!4;UBERON:0000204!1.69e-07!4;UBERON:0010082!1.69e-07!4;UBERON:0000483!1.95e-07!309;UBERON:0000119!3.27e-07!312;UBERON:0003296!9.11e-07!4;UBERON:0010133!9.11e-07!4
|ontology_enrichment_uberon=UBERON:0001049!8.34e-75!56;UBERON:0005068!8.34e-75!56;UBERON:0006241!8.34e-75!56;UBERON:0007135!8.34e-75!56;UBERON:0000073!1.63e-68!53;UBERON:0002616!1.63e-68!53;UBERON:0002780!3.47e-65!41;UBERON:0001890!3.47e-65!41;UBERON:0003080!3.47e-65!41;UBERON:0006240!3.47e-65!41;UBERON:0003528!4.62e-63!34;UBERON:0002020!4.62e-63!34;UBERON:0001893!1.14e-62!34;UBERON:0001869!5.15e-59!32;UBERON:0002791!2.08e-58!32;UBERON:0001016!2.15e-58!89;UBERON:0001017!9.36e-58!81;UBERON:0000955!6.45e-56!68;UBERON:0006238!6.45e-56!68;UBERON:0007023!8.09e-56!114;UBERON:0002346!2.68e-54!86;UBERON:0003075!2.68e-52!82;UBERON:0007284!2.68e-52!82;UBERON:0002619!1.71e-50!22;UBERON:0001950!4.74e-46!20;UBERON:0003056!4.97e-46!61;UBERON:0000956!7.21e-44!25;UBERON:0000203!7.21e-44!25;UBERON:0010371!1.50e-38!104;UBERON:0010314!3.25e-32!132;UBERON:0004121!8.60e-31!171;UBERON:0000924!8.60e-31!171;UBERON:0006601!8.60e-31!171;UBERON:0011216!2.28e-26!223;UBERON:0000125!2.05e-20!9;UBERON:0002308!2.05e-20!9;UBERON:0002420!2.60e-20!9;UBERON:0007245!2.60e-20!9;UBERON:0010009!2.60e-20!9;UBERON:0010011!2.60e-20!9;UBERON:0000454!2.60e-20!9;UBERON:0000200!3.89e-16!6;UBERON:0009663!6.99e-16!7;UBERON:0000025!4.18e-15!192;UBERON:0000477!1.88e-14!373;UBERON:0001872!1.64e-13!5;UBERON:0002021!2.27e-13!5;UBERON:0001871!5.02e-13!6;UBERON:0000349!9.56e-13!5;UBERON:0004111!1.37e-12!240;UBERON:0003076!9.60e-12!15;UBERON:0003057!9.60e-12!15;UBERON:0000064!5.04e-11!218;UBERON:0002298!1.17e-10!6;UBERON:0000369!5.25e-10!4;UBERON:0002435!5.25e-10!4;UBERON:0000204!5.25e-10!4;UBERON:0010082!5.25e-10!4;UBERON:0000481!2.45e-09!342;UBERON:0001870!6.55e-09!3;UBERON:0000988!1.30e-08!3;UBERON:0000483!2.51e-08!306;UBERON:0000119!3.95e-08!309;UBERON:0002240!7.61e-08!3;UBERON:0005174!7.61e-08!3;UBERON:0001137!7.61e-08!3;UBERON:0005383!9.88e-08!3;UBERON:0005382!9.88e-08!3;UBERON:0006947!1.31e-07!3;UBERON:0004054!1.31e-07!3;UBERON:0000922!1.39e-07!592;UBERON:0004733!6.11e-07!12;UBERON:0002028!6.11e-07!12;UBERON:0007277!6.11e-07!12;UBERON:0000923!7.07e-07!560;UBERON:0010316!7.07e-07!560;UBERON:0005291!7.07e-07!560;UBERON:0006598!7.07e-07!560;UBERON:0010317!7.07e-07!560;UBERON:0002532!7.07e-07!560
|tf_chipseq_enrich=SUZ12#23512;3:50.1157809110629:7.93834897779404e-06:0.00022102725377015!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0108884068464403
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}}
}}

Revision as of 14:42, 19 October 2012


Full id: C3006_acute_neuroblastoma_kidney_occipital_parietal_postcentral_paracentral



Phase1 CAGE Peaks

Hg19::chr10:23983671..23983704,+p9@KIAA1217
Hg19::chr10:23983752..23983767,+p19@KIAA1217
Hg19::chr10:23983950..23983961,+p22@KIAA1217


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 tube8.34e-7556
neural rod8.34e-7556
future spinal cord8.34e-7556
neural keel8.34e-7556
regional part of nervous system1.63e-6853
regional part of brain1.63e-6853
regional part of forebrain3.47e-6541
forebrain3.47e-6541
anterior neural tube3.47e-6541
future forebrain3.47e-6541
brain grey matter4.62e-6334
gray matter4.62e-6334
telencephalon1.14e-6234
cerebral hemisphere5.15e-5932
regional part of telencephalon2.08e-5832
nervous system2.15e-5889
central nervous system9.36e-5881
brain6.45e-5668
future brain6.45e-5668
adult organism8.09e-56114
neurectoderm2.68e-5486
neural plate2.68e-5282
presumptive neural plate2.68e-5282
regional part of cerebral cortex1.71e-5022
neocortex4.74e-4620
pre-chordal neural plate4.97e-4661
cerebral cortex7.21e-4425
pallium7.21e-4425
ecto-epithelium1.50e-38104
structure with developmental contribution from neural crest3.25e-32132
ectoderm-derived structure8.60e-31171
ectoderm8.60e-31171
presumptive ectoderm8.60e-31171
organ system subdivision2.28e-26223
neural nucleus2.05e-209
nucleus of brain2.05e-209
basal ganglion2.60e-209
nuclear complex of neuraxis2.60e-209
aggregate regional part of brain2.60e-209
collection of basal ganglia2.60e-209
cerebral subcortex2.60e-209
gyrus3.89e-166
telencephalic nucleus6.99e-167
tube4.18e-15192
anatomical cluster1.88e-14373
parietal lobe1.64e-135
occipital lobe2.27e-135
temporal lobe5.02e-136
limbic system9.56e-135
anatomical conduit1.37e-12240
posterior neural tube9.60e-1215
chordal neural plate9.60e-1215
organ part5.04e-11218
brainstem1.17e-106
corpus striatum5.25e-104
striatum5.25e-104
ventral part of telencephalon5.25e-104
future corpus striatum5.25e-104
multi-tissue structure2.45e-09342
frontal cortex6.55e-093
pons1.30e-083
epithelium2.51e-08306
cell layer3.95e-08309
spinal cord7.61e-083
dorsal region element7.61e-083
dorsum7.61e-083
caudate-putamen9.88e-083
dorsal striatum9.88e-083
male genital duct1.31e-073
internal male genitalia1.31e-073
embryo1.39e-07592
segmental subdivision of hindbrain6.11e-0712
hindbrain6.11e-0712
presumptive hindbrain6.11e-0712
germ layer7.07e-07560
germ layer / neural crest7.07e-07560
embryonic tissue7.07e-07560
presumptive structure7.07e-07560
germ layer / neural crest derived structure7.07e-07560
epiblast (generic)7.07e-07560


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)

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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#23512350.11578091106297.93834897779404e-060.00022102725377015
ZNF263#1012738.221841637010680.001799043925565870.0108884068464403



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.