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Coexpression cluster:C1759: Difference between revisions

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|ontology_enrichment_disease=DOID:171!1.73e-07!10
|ontology_enrichment_disease=DOID:171!1.73e-07!10
|ontology_enrichment_uberon=UBERON:0007023!8.73e-58!115;UBERON:0001049!1.84e-38!57;UBERON:0005068!1.84e-38!57;UBERON:0006241!1.84e-38!57;UBERON:0007135!1.84e-38!57;UBERON:0000073!1.32e-37!94;UBERON:0001016!1.32e-37!94;UBERON:0001017!2.24e-37!82;UBERON:0005743!7.80e-37!86;UBERON:0002346!3.98e-35!90;UBERON:0002616!1.55e-33!59;UBERON:0000955!1.31e-31!69;UBERON:0006238!1.31e-31!69;UBERON:0003075!1.34e-31!86;UBERON:0007284!1.34e-31!86;UBERON:0003080!2.88e-28!42;UBERON:0002780!7.92e-28!41;UBERON:0001890!7.92e-28!41;UBERON:0006240!7.92e-28!41;UBERON:0001893!2.39e-26!34;UBERON:0002020!2.67e-26!34;UBERON:0003528!2.67e-26!34;UBERON:0002791!2.14e-25!33;UBERON:0001869!5.90e-25!32;UBERON:0003056!1.54e-22!61;UBERON:0000924!7.21e-22!173;UBERON:0006601!7.21e-22!173;UBERON:0002619!1.59e-21!22;UBERON:0000153!2.01e-21!129;UBERON:0007811!2.01e-21!129;UBERON:0000956!2.31e-20!25;UBERON:0000203!2.31e-20!25;UBERON:0000033!3.39e-20!123;UBERON:0001950!6.72e-20!20;UBERON:0004121!2.15e-19!169;UBERON:0000922!3.19e-15!612;UBERON:0000468!9.60e-14!659;UBERON:0000062!6.87e-13!511;UBERON:0002050!2.20e-12!605;UBERON:0005423!2.20e-12!605;UBERON:0000923!5.48e-12!604;UBERON:0005291!5.48e-12!604;UBERON:0006598!5.48e-12!604;UBERON:0002532!5.48e-12!604;UBERON:0003076!3.96e-11!15;UBERON:0003057!3.96e-11!15;UBERON:0000467!1.86e-09!625;UBERON:0004732!2.05e-09!13;UBERON:0000480!2.43e-09!626;UBERON:0004733!5.21e-09!12;UBERON:0002028!5.21e-09!12;UBERON:0007277!5.21e-09!12;UBERON:0001871!3.47e-08!7;UBERON:0002420!2.11e-07!9;UBERON:0007245!2.11e-07!9;UBERON:0010009!2.11e-07!9;UBERON:0010011!2.11e-07!9;UBERON:0000454!2.11e-07!9;UBERON:0002308!2.25e-07!9;UBERON:0000125!2.25e-07!9;UBERON:0002298!3.07e-07!8;UBERON:0000025!4.88e-07!194;UBERON:0000200!5.19e-07!6;UBERON:0002680!8.21e-07!9;UBERON:0001895!8.21e-07!9;UBERON:0010092!8.21e-07!9
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}}
}}

Revision as of 17:37, 8 August 2012


Full id: C1759_neuroectodermal_neuroblastoma_peripheral_occipital_postcentral_paracentral_parietal



Phase1 CAGE Peaks

Hg19::chr16:25703274..25703350,+p1@HS3ST4
Hg19::chr8:21645804..21645850,-p3@GFRA2
Hg19::chr8:21646290..21646308,-p4@GFRA2
Hg19::chr8:21646311..21646351,-p1@GFRA2
Hg19::chr8:21646364..21646402,-p2@GFRA2


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


GO IDGO nameFDR corrected p-value
GO:0016167glial cell line-derived neurotrophic factor receptor activity0.00612259915710724
GO:0008467heparin-glucosamine 3-O-sulfotransferase activity0.00765291100983854
GO:0030201heparan sulfate proteoglycan metabolic process0.0122433959859717
GO:0006029proteoglycan metabolic process0.0221856018006757
GO:0008146sulfotransferase activity0.0301459095476488
GO:0016782transferase activity, transferring sulfur-containing groups0.0301459095476488
GO:0004896hematopoietin/interferon-class (D200-domain) cytokine receptor activity0.0301459095476488
GO:0006790sulfur metabolic process0.0328682829093709
GO:0019898extrinsic to membrane0.0363392028844498
GO:0048503GPI anchor binding0.038501975748613



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
adult organism8.73e-58115
neural tube1.84e-3857
neural rod1.84e-3857
future spinal cord1.84e-3857
neural keel1.84e-3857
regional part of nervous system1.32e-3794
nervous system1.32e-3794
central nervous system2.24e-3782
neurectoderm3.98e-3590
regional part of brain1.55e-3359
brain1.31e-3169
future brain1.31e-3169
neural plate1.34e-3186
presumptive neural plate1.34e-3186
anterior neural tube2.88e-2842
regional part of forebrain7.92e-2841
forebrain7.92e-2841
future forebrain7.92e-2841
telencephalon2.39e-2634
gray matter2.67e-2634
brain grey matter2.67e-2634
regional part of telencephalon2.14e-2533
cerebral hemisphere5.90e-2532
pre-chordal neural plate1.54e-2261
ectoderm7.21e-22173
presumptive ectoderm7.21e-22173
regional part of cerebral cortex1.59e-2122
anterior region of body2.01e-21129
craniocervical region2.01e-21129
cerebral cortex2.31e-2025
pallium2.31e-2025
head3.39e-20123
neocortex6.72e-2020
ectoderm-derived structure2.15e-19169
embryo3.19e-15612
multi-cellular organism9.60e-14659
organ6.87e-13511
embryonic structure2.20e-12605
developing anatomical structure2.20e-12605
germ layer5.48e-12604
embryonic tissue5.48e-12604
presumptive structure5.48e-12604
epiblast (generic)5.48e-12604
posterior neural tube3.96e-1115
chordal neural plate3.96e-1115
anatomical system1.86e-09625
segmental subdivision of nervous system2.05e-0913
anatomical group2.43e-09626
segmental subdivision of hindbrain5.21e-0912
hindbrain5.21e-0912
presumptive hindbrain5.21e-0912
temporal lobe3.47e-087
basal ganglion2.11e-079
nuclear complex of neuraxis2.11e-079
aggregate regional part of brain2.11e-079
collection of basal ganglia2.11e-079
cerebral subcortex2.11e-079
nucleus of brain2.25e-079
neural nucleus2.25e-079
brainstem3.07e-078
tube4.88e-07194
gyrus5.19e-076
regional part of metencephalon8.21e-079
metencephalon8.21e-079
future metencephalon8.21e-079
Disease
Ontology termp-valuen
neuroectodermal tumor1.73e-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)

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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


No analysis results for this cluster

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.