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Coexpression cluster:C2684: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004121!2.02e-36!169;UBERON:0000924!3.14e-36!173;UBERON:0006601!3.14e-36!173;UBERON:0005743!5.22e-36!86;UBERON:0001017!2.21e-35!82;UBERON:0007023!3.26e-35!115;UBERON:0003075!1.58e-34!86;UBERON:0007284!1.58e-34!86;UBERON:0000073!3.12e-34!94;UBERON:0001016!3.12e-34!94;UBERON:0002346!9.21e-34!90;UBERON:0001049!2.45e-33!57;UBERON:0005068!2.45e-33!57;UBERON:0006241!2.45e-33!57;UBERON:0007135!2.45e-33!57;UBERON:0002616!6.79e-31!59;UBERON:0000955!1.94e-30!69;UBERON:0006238!1.94e-30!69;UBERON:0000119!3.84e-29!312;UBERON:0004111!7.94e-29!241;UBERON:0000483!8.83e-29!309;UBERON:0000033!2.16e-28!123;UBERON:0000153!1.23e-27!129;UBERON:0007811!1.23e-27!129;UBERON:0003080!2.47e-26!42;UBERON:0000475!2.55e-26!365;UBERON:0002780!6.64e-26!41;UBERON:0001890!6.64e-26!41;UBERON:0006240!6.64e-26!41;UBERON:0000025!1.17e-25!194;UBERON:0000477!6.00e-25!286;UBERON:0003056!2.03e-24!61;UBERON:0002020!5.85e-22!34;UBERON:0003528!5.85e-22!34;UBERON:0001893!5.96e-22!34;UBERON:0002791!2.66e-21!33;UBERON:0001869!5.20e-21!32;UBERON:0000481!4.46e-20!347;UBERON:0000064!1.00e-19!219;UBERON:0000468!3.11e-18!659;UBERON:0000956!8.78e-17!25;UBERON:0000203!8.78e-17!25;UBERON:0002619!4.24e-16!22;UBERON:0000922!1.73e-15!612;UBERON:0000467!2.28e-15!625;UBERON:0000480!4.82e-15!626;UBERON:0001950!8.24e-15!20;UBERON:0002050!2.95e-14!605;UBERON:0005423!2.95e-14!605;UBERON:0000923!6.48e-14!604;UBERON:0005291!6.48e-14!604;UBERON:0006598!6.48e-14!604;UBERON:0002532!6.48e-14!604;UBERON:0000062!1.32e-12!511;UBERON:0003076!3.74e-08!15;UBERON:0003057!3.74e-08!15;UBERON:0004732!5.69e-07!13;UBERON:0002420!9.63e-07!9;UBERON:0007245!9.63e-07!9;UBERON:0010009!9.63e-07!9;UBERON:0010011!9.63e-07!9;UBERON:0000454!9.63e-07!9
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}}
}}

Revision as of 18:30, 8 August 2012


Full id: C2684_adrenal_occipital_parietal_temporal_amygdala_hippocampus_putamen



Phase1 CAGE Peaks

Hg19::chr2:210288760..210288849,+p1@MAP2
Hg19::chr2:213403485..213403534,-p3@ERBB4
Hg19::chr2:213403573..213403584,-p11@ERBB4
Hg19::chr2:213403690..213403704,-p6@ERBB4


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:0007026negative regulation of microtubule depolymerization0.0295010355120949
GO:0031114regulation of microtubule depolymerization0.0295010355120949
GO:0007019microtubule depolymerization0.0295010355120949
GO:0031111negative regulation of microtubule polymerization or depolymerization0.0295010355120949
GO:0031110regulation of microtubule polymerization or depolymerization0.0295010355120949
GO:0031109microtubule polymerization or depolymerization0.0295010355120949
GO:0051261protein depolymerization0.0359437983519393
GO:0051129negative regulation of cellular component organization and biogenesis0.0359437983519393
GO:0051128regulation of cellular component organization and biogenesis0.0463264455314587
GO:0000226microtubule cytoskeleton organization and biogenesis0.0463264455314587
GO:0051248negative regulation of protein metabolic process0.0463264455314587
GO:0046982protein heterodimerization activity0.0463264455314587
GO:0004714transmembrane receptor protein tyrosine kinase activity0.0463264455314587



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
ectoderm-derived structure2.02e-36169
ectoderm3.14e-36173
presumptive ectoderm3.14e-36173
central nervous system2.21e-3582
adult organism3.26e-35115
neural plate1.58e-3486
presumptive neural plate1.58e-3486
regional part of nervous system3.12e-3494
nervous system3.12e-3494
neurectoderm9.21e-3490
neural tube2.45e-3357
neural rod2.45e-3357
future spinal cord2.45e-3357
neural keel2.45e-3357
regional part of brain6.79e-3159
brain1.94e-3069
future brain1.94e-3069
cell layer3.84e-29312
anatomical conduit7.94e-29241
epithelium8.83e-29309
head2.16e-28123
anterior region of body1.23e-27129
craniocervical region1.23e-27129
anterior neural tube2.47e-2642
organism subdivision2.55e-26365
regional part of forebrain6.64e-2641
forebrain6.64e-2641
future forebrain6.64e-2641
tube1.17e-25194
anatomical cluster6.00e-25286
pre-chordal neural plate2.03e-2461
gray matter5.85e-2234
brain grey matter5.85e-2234
telencephalon5.96e-2234
regional part of telencephalon2.66e-2133
cerebral hemisphere5.20e-2132
multi-tissue structure4.46e-20347
organ part1.00e-19219
multi-cellular organism3.11e-18659
cerebral cortex8.78e-1725
pallium8.78e-1725
regional part of cerebral cortex4.24e-1622
embryo1.73e-15612
anatomical system2.28e-15625
anatomical group4.82e-15626
neocortex8.24e-1520
embryonic structure2.95e-14605
developing anatomical structure2.95e-14605
germ layer6.48e-14604
embryonic tissue6.48e-14604
presumptive structure6.48e-14604
epiblast (generic)6.48e-14604
organ1.32e-12511
posterior neural tube3.74e-0815
chordal neural plate3.74e-0815
segmental subdivision of nervous system5.69e-0713
basal ganglion9.63e-079
nuclear complex of neuraxis9.63e-079
aggregate regional part of brain9.63e-079
collection of basal ganglia9.63e-079
cerebral subcortex9.63e-079


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


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.