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Coexpression cluster:C4450: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!1.23e-72!57;UBERON:0005068!1.23e-72!57;UBERON:0006241!1.23e-72!57;UBERON:0007135!1.23e-72!57;UBERON:0001017!4.45e-69!82;UBERON:0000073!1.34e-67!94;UBERON:0001016!1.34e-67!94;UBERON:0005743!3.86e-67!86;UBERON:0003075!4.99e-62!86;UBERON:0007284!4.99e-62!86;UBERON:0000955!1.53e-60!69;UBERON:0006238!1.53e-60!69;UBERON:0002346!2.32e-60!90;UBERON:0002616!2.38e-60!59;UBERON:0007023!1.50e-55!115;UBERON:0003080!1.17e-54!42;UBERON:0002780!3.13e-53!41;UBERON:0001890!3.13e-53!41;UBERON:0006240!3.13e-53!41;UBERON:0001893!4.96e-49!34;UBERON:0002020!5.04e-49!34;UBERON:0003528!5.04e-49!34;UBERON:0002791!1.96e-47!33;UBERON:0001869!1.33e-45!32;UBERON:0003056!3.42e-41!61;UBERON:0004121!1.97e-40!169;UBERON:0000924!3.45e-40!173;UBERON:0006601!3.45e-40!173;UBERON:0000153!1.45e-35!129;UBERON:0007811!1.45e-35!129;UBERON:0000956!2.74e-34!25;UBERON:0000203!2.74e-34!25;UBERON:0000033!3.60e-34!123;UBERON:0002619!1.19e-30!22;UBERON:0001950!1.90e-27!20;UBERON:0003076!3.16e-18!15;UBERON:0003057!3.16e-18!15;UBERON:0000025!6.76e-18!194;UBERON:0002420!2.75e-16!9;UBERON:0007245!2.75e-16!9;UBERON:0010009!2.75e-16!9;UBERON:0010011!2.75e-16!9;UBERON:0000454!2.75e-16!9;UBERON:0002308!4.47e-16!9;UBERON:0000125!4.47e-16!9;UBERON:0000064!1.81e-15!219;UBERON:0002298!4.24e-14!8;UBERON:0004733!1.81e-13!12;UBERON:0002028!1.81e-13!12;UBERON:0007277!1.81e-13!12;UBERON:0004111!2.01e-13!241;UBERON:0000483!3.84e-13!309;UBERON:0000119!8.11e-13!312;UBERON:0009663!8.32e-13!7;UBERON:0000477!9.40e-13!286;UBERON:0004732!3.16e-12!13;UBERON:0000475!4.52e-11!365;UBERON:0001871!5.13e-11!7;UBERON:0000922!5.71e-11!612;UBERON:0000200!8.59e-11!6;UBERON:0000349!5.68e-10!5;UBERON:0000062!6.33e-10!511;UBERON:0002021!2.52e-09!5;UBERON:0000468!4.30e-09!659;UBERON:0002680!5.70e-09!9;UBERON:0001895!5.70e-09!9;UBERON:0010092!5.70e-09!9;UBERON:0000481!9.16e-09!347;UBERON:0000923!2.50e-08!604;UBERON:0005291!2.50e-08!604;UBERON:0006598!2.50e-08!604;UBERON:0002532!2.50e-08!604;UBERON:0002050!2.87e-08!605;UBERON:0005423!2.87e-08!605;UBERON:0000467!4.23e-08!625;UBERON:0000480!4.85e-08!626;UBERON:0000369!7.88e-08!4;UBERON:0002435!7.88e-08!4;UBERON:0000204!7.88e-08!4;UBERON:0010082!7.88e-08!4
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}}
}}

Revision as of 20:02, 8 August 2012


Full id: C4450_brain_hippocampus_amygdala_spinal_corpus_thalamus_globus



Phase1 CAGE Peaks

Hg19::chr5:11589158..11589169,-p25@CTNND2
Hg19::chr7:31092040..31092051,+p7@ADCYAP1R1
Hg19::chrX:13917521..13917525,-p@chrX:13917521..13917525
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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


GO IDGO nameFDR corrected p-value
GO:0007158neuron adhesion0.0248690319985808
GO:0004999vasoactive intestinal polypeptide receptor activity0.0248690319985808



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 tube1.23e-7257
neural rod1.23e-7257
future spinal cord1.23e-7257
neural keel1.23e-7257
central nervous system4.45e-6982
regional part of nervous system1.34e-6794
nervous system1.34e-6794
neural plate4.99e-6286
presumptive neural plate4.99e-6286
brain1.53e-6069
future brain1.53e-6069
neurectoderm2.32e-6090
regional part of brain2.38e-6059
adult organism1.50e-55115
anterior neural tube1.17e-5442
regional part of forebrain3.13e-5341
forebrain3.13e-5341
future forebrain3.13e-5341
telencephalon4.96e-4934
gray matter5.04e-4934
brain grey matter5.04e-4934
regional part of telencephalon1.96e-4733
cerebral hemisphere1.33e-4532
pre-chordal neural plate3.42e-4161
ectoderm-derived structure1.97e-40169
ectoderm3.45e-40173
presumptive ectoderm3.45e-40173
anterior region of body1.45e-35129
craniocervical region1.45e-35129
cerebral cortex2.74e-3425
pallium2.74e-3425
head3.60e-34123
regional part of cerebral cortex1.19e-3022
neocortex1.90e-2720
posterior neural tube3.16e-1815
chordal neural plate3.16e-1815
tube6.76e-18194
basal ganglion2.75e-169
nuclear complex of neuraxis2.75e-169
aggregate regional part of brain2.75e-169
collection of basal ganglia2.75e-169
cerebral subcortex2.75e-169
nucleus of brain4.47e-169
neural nucleus4.47e-169
organ part1.81e-15219
brainstem4.24e-148
segmental subdivision of hindbrain1.81e-1312
hindbrain1.81e-1312
presumptive hindbrain1.81e-1312
anatomical conduit2.01e-13241
epithelium3.84e-13309
cell layer8.11e-13312
telencephalic nucleus8.32e-137
anatomical cluster9.40e-13286
segmental subdivision of nervous system3.16e-1213
organism subdivision4.52e-11365
temporal lobe5.13e-117
embryo5.71e-11612
gyrus8.59e-116
limbic system5.68e-105
organ6.33e-10511
occipital lobe2.52e-095
multi-cellular organism4.30e-09659
regional part of metencephalon5.70e-099
metencephalon5.70e-099
future metencephalon5.70e-099
multi-tissue structure9.16e-09347
germ layer2.50e-08604
embryonic tissue2.50e-08604
presumptive structure2.50e-08604
epiblast (generic)2.50e-08604
embryonic structure2.87e-08605
developing anatomical structure2.87e-08605
anatomical system4.23e-08625
anatomical group4.85e-08626
corpus striatum7.88e-084
striatum7.88e-084
ventral part of telencephalon7.88e-084
future corpus striatum7.88e-084


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.