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Coexpression cluster:C837: Difference between revisions

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|ontology_enrichment_disease=DOID:3095!4.58e-10!22;DOID:2994!4.58e-10!22;DOID:171!6.22e-08!10
|ontology_enrichment_disease=DOID:3095!4.58e-10!22;DOID:2994!4.58e-10!22;DOID:171!6.22e-08!10
|ontology_enrichment_uberon=UBERON:0000073!3.24e-34!94;UBERON:0001016!3.24e-34!94;UBERON:0001017!2.48e-32!82;UBERON:0005743!1.51e-31!86;UBERON:0001049!1.23e-29!57;UBERON:0005068!1.23e-29!57;UBERON:0006241!1.23e-29!57;UBERON:0007135!1.23e-29!57;UBERON:0007023!1.59e-27!115;UBERON:0002346!5.39e-27!90;UBERON:0000955!1.85e-25!69;UBERON:0006238!1.85e-25!69;UBERON:0002616!3.18e-24!59;UBERON:0003075!3.65e-24!86;UBERON:0007284!3.65e-24!86;UBERON:0003080!1.05e-22!42;UBERON:0002780!2.38e-22!41;UBERON:0001890!2.38e-22!41;UBERON:0006240!2.38e-22!41;UBERON:0000924!1.77e-21!173;UBERON:0006601!1.77e-21!173;UBERON:0001893!6.37e-20!34;UBERON:0002020!8.33e-20!34;UBERON:0003528!8.33e-20!34;UBERON:0004121!2.86e-19!169;UBERON:0002791!3.81e-19!33;UBERON:0001869!8.43e-19!32;UBERON:0002619!1.50e-17!22;UBERON:0003056!1.55e-16!61;UBERON:0001950!4.75e-16!20;UBERON:0000956!3.78e-14!25;UBERON:0000203!3.78e-14!25;UBERON:0000153!1.04e-13!129;UBERON:0007811!1.04e-13!129;UBERON:0000033!1.79e-13!123;UBERON:0003076!4.62e-08!15;UBERON:0003057!4.62e-08!15;UBERON:0002420!1.44e-07!9;UBERON:0007245!1.44e-07!9;UBERON:0010009!1.44e-07!9;UBERON:0010011!1.44e-07!9;UBERON:0000454!1.44e-07!9;UBERON:0002308!3.49e-07!9;UBERON:0000125!3.49e-07!9;UBERON:0004732!7.54e-07!13
|ontology_enrichment_uberon=UBERON:0000073!3.24e-34!94;UBERON:0001016!3.24e-34!94;UBERON:0001017!2.48e-32!82;UBERON:0005743!1.51e-31!86;UBERON:0001049!1.23e-29!57;UBERON:0005068!1.23e-29!57;UBERON:0006241!1.23e-29!57;UBERON:0007135!1.23e-29!57;UBERON:0007023!1.59e-27!115;UBERON:0002346!5.39e-27!90;UBERON:0000955!1.85e-25!69;UBERON:0006238!1.85e-25!69;UBERON:0002616!3.18e-24!59;UBERON:0003075!3.65e-24!86;UBERON:0007284!3.65e-24!86;UBERON:0003080!1.05e-22!42;UBERON:0002780!2.38e-22!41;UBERON:0001890!2.38e-22!41;UBERON:0006240!2.38e-22!41;UBERON:0000924!1.77e-21!173;UBERON:0006601!1.77e-21!173;UBERON:0001893!6.37e-20!34;UBERON:0002020!8.33e-20!34;UBERON:0003528!8.33e-20!34;UBERON:0004121!2.86e-19!169;UBERON:0002791!3.81e-19!33;UBERON:0001869!8.43e-19!32;UBERON:0002619!1.50e-17!22;UBERON:0003056!1.55e-16!61;UBERON:0001950!4.75e-16!20;UBERON:0000956!3.78e-14!25;UBERON:0000203!3.78e-14!25;UBERON:0000153!1.04e-13!129;UBERON:0007811!1.04e-13!129;UBERON:0000033!1.79e-13!123;UBERON:0003076!4.62e-08!15;UBERON:0003057!4.62e-08!15;UBERON:0002420!1.44e-07!9;UBERON:0007245!1.44e-07!9;UBERON:0010009!1.44e-07!9;UBERON:0010011!1.44e-07!9;UBERON:0000454!1.44e-07!9;UBERON:0002308!3.49e-07!9;UBERON:0000125!3.49e-07!9;UBERON:0004732!7.54e-07!13
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}}
}}

Revision as of 20:53, 8 August 2012


Full id: C837_neuroectodermal_duodenum_temporal_occipital_medial_carcinoid_parietal



Phase1 CAGE Peaks

Hg19::chr15:77907249..77907288,-p9@LINGO1
Hg19::chr15:77907545..77907560,-p4@LINGO1
Hg19::chr15:77907829..77907849,-p11@LINGO1
Hg19::chr15:77907867..77907879,-p12@LINGO1
Hg19::chr15:77907974..77907985,-p8@LINGO1
Hg19::chr15:77908039..77908050,-p14@LINGO1
Hg19::chr15:78111788..78111799,-p@chr15:78111788..78111799
-
Hg19::chr3:51741072..51741106,+p1@GRM2
Hg19::chr6:110422944..110422955,-p7@AK056044
Hg19::chr8:50823900..50823915,+p6@SNTG1


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:0014047glutamate secretion0.00759426602163143
GO:0016013syntrophin complex0.00759426602163143
GO:0042734presynaptic membrane0.0189784004164746
GO:0031280negative regulation of cyclase activity0.0189784004164746
GO:0007194negative regulation of adenylate cyclase activity0.0189784004164746
GO:0051350negative regulation of lyase activity0.0189784004164746
GO:0016010dystrophin-associated glycoprotein complex0.0238536438879483
GO:0030424axon0.0245064420408919
GO:0005605basal lamina0.0245064420408919
GO:0007269neurotransmitter secretion0.0245064420408919
GO:0045761regulation of adenylate cyclase activity0.0245064420408919
GO:0031279regulation of cyclase activity0.0245064420408919
GO:0051339regulation of lyase activity0.0245064420408919
GO:0045055regulated secretory pathway0.0287065807247769
GO:0008067metabotropic glutamate, GABA-B-like receptor activity0.0288115129303549
GO:0003001generation of a signal involved in cell-cell signaling0.029956787610063
GO:0005604basement membrane0.029956787610063
GO:0001505regulation of neurotransmitter levels0.029956787610063
GO:0043005neuron projection0.029956787610063
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.029956787610063
GO:0043086negative regulation of catalytic activity0.029956787610063
GO:0019933cAMP-mediated signaling0.029956787610063
GO:0008066glutamate receptor activity0.0309534539371326
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.0368968572996878
GO:0019935cyclic-nucleotide-mediated signaling0.0369292580465969
GO:0044420extracellular matrix part0.0381182985017164
GO:0044459plasma membrane part0.0412763404122513
GO:0044456synapse part0.0434629625940273



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
regional part of nervous system3.24e-3494
nervous system3.24e-3494
central nervous system2.48e-3282
neural tube1.23e-2957
neural rod1.23e-2957
future spinal cord1.23e-2957
neural keel1.23e-2957
adult organism1.59e-27115
neurectoderm5.39e-2790
brain1.85e-2569
future brain1.85e-2569
regional part of brain3.18e-2459
neural plate3.65e-2486
presumptive neural plate3.65e-2486
anterior neural tube1.05e-2242
regional part of forebrain2.38e-2241
forebrain2.38e-2241
future forebrain2.38e-2241
ectoderm1.77e-21173
presumptive ectoderm1.77e-21173
telencephalon6.37e-2034
gray matter8.33e-2034
brain grey matter8.33e-2034
ectoderm-derived structure2.86e-19169
regional part of telencephalon3.81e-1933
cerebral hemisphere8.43e-1932
regional part of cerebral cortex1.50e-1722
pre-chordal neural plate1.55e-1661
neocortex4.75e-1620
cerebral cortex3.78e-1425
pallium3.78e-1425
anterior region of body1.04e-13129
craniocervical region1.04e-13129
head1.79e-13123
posterior neural tube4.62e-0815
chordal neural plate4.62e-0815
basal ganglion1.44e-079
nuclear complex of neuraxis1.44e-079
aggregate regional part of brain1.44e-079
collection of basal ganglia1.44e-079
cerebral subcortex1.44e-079
nucleus of brain3.49e-079
neural nucleus3.49e-079
segmental subdivision of nervous system7.54e-0713
Disease
Ontology termp-valuen
germ cell and embryonal cancer4.58e-1022
germ cell cancer4.58e-1022
neuroectodermal tumor6.22e-0810


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.