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Coexpression cluster:C2770: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!2.49e-64!57;UBERON:0005068!2.49e-64!57;UBERON:0006241!2.49e-64!57;UBERON:0007135!2.49e-64!57;UBERON:0005743!5.54e-54!86;UBERON:0002616!1.99e-53!59;UBERON:0001017!5.60e-53!82;UBERON:0007023!2.29e-51!115;UBERON:0003075!1.04e-50!86;UBERON:0007284!1.04e-50!86;UBERON:0000073!1.06e-50!94;UBERON:0001016!1.06e-50!94;UBERON:0002780!2.55e-50!41;UBERON:0001890!2.55e-50!41;UBERON:0006240!2.55e-50!41;UBERON:0000955!4.01e-49!69;UBERON:0006238!4.01e-49!69;UBERON:0003080!7.66e-49!42;UBERON:0002346!1.19e-47!90;UBERON:0002020!1.01e-39!34;UBERON:0003528!1.01e-39!34;UBERON:0001893!1.43e-39!34;UBERON:0002791!7.19e-38!33;UBERON:0001869!8.58e-37!32;UBERON:0003056!8.25e-36!61;UBERON:0002619!3.09e-31!22;UBERON:0004121!1.01e-28!169;UBERON:0000033!2.76e-28!123;UBERON:0001950!4.05e-28!20;UBERON:0000924!1.35e-27!173;UBERON:0006601!1.35e-27!173;UBERON:0000153!2.53e-27!129;UBERON:0007811!2.53e-27!129;UBERON:0000956!8.67e-27!25;UBERON:0000203!8.67e-27!25;UBERON:0000025!2.99e-16!194;UBERON:0003076!6.09e-16!15;UBERON:0003057!6.09e-16!15;UBERON:0002308!1.56e-14!9;UBERON:0000125!1.56e-14!9;UBERON:0002420!3.19e-14!9;UBERON:0007245!3.19e-14!9;UBERON:0010009!3.19e-14!9;UBERON:0010011!3.19e-14!9;UBERON:0000454!3.19e-14!9;UBERON:0004111!8.01e-13!241;UBERON:0000483!1.11e-12!309;UBERON:0000119!2.30e-12!312;UBERON:0000062!2.45e-12!511;UBERON:0001894!3.76e-12!7;UBERON:0006222!3.76e-12!7;UBERON:0004733!8.43e-12!12;UBERON:0002028!8.43e-12!12;UBERON:0007277!8.43e-12!12;UBERON:0000200!1.02e-11!6;UBERON:0000922!1.61e-11!612;UBERON:0009663!2.99e-11!7;UBERON:0002298!5.71e-11!8;UBERON:0000477!6.45e-11!286;UBERON:0004732!1.04e-10!13;UBERON:0001871!1.87e-10!7;UBERON:0000923!7.99e-10!604;UBERON:0005291!7.99e-10!604;UBERON:0006598!7.99e-10!604;UBERON:0002532!7.99e-10!604;UBERON:0002050!9.27e-10!605;UBERON:0005423!9.27e-10!605;UBERON:0000481!1.10e-09!347;UBERON:0001872!1.13e-09!5;UBERON:0000475!1.35e-09!365;UBERON:0000349!2.76e-09!5;UBERON:0000064!3.45e-09!219;UBERON:0000480!5.02e-09!626;UBERON:0000467!1.38e-08!625;UBERON:0000468!1.51e-08!659;UBERON:0003296!6.36e-08!4;UBERON:0010133!6.36e-08!4;UBERON:0002680!1.67e-07!9;UBERON:0001895!1.67e-07!9;UBERON:0010092!1.67e-07!9;UBERON:0000369!2.39e-07!4;UBERON:0002435!2.39e-07!4;UBERON:0000204!2.39e-07!4;UBERON:0010082!2.39e-07!4;UBERON:0000988!9.73e-07!3
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}}
}}

Revision as of 18:35, 8 August 2012


Full id: C2770_melanoma_pons_cerebellum_medial_pituitary_parietal_locus



Phase1 CAGE Peaks

Hg19::chr4:114037833..114037852,+p12@ANK2
Hg19::chr4:114037991..114038015,+p8@ANK2
Hg19::chr4:114038031..114038042,+p22@ANK2
Hg19::chr6:72926217..72926229,+p15@RIMS1


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:0016079synaptic vesicle exocytosis0.0196401586040074
GO:0042734presynaptic membrane0.0196401586040074
GO:0017156calcium ion-dependent exocytosis0.0196401586040074
GO:0048489synaptic vesicle transport0.0203940481014304
GO:0017137Rab GTPase binding0.0244696150905867
GO:0006944membrane fusion0.0258888161799637
GO:0007269neurotransmitter secretion0.0258888161799637
GO:0045055regulated secretory pathway0.0274886381140926
GO:0003001generation of a signal involved in cell-cell signaling0.0274886381140926
GO:0017016Ras GTPase binding0.0274886381140926
GO:0006836neurotransmitter transport0.0274886381140926
GO:0001505regulation of neurotransmitter levels0.0274886381140926
GO:0005200structural constituent of cytoskeleton0.0274886381140926
GO:0031267small GTPase binding0.0274886381140926
GO:0051020GTPase binding0.0292729170215506
GO:0006887exocytosis0.031397776726905
GO:0044456synapse part0.0428304475215015



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 tube2.49e-6457
neural rod2.49e-6457
future spinal cord2.49e-6457
neural keel2.49e-6457
regional part of brain1.99e-5359
central nervous system5.60e-5382
adult organism2.29e-51115
neural plate1.04e-5086
presumptive neural plate1.04e-5086
regional part of nervous system1.06e-5094
nervous system1.06e-5094
regional part of forebrain2.55e-5041
forebrain2.55e-5041
future forebrain2.55e-5041
brain4.01e-4969
future brain4.01e-4969
anterior neural tube7.66e-4942
neurectoderm1.19e-4790
gray matter1.01e-3934
brain grey matter1.01e-3934
telencephalon1.43e-3934
regional part of telencephalon7.19e-3833
cerebral hemisphere8.58e-3732
pre-chordal neural plate8.25e-3661
regional part of cerebral cortex3.09e-3122
ectoderm-derived structure1.01e-28169
head2.76e-28123
neocortex4.05e-2820
ectoderm1.35e-27173
presumptive ectoderm1.35e-27173
anterior region of body2.53e-27129
craniocervical region2.53e-27129
cerebral cortex8.67e-2725
pallium8.67e-2725
tube2.99e-16194
posterior neural tube6.09e-1615
chordal neural plate6.09e-1615
nucleus of brain1.56e-149
neural nucleus1.56e-149
basal ganglion3.19e-149
nuclear complex of neuraxis3.19e-149
aggregate regional part of brain3.19e-149
collection of basal ganglia3.19e-149
cerebral subcortex3.19e-149
anatomical conduit8.01e-13241
epithelium1.11e-12309
cell layer2.30e-12312
organ2.45e-12511
diencephalon3.76e-127
future diencephalon3.76e-127
segmental subdivision of hindbrain8.43e-1212
hindbrain8.43e-1212
presumptive hindbrain8.43e-1212
gyrus1.02e-116
embryo1.61e-11612
telencephalic nucleus2.99e-117
brainstem5.71e-118
anatomical cluster6.45e-11286
segmental subdivision of nervous system1.04e-1013
temporal lobe1.87e-107
germ layer7.99e-10604
embryonic tissue7.99e-10604
presumptive structure7.99e-10604
epiblast (generic)7.99e-10604
embryonic structure9.27e-10605
developing anatomical structure9.27e-10605
multi-tissue structure1.10e-09347
parietal lobe1.13e-095
organism subdivision1.35e-09365
limbic system2.76e-095
organ part3.45e-09219
anatomical group5.02e-09626
anatomical system1.38e-08625
multi-cellular organism1.51e-08659
gland of diencephalon6.36e-084
neuroendocrine gland6.36e-084
regional part of metencephalon1.67e-079
metencephalon1.67e-079
future metencephalon1.67e-079
corpus striatum2.39e-074
striatum2.39e-074
ventral part of telencephalon2.39e-074
future corpus striatum2.39e-074
pons9.73e-073


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.

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