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Coexpression cluster:C2676: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!1.81e-52!82;UBERON:0001049!2.57e-51!57;UBERON:0005068!2.57e-51!57;UBERON:0006241!2.57e-51!57;UBERON:0007135!2.57e-51!57;UBERON:0005743!1.42e-50!86;UBERON:0000073!6.24e-50!94;UBERON:0001016!6.24e-50!94;UBERON:0007023!1.12e-49!115;UBERON:0000955!2.85e-45!69;UBERON:0006238!2.85e-45!69;UBERON:0002616!1.86e-44!59;UBERON:0002780!1.19e-37!41;UBERON:0001890!1.19e-37!41;UBERON:0006240!1.19e-37!41;UBERON:0003075!2.99e-37!86;UBERON:0007284!2.99e-37!86;UBERON:0003080!2.16e-36!42;UBERON:0002346!4.05e-36!90;UBERON:0001893!4.90e-34!34;UBERON:0002020!7.86e-34!34;UBERON:0003528!7.86e-34!34;UBERON:0002791!7.80e-33!33;UBERON:0001869!6.47e-32!32;UBERON:0002619!5.41e-27!22;UBERON:0004121!6.05e-27!169;UBERON:0000924!1.13e-26!173;UBERON:0006601!1.13e-26!173;UBERON:0003056!5.92e-25!61;UBERON:0001950!8.94e-25!20;UBERON:0000956!1.03e-24!25;UBERON:0000203!1.03e-24!25;UBERON:0000153!6.13e-24!129;UBERON:0007811!6.13e-24!129;UBERON:0000033!1.90e-23!123;UBERON:0003076!1.28e-15!15;UBERON:0003057!1.28e-15!15;UBERON:0004732!6.48e-14!13;UBERON:0000025!7.38e-14!194;UBERON:0000477!4.50e-13!286;UBERON:0004733!8.22e-13!12;UBERON:0002028!8.22e-13!12;UBERON:0007277!8.22e-13!12;UBERON:0004111!6.06e-12!241;UBERON:0000064!4.20e-11!219;UBERON:0002420!8.70e-11!9;UBERON:0007245!8.70e-11!9;UBERON:0010009!8.70e-11!9;UBERON:0010011!8.70e-11!9;UBERON:0000454!8.70e-11!9;UBERON:0002308!1.70e-10!9;UBERON:0000125!1.70e-10!9;UBERON:0001871!2.97e-10!7;UBERON:0002680!6.50e-10!9;UBERON:0001895!6.50e-10!9;UBERON:0010092!6.50e-10!9;UBERON:0000483!1.92e-09!309;UBERON:0000119!4.15e-09!312;UBERON:0000468!4.27e-09!659;UBERON:0000200!1.22e-08!6;UBERON:0009663!1.55e-08!7;UBERON:0000475!3.49e-08!365;UBERON:0000467!5.67e-08!625;UBERON:0000480!6.85e-08!626;UBERON:0000922!8.63e-08!612;UBERON:0000481!1.35e-07!347;UBERON:0000062!2.00e-07!511;UBERON:0002298!2.90e-07!8;UBERON:0001872!3.05e-07!5;UBERON:0000349!3.57e-07!5;UBERON:0002021!5.63e-07!5;UBERON:0002037!6.33e-07!6;UBERON:0006215!6.33e-07!6;UBERON:0002050!9.25e-07!605;UBERON:0005423!9.25e-07!605
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}}
}}

Revision as of 18:30, 8 August 2012


Full id: C2676_small_cerebellum_medial_carcinoid_frontal_amygdala_occipital



Phase1 CAGE Peaks

Hg19::chr2:183387244..183387259,-p3@PDE1A
Hg19::chr2:183387381..183387407,-p2@PDE1A
Hg19::chr2:183387430..183387463,-p4@PDE1A
Hg19::chr6:35026025..35026047,+p2@ANKS1A


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:0004117calmodulin-dependent cyclic-nucleotide phosphodiesterase activity0.00264916256568538
GO:00041143',5'-cyclic-nucleotide phosphodiesterase activity0.0138255559698253
GO:0004112cyclic-nucleotide phosphodiesterase activity0.0138255559698253
GO:0008081phosphoric diester hydrolase activity0.024851546815114
GO:0005516calmodulin binding0.024851546815114



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
central nervous system1.81e-5282
neural tube2.57e-5157
neural rod2.57e-5157
future spinal cord2.57e-5157
neural keel2.57e-5157
regional part of nervous system6.24e-5094
nervous system6.24e-5094
adult organism1.12e-49115
brain2.85e-4569
future brain2.85e-4569
regional part of brain1.86e-4459
regional part of forebrain1.19e-3741
forebrain1.19e-3741
future forebrain1.19e-3741
neural plate2.99e-3786
presumptive neural plate2.99e-3786
anterior neural tube2.16e-3642
neurectoderm4.05e-3690
telencephalon4.90e-3434
gray matter7.86e-3434
brain grey matter7.86e-3434
regional part of telencephalon7.80e-3333
cerebral hemisphere6.47e-3232
regional part of cerebral cortex5.41e-2722
ectoderm-derived structure6.05e-27169
ectoderm1.13e-26173
presumptive ectoderm1.13e-26173
pre-chordal neural plate5.92e-2561
neocortex8.94e-2520
cerebral cortex1.03e-2425
pallium1.03e-2425
anterior region of body6.13e-24129
craniocervical region6.13e-24129
head1.90e-23123
posterior neural tube1.28e-1515
chordal neural plate1.28e-1515
segmental subdivision of nervous system6.48e-1413
tube7.38e-14194
anatomical cluster4.50e-13286
segmental subdivision of hindbrain8.22e-1312
hindbrain8.22e-1312
presumptive hindbrain8.22e-1312
anatomical conduit6.06e-12241
organ part4.20e-11219
basal ganglion8.70e-119
nuclear complex of neuraxis8.70e-119
aggregate regional part of brain8.70e-119
collection of basal ganglia8.70e-119
cerebral subcortex8.70e-119
nucleus of brain1.70e-109
neural nucleus1.70e-109
temporal lobe2.97e-107
regional part of metencephalon6.50e-109
metencephalon6.50e-109
future metencephalon6.50e-109
epithelium1.92e-09309
cell layer4.15e-09312
multi-cellular organism4.27e-09659
gyrus1.22e-086
telencephalic nucleus1.55e-087
organism subdivision3.49e-08365
anatomical system5.67e-08625
anatomical group6.85e-08626
embryo8.63e-08612
multi-tissue structure1.35e-07347
organ2.00e-07511
brainstem2.90e-078
parietal lobe3.05e-075
limbic system3.57e-075
occipital lobe5.63e-075
cerebellum6.33e-076
rhombic lip6.33e-076
embryonic structure9.25e-07605
developing anatomical structure9.25e-07605


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.