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Coexpression cluster:C3026: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!5.91e-43!115;UBERON:0005743!8.32e-32!86;UBERON:0001049!2.61e-31!57;UBERON:0005068!2.61e-31!57;UBERON:0006241!2.61e-31!57;UBERON:0007135!2.61e-31!57;UBERON:0001017!4.58e-31!82;UBERON:0000073!2.40e-29!94;UBERON:0001016!2.40e-29!94;UBERON:0000955!2.66e-27!69;UBERON:0006238!2.66e-27!69;UBERON:0002616!1.70e-26!59;UBERON:0003080!1.81e-23!42;UBERON:0003075!1.81e-23!86;UBERON:0007284!1.81e-23!86;UBERON:0002780!8.73e-23!41;UBERON:0001890!8.73e-23!41;UBERON:0006240!8.73e-23!41;UBERON:0004121!1.17e-22!169;UBERON:0002346!1.98e-22!90;UBERON:0000924!3.73e-22!173;UBERON:0006601!3.73e-22!173;UBERON:0000033!5.16e-22!123;UBERON:0000153!2.05e-21!129;UBERON:0007811!2.05e-21!129;UBERON:0002020!3.64e-19!34;UBERON:0003528!3.64e-19!34;UBERON:0001893!5.13e-19!34;UBERON:0002791!1.80e-18!33;UBERON:0000475!1.13e-17!365;UBERON:0001869!1.22e-17!32;UBERON:0003056!5.59e-16!61;UBERON:0000481!1.24e-14!347;UBERON:0000956!6.38e-14!25;UBERON:0000203!6.38e-14!25;UBERON:0000477!3.69e-13!286;UBERON:0002619!7.13e-13!22;UBERON:0000062!1.76e-12!511;UBERON:0004111!4.24e-12!241;UBERON:0001950!1.25e-11!20;UBERON:0000025!2.80e-10!194;UBERON:0000468!1.33e-09!659;UBERON:0000467!2.24e-09!625;UBERON:0000480!3.58e-09!626;UBERON:0003076!6.43e-09!15;UBERON:0003057!6.43e-09!15;UBERON:0000922!2.09e-08!612;UBERON:0000483!2.30e-08!309;UBERON:0002050!2.87e-08!605;UBERON:0005423!2.87e-08!605;UBERON:0000119!3.19e-08!312;UBERON:0000923!4.50e-08!604;UBERON:0005291!4.50e-08!604;UBERON:0006598!4.50e-08!604;UBERON:0002532!4.50e-08!604;UBERON:0004732!1.36e-07!13;UBERON:0000064!2.56e-07!219;UBERON:0002298!4.25e-07!8;UBERON:0004733!6.34e-07!12;UBERON:0002028!6.34e-07!12;UBERON:0007277!6.34e-07!12;UBERON:0002308!9.58e-07!9;UBERON:0000125!9.58e-07!9
|ontology_enrichment_uberon=UBERON:0007023!1.95e-58!114;UBERON:0001049!1.14e-38!56;UBERON:0005068!1.14e-38!56;UBERON:0006241!1.14e-38!56;UBERON:0007135!1.14e-38!56;UBERON:0001017!4.77e-38!81;UBERON:0000073!9.74e-36!53;UBERON:0002616!9.74e-36!53;UBERON:0001016!3.00e-34!89;UBERON:0000955!7.85e-33!68;UBERON:0006238!7.85e-33!68;UBERON:0003075!5.27e-30!82;UBERON:0007284!5.27e-30!82;UBERON:0011216!1.04e-29!223;UBERON:0002346!2.87e-29!86;UBERON:0002780!3.90e-29!41;UBERON:0001890!3.90e-29!41;UBERON:0003080!3.90e-29!41;UBERON:0006240!3.90e-29!41;UBERON:0004121!1.70e-26!171;UBERON:0000924!1.70e-26!171;UBERON:0006601!1.70e-26!171;UBERON:0010371!2.14e-25!104;UBERON:0003528!1.83e-24!34;UBERON:0002020!1.83e-24!34;UBERON:0001893!3.51e-24!34;UBERON:0002791!1.54e-22!32;UBERON:0010314!1.83e-22!132;UBERON:0001869!2.84e-22!32;UBERON:0003056!1.39e-19!61;UBERON:0000477!4.17e-18!373;UBERON:0000956!2.87e-17!25;UBERON:0000203!2.87e-17!25;UBERON:0002619!8.35e-16!22;UBERON:0000481!3.76e-14!342;UBERON:0001950!3.92e-14!20;UBERON:0004111!6.15e-12!240;UBERON:0003076!1.70e-10!15;UBERON:0003057!1.70e-10!15;UBERON:0000025!2.25e-10!192;UBERON:0000062!2.59e-09!503;UBERON:0004732!9.76e-09!13;UBERON:0000125!1.01e-08!9;UBERON:0002308!1.01e-08!9;UBERON:0002420!5.68e-08!9;UBERON:0007245!5.68e-08!9;UBERON:0010009!5.68e-08!9;UBERON:0010011!5.68e-08!9;UBERON:0000454!5.68e-08!9;UBERON:0004733!8.51e-08!12;UBERON:0002028!8.51e-08!12;UBERON:0007277!8.51e-08!12;UBERON:0002298!1.85e-07!6;UBERON:0000483!5.71e-07!306;UBERON:0009663!8.53e-07!7
|tf_chipseq_enrich=NFYA#4800;2:12.2837204665537:0.00851601140372443:0.0324611743126966!NFYB#4801;2:11.1731955023576:0.0102546713505453:0.038109369860143!NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.0460073682941841!SP2#6668;2:17.4356869958964:0.00427356848176974:0.0203060609038922
|tf_chipseq_enrich=NFYA#4800;2:12.2837204665537:0.00851601140372443:0.0324611743126966!NFYB#4801;2:11.1731955023576:0.0102546713505453:0.038109369860143!NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.0460073682941841!SP2#6668;2:17.4356869958964:0.00427356848176974:0.0203060609038922
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}}
}}

Revision as of 14:43, 19 October 2012


Full id: C3026_medulla_aorta_optic_spinal_locus_corpus_skeletal



Phase1 CAGE Peaks

Hg19::chr10:5454633..5454661,+p4@NET1
Hg19::chr10:5454672..5454689,+p1@CU690984
Hg19::chr4:79892654..79892672,+p5@LOC100505875


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:0005089Rho guanyl-nucleotide exchange factor activity0.0288031319910514
GO:0035023regulation of Rho protein signal transduction0.0288031319910514
GO:0001558regulation of cell growth0.0288031319910514
GO:0005088Ras guanyl-nucleotide exchange factor activity0.0288031319910514
GO:0007266Rho protein signal transduction0.0288031319910514
GO:0016049cell growth0.0288031319910514
GO:0040008regulation of growth0.0288031319910514
GO:0008361regulation of cell size0.0288031319910514
GO:0005085guanyl-nucleotide exchange factor activity0.0356450410141685
GO:0046578regulation of Ras protein signal transduction0.0356450410141685
GO:0007265Ras protein signal transduction0.0356450410141685
GO:0005083small GTPase regulator activity0.0356450410141685
GO:0051056regulation of small GTPase mediated signal transduction0.0356450410141685
GO:0032989cellular structure morphogenesis0.0356450410141685
GO:0000902cell morphogenesis0.0356450410141685
GO:0030695GTPase regulator activity0.0489373601789709



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
adult organism1.95e-58114
neural tube1.14e-3856
neural rod1.14e-3856
future spinal cord1.14e-3856
neural keel1.14e-3856
central nervous system4.77e-3881
regional part of nervous system9.74e-3653
regional part of brain9.74e-3653
nervous system3.00e-3489
brain7.85e-3368
future brain7.85e-3368
neural plate5.27e-3082
presumptive neural plate5.27e-3082
organ system subdivision1.04e-29223
neurectoderm2.87e-2986
regional part of forebrain3.90e-2941
forebrain3.90e-2941
anterior neural tube3.90e-2941
future forebrain3.90e-2941
ectoderm-derived structure1.70e-26171
ectoderm1.70e-26171
presumptive ectoderm1.70e-26171
ecto-epithelium2.14e-25104
brain grey matter1.83e-2434
gray matter1.83e-2434
telencephalon3.51e-2434
regional part of telencephalon1.54e-2232
structure with developmental contribution from neural crest1.83e-22132
cerebral hemisphere2.84e-2232
pre-chordal neural plate1.39e-1961
anatomical cluster4.17e-18373
cerebral cortex2.87e-1725
pallium2.87e-1725
regional part of cerebral cortex8.35e-1622
multi-tissue structure3.76e-14342
neocortex3.92e-1420
anatomical conduit6.15e-12240
posterior neural tube1.70e-1015
chordal neural plate1.70e-1015
tube2.25e-10192
organ2.59e-09503
segmental subdivision of nervous system9.76e-0913
neural nucleus1.01e-089
nucleus of brain1.01e-089
basal ganglion5.68e-089
nuclear complex of neuraxis5.68e-089
aggregate regional part of brain5.68e-089
collection of basal ganglia5.68e-089
cerebral subcortex5.68e-089
segmental subdivision of hindbrain8.51e-0812
hindbrain8.51e-0812
presumptive hindbrain8.51e-0812
brainstem1.85e-076
epithelium5.71e-07306
telencephalic nucleus8.53e-077


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
NFYA#4800212.28372046655370.008516011403724430.0324611743126966
NFYB#4801211.17319550235760.01025467135054530.038109369860143
NR3C1#290829.982015554115360.01278474365547170.0460073682941841
SP2#6668217.43568699589640.004273568481769740.0203060609038922



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.