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Coexpression cluster:C2251: Difference between revisions

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|full_id=C2251_adipose_spinal_substantia_medulla_corpus_Anulus_tenocyte
|full_id=C2251_adipose_spinal_substantia_medulla_corpus_Anulus_tenocyte
|id=C2251
|id=C2251
|ontology_enrichment_celltype=CL:0000055!3.65e-09!180;CL:0000057!4.68e-09!75;CL:0002620!8.92e-07!23
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.75e-45!115;UBERON:0001049!2.31e-26!57;UBERON:0005068!2.31e-26!57;UBERON:0006241!2.31e-26!57;UBERON:0007135!2.31e-26!57;UBERON:0002616!3.06e-23!59;UBERON:0000477!1.10e-21!286;UBERON:0003075!5.52e-21!86;UBERON:0007284!5.52e-21!86;UBERON:0000475!2.24e-20!365;UBERON:0000955!4.72e-20!69;UBERON:0006238!4.72e-20!69;UBERON:0003080!2.95e-19!42;UBERON:0004111!3.49e-19!241;UBERON:0005743!3.70e-19!86;UBERON:0001017!4.36e-19!82;UBERON:0002346!1.39e-18!90;UBERON:0002780!1.47e-18!41;UBERON:0001890!1.47e-18!41;UBERON:0006240!1.47e-18!41;UBERON:0000153!1.10e-17!129;UBERON:0007811!1.10e-17!129;UBERON:0000033!1.32e-17!123;UBERON:0000073!1.37e-16!94;UBERON:0001016!1.37e-16!94;UBERON:0000468!1.47e-15!659;UBERON:0000025!1.96e-15!194;UBERON:0002020!2.04e-15!34;UBERON:0003528!2.04e-15!34;UBERON:0001893!2.24e-15!34;UBERON:0000481!6.51e-15!347;UBERON:0002791!9.05e-15!33;UBERON:0003056!4.04e-14!61;UBERON:0001869!5.95e-14!32;UBERON:0000119!6.61e-14!312;UBERON:0000467!6.92e-14!625;UBERON:0000483!8.81e-14!309;UBERON:0000480!1.10e-13!626;UBERON:0004121!7.47e-12!169;UBERON:0002619!3.21e-11!22;UBERON:0000924!9.46e-11!173;UBERON:0006601!9.46e-11!173;UBERON:0001950!6.46e-10!20;UBERON:0000956!7.41e-10!25;UBERON:0000203!7.41e-10!25;UBERON:0000062!3.39e-09!511;UBERON:0000914!2.70e-08!83;UBERON:0002329!2.70e-08!83;UBERON:0003077!2.70e-08!83;UBERON:0003059!2.70e-08!83;UBERON:0007282!2.70e-08!83;UBERON:0009618!2.70e-08!83;UBERON:0007285!2.70e-08!83;UBERON:0000479!2.75e-08!787;UBERON:0003076!2.82e-08!15;UBERON:0003057!2.82e-08!15;UBERON:0002308!1.91e-07!9;UBERON:0000125!1.91e-07!9;UBERON:0002298!1.91e-07!8;UBERON:0002420!3.10e-07!9;UBERON:0007245!3.10e-07!9;UBERON:0010009!3.10e-07!9;UBERON:0010011!3.10e-07!9;UBERON:0000454!3.10e-07!9;UBERON:0000064!3.44e-07!219;UBERON:0002385!4.91e-07!63;UBERON:0001015!4.91e-07!63;UBERON:0000383!4.91e-07!63;UBERON:0002050!5.37e-07!605;UBERON:0005423!5.37e-07!605;UBERON:0000922!7.52e-07!612;UBERON:0000923!7.72e-07!604;UBERON:0005291!7.72e-07!604;UBERON:0006598!7.72e-07!604;UBERON:0002532!7.72e-07!604;UBERON:0004732!7.82e-07!13
|ontology_enrichment_uberon=UBERON:0007023!1.07e-53!114;UBERON:0001049!1.16e-27!56;UBERON:0005068!1.16e-27!56;UBERON:0006241!1.16e-27!56;UBERON:0007135!1.16e-27!56;UBERON:0000073!4.64e-25!53;UBERON:0002616!4.64e-25!53;UBERON:0010314!2.80e-22!132;UBERON:0002780!5.86e-22!41;UBERON:0001890!5.86e-22!41;UBERON:0003080!5.86e-22!41;UBERON:0006240!5.86e-22!41;UBERON:0003075!1.84e-21!82;UBERON:0007284!1.84e-21!82;UBERON:0000955!1.38e-19!68;UBERON:0006238!1.38e-19!68;UBERON:0002346!2.01e-19!86;UBERON:0001893!1.02e-18!34;UBERON:0003528!1.06e-18!34;UBERON:0002020!1.06e-18!34;UBERON:0001017!1.50e-18!81;UBERON:0002791!4.82e-17!32;UBERON:0001869!6.36e-17!32;UBERON:0001016!1.25e-15!89;UBERON:0010371!7.66e-15!104;UBERON:0003056!7.92e-15!61;UBERON:0002619!1.98e-14!22;UBERON:0000481!1.73e-13!342;UBERON:0000477!2.18e-13!373;UBERON:0004111!7.99e-13!240;UBERON:0001950!9.23e-13!20;UBERON:0000956!9.27e-12!25;UBERON:0000203!9.27e-12!25;UBERON:0000467!1.53e-11!624;UBERON:0000480!2.04e-11!625;UBERON:0000468!3.16e-11!656;UBERON:0011216!6.30e-11!223;UBERON:0000025!1.93e-10!192;UBERON:0000483!8.76e-10!306;UBERON:0000119!1.22e-09!309;UBERON:0004121!1.73e-09!171;UBERON:0000924!1.73e-09!171;UBERON:0006601!1.73e-09!171;UBERON:0000125!6.22e-09!9;UBERON:0002308!6.22e-09!9;UBERON:0002420!8.03e-09!9;UBERON:0007245!8.03e-09!9;UBERON:0010009!8.03e-09!9;UBERON:0010011!8.03e-09!9;UBERON:0000454!8.03e-09!9;UBERON:0000062!1.17e-08!503;UBERON:0000479!2.52e-08!773;UBERON:0009663!3.40e-07!7;UBERON:0002298!4.43e-07!6;UBERON:0003076!5.84e-07!15;UBERON:0003057!5.84e-07!15
|tf_chipseq_enrich=EP300#2033;3:5.0804562946674:0.0114429840539824:0.0418758124536201!RAD21#5885;3:7.76627542159225:0.003341119385872:0.017264158299084
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}}
}}

Revision as of 13:48, 19 October 2012


Full id: C2251_adipose_spinal_substantia_medulla_corpus_Anulus_tenocyte



Phase1 CAGE Peaks

Hg19::chr13:113633442..113633469,+p7@MCF2L
Hg19::chr3:16216111..16216120,+p4@GALNTL2
Hg19::chr3:16216137..16216203,+p1@GALNTL2
Hg19::chr3:16216210..16216221,+p2@GALNTL2


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


No GOStat results

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 organism1.07e-53114
neural tube1.16e-2756
neural rod1.16e-2756
future spinal cord1.16e-2756
neural keel1.16e-2756
regional part of nervous system4.64e-2553
regional part of brain4.64e-2553
structure with developmental contribution from neural crest2.80e-22132
regional part of forebrain5.86e-2241
forebrain5.86e-2241
anterior neural tube5.86e-2241
future forebrain5.86e-2241
neural plate1.84e-2182
presumptive neural plate1.84e-2182
brain1.38e-1968
future brain1.38e-1968
neurectoderm2.01e-1986
telencephalon1.02e-1834
brain grey matter1.06e-1834
gray matter1.06e-1834
central nervous system1.50e-1881
regional part of telencephalon4.82e-1732
cerebral hemisphere6.36e-1732
nervous system1.25e-1589
ecto-epithelium7.66e-15104
pre-chordal neural plate7.92e-1561
regional part of cerebral cortex1.98e-1422
multi-tissue structure1.73e-13342
anatomical cluster2.18e-13373
anatomical conduit7.99e-13240
neocortex9.23e-1320
cerebral cortex9.27e-1225
pallium9.27e-1225
anatomical system1.53e-11624
anatomical group2.04e-11625
multi-cellular organism3.16e-11656
organ system subdivision6.30e-11223
tube1.93e-10192
epithelium8.76e-10306
cell layer1.22e-09309
ectoderm-derived structure1.73e-09171
ectoderm1.73e-09171
presumptive ectoderm1.73e-09171
neural nucleus6.22e-099
nucleus of brain6.22e-099
basal ganglion8.03e-099
nuclear complex of neuraxis8.03e-099
aggregate regional part of brain8.03e-099
collection of basal ganglia8.03e-099
cerebral subcortex8.03e-099
organ1.17e-08503
tissue2.52e-08773
telencephalic nucleus3.40e-077
brainstem4.43e-076
posterior neural tube5.84e-0715
chordal neural plate5.84e-0715


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
EP300#203335.08045629466740.01144298405398240.0418758124536201
RAD21#588537.766275421592250.0033411193858720.017264158299084



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.