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Coexpression cluster:C2486: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!9.45e-40!115;UBERON:0001049!5.47e-22!57;UBERON:0005068!5.47e-22!57;UBERON:0006241!5.47e-22!57;UBERON:0007135!5.47e-22!57;UBERON:0002616!1.22e-20!59;UBERON:0003075!1.07e-19!86;UBERON:0007284!1.07e-19!86;UBERON:0005743!6.52e-18!86;UBERON:0001017!1.17e-17!82;UBERON:0002346!1.38e-17!90;UBERON:0000073!2.77e-17!94;UBERON:0001016!2.77e-17!94;UBERON:0000475!6.64e-17!365;UBERON:0003080!6.17e-16!42;UBERON:0000955!1.20e-15!69;UBERON:0006238!1.20e-15!69;UBERON:0002780!1.55e-15!41;UBERON:0001890!1.55e-15!41;UBERON:0006240!1.55e-15!41;UBERON:0002020!7.84e-15!34;UBERON:0003528!7.84e-15!34;UBERON:0001893!8.49e-15!34;UBERON:0003056!1.15e-14!61;UBERON:0004121!1.15e-14!169;UBERON:0002791!3.08e-14!33;UBERON:0000033!5.46e-14!123;UBERON:0000119!7.09e-14!312;UBERON:0000025!1.02e-13!194;UBERON:0000924!1.63e-13!173;UBERON:0006601!1.63e-13!173;UBERON:0001869!1.67e-13!32;UBERON:0004111!2.25e-13!241;UBERON:0000483!2.25e-13!309;UBERON:0000153!4.70e-13!129;UBERON:0007811!4.70e-13!129;UBERON:0000481!2.98e-12!347;UBERON:0000064!1.15e-11!219;UBERON:0000477!1.55e-11!286;UBERON:0000956!6.55e-10!25;UBERON:0000203!6.55e-10!25;UBERON:0002619!7.01e-10!22;UBERON:0001950!5.73e-09!20;UBERON:0000464!1.41e-08!104;UBERON:0000468!3.09e-08!659;UBERON:0002553!6.06e-08!70;UBERON:0003886!1.04e-07!63;UBERON:0003103!1.53e-07!69;UBERON:0003076!2.63e-07!15;UBERON:0003057!2.63e-07!15;UBERON:0000466!4.65e-07!126
|ontology_enrichment_uberon=UBERON:0007023!1.12e-39!114;UBERON:0003075!6.60e-23!82;UBERON:0007284!6.60e-23!82;UBERON:0001049!9.45e-23!56;UBERON:0005068!9.45e-23!56;UBERON:0006241!9.45e-23!56;UBERON:0007135!9.45e-23!56;UBERON:0010371!1.72e-21!104;UBERON:0000073!3.51e-21!53;UBERON:0002616!3.51e-21!53;UBERON:0002346!1.31e-20!86;UBERON:0010314!4.55e-19!132;UBERON:0001017!3.29e-18!81;UBERON:0001016!2.90e-17!89;UBERON:0002780!1.15e-16!41;UBERON:0001890!1.15e-16!41;UBERON:0003080!1.15e-16!41;UBERON:0006240!1.15e-16!41;UBERON:0003056!1.98e-16!61;UBERON:0000477!2.07e-16!373;UBERON:0000955!2.26e-16!68;UBERON:0006238!2.26e-16!68;UBERON:0001893!1.10e-15!34;UBERON:0003528!1.16e-15!34;UBERON:0002020!1.16e-15!34;UBERON:0004121!2.74e-15!171;UBERON:0000924!2.74e-15!171;UBERON:0006601!2.74e-15!171;UBERON:0000119!4.22e-15!309;UBERON:0000481!4.32e-15!342;UBERON:0000483!1.51e-14!306;UBERON:0002791!2.10e-14!32;UBERON:0001869!2.38e-14!32;UBERON:0000025!2.95e-14!192;UBERON:0004111!1.23e-13!240;UBERON:0011216!5.20e-13!223;UBERON:0000064!3.38e-12!218;UBERON:0000956!1.61e-10!25;UBERON:0000203!1.61e-10!25;UBERON:0002619!1.74e-10!22;UBERON:0001950!1.79e-09!20;UBERON:0000468!9.24e-09!656;UBERON:0003103!9.20e-08!68;UBERON:0000464!2.34e-07!95;UBERON:0000922!2.42e-07!592;UBERON:0003076!2.55e-07!15;UBERON:0003057!2.55e-07!15;UBERON:0000125!7.68e-07!9;UBERON:0002308!7.68e-07!9;UBERON:0000062!9.64e-07!503
|tf_chipseq_enrich=CTCFL#140690;3:14.8098557692308:0.000499629176756334:0.00440902168071438!HMGN3#9324;3:6.13391079251294:0.00664069668332472:0.0282953661992473!NR3C1#2908;3:11.2297674983798:0.00113167206806385:0.00775478637336926!NRF1#4899;3:9.15770958578318:0.00206195379173342:0.0119624703952254!RAD21#5885;3:7.76627542159225:0.003341119385872:0.0172675755909089!SMC3#9126;3:11.2836996336996:0.00111580236686805:0.00765658892203238!ZBTB7A#51341;3:5.51393198090692:0.00903835282108109:0.0342459922464406
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}}
}}

Revision as of 14:04, 19 October 2012


Full id: C2486_optic_Adipocyte_aorta_embryonic_diencephalon_basal_corpus



Phase1 CAGE Peaks

Hg19::chr19:38743538..38743565,+p@chr19:38743538..38743565
+
Hg19::chr19:38746979..38747050,-p1@PPP1R14A
Hg19::chr19:38747153..38747169,-p3@PPP1R14A
Hg19::chr19:38747174..38747218,-p2@PPP1R14A


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 organism1.12e-39114
neural plate6.60e-2382
presumptive neural plate6.60e-2382
neural tube9.45e-2356
neural rod9.45e-2356
future spinal cord9.45e-2356
neural keel9.45e-2356
ecto-epithelium1.72e-21104
regional part of nervous system3.51e-2153
regional part of brain3.51e-2153
neurectoderm1.31e-2086
structure with developmental contribution from neural crest4.55e-19132
central nervous system3.29e-1881
nervous system2.90e-1789
regional part of forebrain1.15e-1641
forebrain1.15e-1641
anterior neural tube1.15e-1641
future forebrain1.15e-1641
pre-chordal neural plate1.98e-1661
anatomical cluster2.07e-16373
brain2.26e-1668
future brain2.26e-1668
telencephalon1.10e-1534
brain grey matter1.16e-1534
gray matter1.16e-1534
ectoderm-derived structure2.74e-15171
ectoderm2.74e-15171
presumptive ectoderm2.74e-15171
cell layer4.22e-15309
multi-tissue structure4.32e-15342
epithelium1.51e-14306
regional part of telencephalon2.10e-1432
cerebral hemisphere2.38e-1432
tube2.95e-14192
anatomical conduit1.23e-13240
organ system subdivision5.20e-13223
organ part3.38e-12218
cerebral cortex1.61e-1025
pallium1.61e-1025
regional part of cerebral cortex1.74e-1022
neocortex1.79e-0920
multi-cellular organism9.24e-09656
compound organ9.20e-0868
anatomical space2.34e-0795
embryo2.42e-07592
posterior neural tube2.55e-0715
chordal neural plate2.55e-0715
neural nucleus7.68e-079
nucleus of brain7.68e-079
organ9.64e-07503


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
CTCFL#140690314.80985576923080.0004996291767563340.00440902168071438
HMGN3#932436.133910792512940.006640696683324720.0282953661992473
NR3C1#2908311.22976749837980.001131672068063850.00775478637336926
NRF1#489939.157709585783180.002061953791733420.0119624703952254
RAD21#588537.766275421592250.0033411193858720.0172675755909089
SMC3#9126311.28369963369960.001115802366868050.00765658892203238
ZBTB7A#5134135.513931980906920.009038352821081090.0342459922464406



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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