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Coexpression cluster:C3045: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.02e-29!115;UBERON:0001049!4.17e-29!57;UBERON:0005068!4.17e-29!57;UBERON:0006241!4.17e-29!57;UBERON:0007135!4.17e-29!57;UBERON:0001017!3.25e-25!82;UBERON:0002616!4.66e-25!59;UBERON:0000073!4.98e-25!94;UBERON:0001016!4.98e-25!94;UBERON:0005743!1.42e-23!86;UBERON:0000955!1.44e-23!69;UBERON:0006238!1.44e-23!69;UBERON:0003075!3.48e-23!86;UBERON:0007284!3.48e-23!86;UBERON:0002346!3.51e-23!90;UBERON:0003080!1.92e-22!42;UBERON:0002780!4.72e-22!41;UBERON:0001890!4.72e-22!41;UBERON:0006240!4.72e-22!41;UBERON:0002020!1.50e-18!34;UBERON:0003528!1.50e-18!34;UBERON:0000924!1.93e-18!173;UBERON:0006601!1.93e-18!173;UBERON:0001893!2.48e-18!34;UBERON:0004121!3.65e-18!169;UBERON:0002791!9.61e-18!33;UBERON:0001869!1.36e-17!32;UBERON:0000033!7.94e-17!123;UBERON:0000153!1.66e-16!129;UBERON:0007811!1.66e-16!129;UBERON:0003056!4.49e-16!61;UBERON:0000475!1.20e-15!365;UBERON:0002619!2.61e-15!22;UBERON:0001950!5.10e-14!20;UBERON:0000025!6.50e-14!194;UBERON:0000956!2.05e-13!25;UBERON:0000203!2.05e-13!25;UBERON:0004111!3.51e-13!241;UBERON:0000477!2.78e-11!286;UBERON:0000481!1.01e-10!347;UBERON:0000119!1.23e-10!312;UBERON:0000483!1.42e-10!309;UBERON:0003076!8.23e-08!15;UBERON:0003057!8.23e-08!15;UBERON:0000468!3.85e-07!659;UBERON:0002420!8.05e-07!9;UBERON:0007245!8.05e-07!9;UBERON:0010009!8.05e-07!9;UBERON:0010011!8.05e-07!9;UBERON:0000454!8.05e-07!9;UBERON:0000064!9.09e-07!219
|ontology_enrichment_uberon=UBERON:0001049!1.37e-27!56;UBERON:0005068!1.37e-27!56;UBERON:0006241!1.37e-27!56;UBERON:0007135!1.37e-27!56;UBERON:0007023!3.93e-26!114;UBERON:0000073!6.07e-26!53;UBERON:0002616!6.07e-26!53;UBERON:0001016!3.09e-25!89;UBERON:0001017!8.77e-25!81;UBERON:0000955!5.97e-23!68;UBERON:0006238!5.97e-23!68;UBERON:0003075!2.58e-22!82;UBERON:0007284!2.58e-22!82;UBERON:0002346!5.66e-22!86;UBERON:0002780!1.45e-21!41;UBERON:0001890!1.45e-21!41;UBERON:0003080!1.45e-21!41;UBERON:0006240!1.45e-21!41;UBERON:0010314!1.66e-18!132;UBERON:0003528!3.16e-18!34;UBERON:0002020!3.16e-18!34;UBERON:0001893!5.71e-18!34;UBERON:0001869!1.94e-17!32;UBERON:0002791!4.19e-17!32;UBERON:0004121!1.24e-16!171;UBERON:0000924!1.24e-16!171;UBERON:0006601!1.24e-16!171;UBERON:0003056!1.30e-16!61;UBERON:0002619!2.34e-15!22;UBERON:0010371!2.00e-14!104;UBERON:0001950!4.18e-14!20;UBERON:0011216!2.06e-13!223;UBERON:0000956!2.39e-13!25;UBERON:0000203!2.39e-13!25;UBERON:0000025!1.59e-12!192;UBERON:0000477!7.93e-12!373;UBERON:0004111!2.23e-11!240;UBERON:0000481!4.31e-11!342;UBERON:0000119!2.45e-09!309;UBERON:0000483!3.25e-09!306;UBERON:0000064!5.32e-08!218;UBERON:0003076!3.06e-07!15;UBERON:0003057!3.06e-07!15
|pathway_enrichment=1.58091305570944e-05;0.00879764861457124;2;114;Oocyte meiosis (KEGG):04114!2.77966780871129e-05;0.00879764861457124;2;151;Wnt signaling pathway (KEGG):04310
|pathway_enrichment=1.58091305570944e-05;0.00879764861457124;2;114;Oocyte meiosis (KEGG):04114!2.77966780871129e-05;0.00879764861457124;2;151;Wnt signaling pathway (KEGG):04310
|tf_chipseq_enrich=BCLAF1#9774;3:21.6526476101218:9.8473954032885e-05:0.0013882993095627!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.031899441353459!ELK4#2005;2:10.823787772312:0.0109128471951648:0.0401722480073249!FAM48A#55578;1:385.05625:0.00259478966140747:0.014348347405503!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0127589782211264!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156129227126221!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0185667252071482!MEF2A#4205;2:12.495487273096:0.00823502947802974:0.0324709572113092!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0293159243965195!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0268527451311305!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00469276767888513!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172223222289507!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00879344366748451!SIX5#147912;2:11.391143570306:0.00987382008142903:0.0370566298506672!STAT1#6772;2:13.8043916647995:0.00677093170844408:0.0287424028247852
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}}
}}

Revision as of 14:45, 19 October 2012


Full id: C3045_occipital_brain_hippocampus_medial_cerebellum_temporal_amygdala



Phase1 CAGE Peaks

Hg19::chr10:75255724..75255792,-p1@PPP3CB
Hg19::chr2:86790580..86790591,-p4@CHMP3
p4@RNF103-CHMP3
Hg19::chr5:171433662..171433686,-p2@FBXW11


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


p.valueFDRnGenesnPathwayName
1.58091305570944e-050.008797648614571242114Oocyte meiosis (KEGG):04114
2.77966780871129e-050.008797648614571242151Wnt signaling pathway (KEGG):04310



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:0005955calcineurin complex0.0134222261032357
GO:0008287protein serine/threonine phosphatase complex0.03969244056313
GO:0004722protein serine/threonine phosphatase activity0.03969244056313
GO:0016567protein ubiquitination0.03969244056313
GO:0043687post-translational protein modification0.03969244056313
GO:0032446protein modification by small protein conjugation0.03969244056313
GO:0000151ubiquitin ligase complex0.03969244056313
GO:0006464protein modification process0.03969244056313
GO:0043412biopolymer modification0.03969244056313
GO:0043234protein complex0.03969244056313
GO:0005516calmodulin binding0.03969244056313
GO:0016055Wnt receptor signaling pathway0.03969244056313
GO:0004842ubiquitin-protein ligase activity0.03969244056313
GO:0008639small protein conjugating enzyme activity0.03969244056313
GO:0032991macromolecular complex0.0485798812421496
GO:0019787small conjugating protein ligase activity0.0485798812421496
GO:0006470protein amino acid dephosphorylation0.0485798812421496



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 tube1.37e-2756
neural rod1.37e-2756
future spinal cord1.37e-2756
neural keel1.37e-2756
adult organism3.93e-26114
regional part of nervous system6.07e-2653
regional part of brain6.07e-2653
nervous system3.09e-2589
central nervous system8.77e-2581
brain5.97e-2368
future brain5.97e-2368
neural plate2.58e-2282
presumptive neural plate2.58e-2282
neurectoderm5.66e-2286
regional part of forebrain1.45e-2141
forebrain1.45e-2141
anterior neural tube1.45e-2141
future forebrain1.45e-2141
structure with developmental contribution from neural crest1.66e-18132
brain grey matter3.16e-1834
gray matter3.16e-1834
telencephalon5.71e-1834
cerebral hemisphere1.94e-1732
regional part of telencephalon4.19e-1732
ectoderm-derived structure1.24e-16171
ectoderm1.24e-16171
presumptive ectoderm1.24e-16171
pre-chordal neural plate1.30e-1661
regional part of cerebral cortex2.34e-1522
ecto-epithelium2.00e-14104
neocortex4.18e-1420
organ system subdivision2.06e-13223
cerebral cortex2.39e-1325
pallium2.39e-1325
tube1.59e-12192
anatomical cluster7.93e-12373
anatomical conduit2.23e-11240
multi-tissue structure4.31e-11342
cell layer2.45e-09309
epithelium3.25e-09306
organ part5.32e-08218
posterior neural tube3.06e-0715
chordal neural plate3.06e-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
BCLAF1#9774321.65264761012189.8473954032885e-050.0013882993095627
EGR1#195834.988179094810140.008056488137383440.031899441353459
ELK4#2005210.8237877723120.01091284719516480.0401722480073249
FAM48A#555781385.056250.002594789661407470.014348347405503
IRF1#365937.63716375356390.002244692747297240.0127589782211264
JUND#372736.994663941871030.002921845042734990.0156129227126221
MAX#414936.452555509007120.003721913834265510.0185667252071482
MEF2A#4205212.4954872730960.008235029478029740.0324709572113092
MYC#460935.22228187160940.007020843755740150.0293159243965195
NFKB1#479035.488063424193840.006049381815655430.0268527451311305
NRF1#4899312.21027944771090.0005492172401020010.00469276767888513
PAX5#507936.669565531177830.003370290999677260.0172223222289507
POU2F2#545239.106124057742520.001324165192682130.00879344366748451
SIX5#147912211.3911435703060.009873820081429030.0370566298506672
STAT1#6772213.80439166479950.006770931708444080.0287424028247852



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.