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Coexpression cluster:C4279: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!9.38e-43!115;UBERON:0000073!3.35e-35!94;UBERON:0001016!3.35e-35!94;UBERON:0005743!1.21e-34!86;UBERON:0001017!2.01e-33!82;UBERON:0001049!5.48e-31!57;UBERON:0005068!5.48e-31!57;UBERON:0006241!5.48e-31!57;UBERON:0007135!5.48e-31!57;UBERON:0000955!5.31e-29!69;UBERON:0006238!5.31e-29!69;UBERON:0002616!7.28e-29!59;UBERON:0002346!4.24e-27!90;UBERON:0003075!2.19e-26!86;UBERON:0007284!2.19e-26!86;UBERON:0000924!9.92e-26!173;UBERON:0006601!9.92e-26!173;UBERON:0004121!6.95e-25!169;UBERON:0003080!7.61e-24!42;UBERON:0002780!1.95e-23!41;UBERON:0001890!1.95e-23!41;UBERON:0006240!1.95e-23!41;UBERON:0000153!8.67e-21!129;UBERON:0007811!8.67e-21!129;UBERON:0000033!2.36e-20!123;UBERON:0001893!9.94e-20!34;UBERON:0002020!1.01e-19!34;UBERON:0003528!1.01e-19!34;UBERON:0003056!1.36e-19!61;UBERON:0002791!4.02e-19!33;UBERON:0001869!1.25e-18!32;UBERON:0000956!1.30e-14!25;UBERON:0000203!1.30e-14!25;UBERON:0002619!9.07e-14!22;UBERON:0001950!8.81e-13!20;UBERON:0000475!4.10e-10!365;UBERON:0000064!5.48e-10!219;UBERON:0000062!1.11e-09!511;UBERON:0000481!2.57e-08!347;UBERON:0003076!2.94e-08!15;UBERON:0003057!2.94e-08!15;UBERON:0004111!7.05e-08!241;UBERON:0000477!1.47e-07!286;UBERON:0000468!1.47e-07!659;UBERON:0000922!2.61e-07!612;UBERON:0000025!2.71e-07!194;UBERON:0004732!3.85e-07!13
|ontology_enrichment_uberon=UBERON:0007023!9.38e-43!115;UBERON:0000073!3.35e-35!94;UBERON:0001016!3.35e-35!94;UBERON:0005743!1.21e-34!86;UBERON:0001017!2.01e-33!82;UBERON:0001049!5.48e-31!57;UBERON:0005068!5.48e-31!57;UBERON:0006241!5.48e-31!57;UBERON:0007135!5.48e-31!57;UBERON:0000955!5.31e-29!69;UBERON:0006238!5.31e-29!69;UBERON:0002616!7.28e-29!59;UBERON:0002346!4.24e-27!90;UBERON:0003075!2.19e-26!86;UBERON:0007284!2.19e-26!86;UBERON:0000924!9.92e-26!173;UBERON:0006601!9.92e-26!173;UBERON:0004121!6.95e-25!169;UBERON:0003080!7.61e-24!42;UBERON:0002780!1.95e-23!41;UBERON:0001890!1.95e-23!41;UBERON:0006240!1.95e-23!41;UBERON:0000153!8.67e-21!129;UBERON:0007811!8.67e-21!129;UBERON:0000033!2.36e-20!123;UBERON:0001893!9.94e-20!34;UBERON:0002020!1.01e-19!34;UBERON:0003528!1.01e-19!34;UBERON:0003056!1.36e-19!61;UBERON:0002791!4.02e-19!33;UBERON:0001869!1.25e-18!32;UBERON:0000956!1.30e-14!25;UBERON:0000203!1.30e-14!25;UBERON:0002619!9.07e-14!22;UBERON:0001950!8.81e-13!20;UBERON:0000475!4.10e-10!365;UBERON:0000064!5.48e-10!219;UBERON:0000062!1.11e-09!511;UBERON:0000481!2.57e-08!347;UBERON:0003076!2.94e-08!15;UBERON:0003057!2.94e-08!15;UBERON:0004111!7.05e-08!241;UBERON:0000477!1.47e-07!286;UBERON:0000468!1.47e-07!659;UBERON:0000922!2.61e-07!612;UBERON:0000025!2.71e-07!194;UBERON:0004732!3.85e-07!13
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}}
}}

Revision as of 12:32, 5 September 2012


Full id: C4279_skeletal_diaphragm_heart_tongue_left_penis_throat



Phase1 CAGE Peaks

Hg19::chr3:12838161..12838215,+p1@CAND2
Hg19::chr6:146056648..146056679,-p2@EPM2A
Hg19::chr6:146056691..146056735,-p3@EPM2A


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:0017025TATA-binding protein binding0.00777099123786688
GO:0005844polysome0.0174829288234617
GO:0005977glycogen metabolic process0.0370821653336492
GO:0006073glucan metabolic process0.0370821653336492
GO:0006112energy reserve metabolic process0.0370821653336492
GO:0008138protein tyrosine/serine/threonine phosphatase activity0.0370821653336492
GO:0043687post-translational protein modification0.0370821653336492
GO:0044264cellular polysaccharide metabolic process0.0370821653336492
GO:0005976polysaccharide metabolic process0.0370821653336492
GO:0006464protein modification process0.0378194588250887
GO:0043412biopolymer modification0.0378194588250887
GO:0015980energy derivation by oxidation of organic compounds0.0378194588250887



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 organism9.38e-43115
regional part of nervous system3.35e-3594
nervous system3.35e-3594
central nervous system2.01e-3382
neural tube5.48e-3157
neural rod5.48e-3157
future spinal cord5.48e-3157
neural keel5.48e-3157
brain5.31e-2969
future brain5.31e-2969
regional part of brain7.28e-2959
neurectoderm4.24e-2790
neural plate2.19e-2686
presumptive neural plate2.19e-2686
ectoderm9.92e-26173
presumptive ectoderm9.92e-26173
ectoderm-derived structure6.95e-25169
anterior neural tube7.61e-2442
regional part of forebrain1.95e-2341
forebrain1.95e-2341
future forebrain1.95e-2341
anterior region of body8.67e-21129
craniocervical region8.67e-21129
head2.36e-20123
telencephalon9.94e-2034
gray matter1.01e-1934
brain grey matter1.01e-1934
pre-chordal neural plate1.36e-1961
regional part of telencephalon4.02e-1933
cerebral hemisphere1.25e-1832
cerebral cortex1.30e-1425
pallium1.30e-1425
regional part of cerebral cortex9.07e-1422
neocortex8.81e-1320
organism subdivision4.10e-10365
organ part5.48e-10219
organ1.11e-09511
multi-tissue structure2.57e-08347
posterior neural tube2.94e-0815
chordal neural plate2.94e-0815
anatomical conduit7.05e-08241
anatomical cluster1.47e-07286
multi-cellular organism1.47e-07659
embryo2.61e-07612
tube2.71e-07194
segmental subdivision of nervous system3.85e-0713


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#9774214.43509840674790.006201147435546130.0273925321245613
CCNT2#90536.336201576962630.003930750035764890.0190577783290121
E2F4#1874312.66806031528440.0004917987006298980.00438026304750861
E2F6#187635.017155731697390.00791769806886330.032335528432879
ELF1#199734.258097958807540.01295179875054610.0463720572405994
GTF2B#2959331.94382993432423.06634405746243e-050.000628796204628547
HMGN3#932438.178547723350590.001827766942164210.0108943129592905
JUNB#3726220.40708843988080.003131462199438740.0164518728631814
SETDB1#9869226.8800174520070.001814468907964410.010896516490075
TFAP2A#7020211.01242291536330.01054990655215560.0390287871630684
YY1#752834.911170749853860.008441455341808260.0330366916901414



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.