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Coexpression cluster:C751: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005743!3.42e-37!86;UBERON:0001017!2.81e-35!82;UBERON:0007023!3.87e-35!115;UBERON:0003075!1.16e-34!86;UBERON:0007284!1.16e-34!86;UBERON:0000073!3.11e-34!94;UBERON:0001016!3.11e-34!94;UBERON:0002346!1.44e-33!90;UBERON:0001049!1.64e-31!57;UBERON:0005068!1.64e-31!57;UBERON:0006241!1.64e-31!57;UBERON:0007135!1.64e-31!57;UBERON:0000955!5.73e-30!69;UBERON:0006238!5.73e-30!69;UBERON:0004111!1.28e-28!241;UBERON:0004121!2.22e-28!169;UBERON:0000483!4.25e-28!309;UBERON:0000924!4.72e-28!173;UBERON:0006601!4.72e-28!173;UBERON:0002616!4.82e-28!59;UBERON:0000119!2.52e-27!312;UBERON:0000025!3.47e-27!194;UBERON:0000033!8.39e-25!123;UBERON:0000153!2.53e-24!129;UBERON:0007811!2.53e-24!129;UBERON:0002780!5.94e-24!41;UBERON:0001890!5.94e-24!41;UBERON:0006240!5.94e-24!41;UBERON:0003056!8.27e-24!61;UBERON:0003080!1.67e-23!42;UBERON:0000477!1.26e-22!286;UBERON:0000475!4.33e-21!365;UBERON:0000468!2.60e-20!659;UBERON:0002020!7.50e-20!34;UBERON:0003528!7.50e-20!34;UBERON:0001893!8.70e-20!34;UBERON:0002791!3.72e-19!33;UBERON:0001869!6.72e-19!32;UBERON:0000467!2.04e-17!625;UBERON:0000480!3.36e-17!626;UBERON:0000064!3.61e-16!219;UBERON:0000922!4.44e-16!612;UBERON:0000481!1.28e-15!347;UBERON:0000956!9.45e-15!25;UBERON:0000203!9.45e-15!25;UBERON:0002619!2.12e-14!22;UBERON:0002050!9.49e-14!605;UBERON:0005423!9.49e-14!605;UBERON:0000923!2.07e-13!604;UBERON:0005291!2.07e-13!604;UBERON:0006598!2.07e-13!604;UBERON:0002532!2.07e-13!604;UBERON:0001950!3.34e-13!20;UBERON:0003103!1.09e-10!69;UBERON:0000062!1.18e-10!511;UBERON:0003076!4.42e-09!15;UBERON:0003057!4.42e-09!15;UBERON:0004732!4.77e-08!13;UBERON:0004733!1.12e-07!12;UBERON:0002028!1.12e-07!12;UBERON:0007277!1.12e-07!12;UBERON:0004872!2.94e-07!84
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}}
}}

Revision as of 20:47, 8 August 2012


Full id: C751_heart_pineal_left_cerebellum_pons_putamen_Mesothelial



Phase1 CAGE Peaks

Hg19::chr13:30079614..30079618,+p@chr13:30079614..30079618
+
Hg19::chr16:58497281..58497330,+p6@NDRG4
Hg19::chr16:58497337..58497348,+p9@NDRG4
Hg19::chr16:58497587..58497668,+p2@NDRG4
Hg19::chr16:58498177..58498193,+p4@NDRG4
Hg19::chr16:58498194..58498236,+p3@NDRG4
Hg19::chr1:62417957..62417993,+p4@INADL
Hg19::chr1:62417997..62418034,+p3@INADL
Hg19::chr2:220492344..220492368,+p1@SLC4A3
Hg19::chr2:220492373..220492391,+p2@SLC4A3
Hg19::chr5:31639211..31639288,+p1@PDZD2


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:0005911intercellular junction0.0104492723300696
GO:0030054cell junction0.0261672940711137
GO:0044459plasma membrane part0.0261672940711137
GO:0015106bicarbonate transmembrane transporter activity0.032980560816889
GO:0005452inorganic anion exchanger activity0.032980560816889
GO:0015380anion exchanger activity0.032980560816889
GO:0015301anion:anion antiporter activity0.032980560816889
GO:0015108chloride transmembrane transporter activity0.032980560816889
GO:0005886plasma membrane0.0392005153929385



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>cell_data<br>uberon_data<br><br>


Cell Type
Ontology termp-valuen
embryonic cell3.45e-08248
Uber Anatomy
Ontology termp-valuen
central nervous system2.81e-3582
adult organism3.87e-35115
neural plate1.16e-3486
presumptive neural plate1.16e-3486
regional part of nervous system3.11e-3494
nervous system3.11e-3494
neurectoderm1.44e-3390
neural tube1.64e-3157
neural rod1.64e-3157
future spinal cord1.64e-3157
neural keel1.64e-3157
brain5.73e-3069
future brain5.73e-3069
anatomical conduit1.28e-28241
ectoderm-derived structure2.22e-28169
epithelium4.25e-28309
ectoderm4.72e-28173
presumptive ectoderm4.72e-28173
regional part of brain4.82e-2859
cell layer2.52e-27312
tube3.47e-27194
head8.39e-25123
anterior region of body2.53e-24129
craniocervical region2.53e-24129
regional part of forebrain5.94e-2441
forebrain5.94e-2441
future forebrain5.94e-2441
pre-chordal neural plate8.27e-2461
anterior neural tube1.67e-2342
anatomical cluster1.26e-22286
organism subdivision4.33e-21365
multi-cellular organism2.60e-20659
gray matter7.50e-2034
brain grey matter7.50e-2034
telencephalon8.70e-2034
regional part of telencephalon3.72e-1933
cerebral hemisphere6.72e-1932
anatomical system2.04e-17625
anatomical group3.36e-17626
organ part3.61e-16219
embryo4.44e-16612
multi-tissue structure1.28e-15347
cerebral cortex9.45e-1525
pallium9.45e-1525
regional part of cerebral cortex2.12e-1422
embryonic structure9.49e-14605
developing anatomical structure9.49e-14605
germ layer2.07e-13604
embryonic tissue2.07e-13604
presumptive structure2.07e-13604
epiblast (generic)2.07e-13604
neocortex3.34e-1320
compound organ1.09e-1069
organ1.18e-10511
posterior neural tube4.42e-0915
chordal neural plate4.42e-0915
segmental subdivision of nervous system4.77e-0813
segmental subdivision of hindbrain1.12e-0712
hindbrain1.12e-0712
presumptive hindbrain1.12e-0712
splanchnic layer of lateral plate mesoderm2.94e-0784


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


No analysis results for this cluster

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.