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Difference between revisions of "Coexpression cluster:C2121"

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|ontology_enrichment_disease=
 
|ontology_enrichment_disease=
 
|ontology_enrichment_uberon=UBERON:0005743!2.93e-52!86;UBERON:0000073!1.29e-51!94;UBERON:0001016!1.29e-51!94;UBERON:0001017!1.41e-51!82;UBERON:0001049!1.46e-47!57;UBERON:0005068!1.46e-47!57;UBERON:0006241!1.46e-47!57;UBERON:0007135!1.46e-47!57;UBERON:0002616!1.12e-43!59;UBERON:0000955!2.10e-40!69;UBERON:0006238!2.10e-40!69;UBERON:0003075!1.65e-39!86;UBERON:0007284!1.65e-39!86;UBERON:0002346!1.45e-37!90;UBERON:0002780!2.49e-34!41;UBERON:0001890!2.49e-34!41;UBERON:0006240!2.49e-34!41;UBERON:0003080!4.11e-33!42;UBERON:0003056!3.26e-31!61;UBERON:0007023!1.03e-30!115;UBERON:0002020!3.44e-30!34;UBERON:0003528!3.44e-30!34;UBERON:0001893!5.80e-30!34;UBERON:0004121!9.21e-30!169;UBERON:0002791!4.62e-29!33;UBERON:0000924!5.76e-29!173;UBERON:0006601!5.76e-29!173;UBERON:0000153!2.37e-28!129;UBERON:0007811!2.37e-28!129;UBERON:0000033!3.09e-28!123;UBERON:0001869!6.44e-28!32;UBERON:0002619!2.64e-22!22;UBERON:0000956!1.57e-21!25;UBERON:0000203!1.57e-21!25;UBERON:0001950!2.92e-20!20;UBERON:0003076!2.82e-15!15;UBERON:0003057!2.82e-15!15;UBERON:0004732!1.02e-12!13;UBERON:0000475!1.84e-12!365;UBERON:0004733!4.50e-12!12;UBERON:0002028!4.50e-12!12;UBERON:0007277!4.50e-12!12;UBERON:0000922!3.07e-11!612;UBERON:0000468!5.30e-11!659;UBERON:0000119!3.16e-10!312;UBERON:0002308!4.07e-10!9;UBERON:0000125!4.07e-10!9;UBERON:0002420!4.90e-10!9;UBERON:0007245!4.90e-10!9;UBERON:0010009!4.90e-10!9;UBERON:0010011!4.90e-10!9;UBERON:0000454!4.90e-10!9;UBERON:0000483!1.65e-09!309;UBERON:0000025!3.27e-09!194;UBERON:0002680!5.24e-09!9;UBERON:0001895!5.24e-09!9;UBERON:0010092!5.24e-09!9;UBERON:0002050!1.37e-08!605;UBERON:0005423!1.37e-08!605;UBERON:0000481!1.70e-08!347;UBERON:0001871!1.96e-08!7;UBERON:0000062!2.14e-08!511;UBERON:0000923!2.60e-08!604;UBERON:0005291!2.60e-08!604;UBERON:0006598!2.60e-08!604;UBERON:0002532!2.60e-08!604;UBERON:0009663!5.07e-08!7;UBERON:0000467!1.00e-07!625;UBERON:0000480!1.24e-07!626;UBERON:0000064!1.90e-07!219;UBERON:0002298!1.91e-07!8;UBERON:0000200!7.26e-07!6
 
|ontology_enrichment_uberon=UBERON:0005743!2.93e-52!86;UBERON:0000073!1.29e-51!94;UBERON:0001016!1.29e-51!94;UBERON:0001017!1.41e-51!82;UBERON:0001049!1.46e-47!57;UBERON:0005068!1.46e-47!57;UBERON:0006241!1.46e-47!57;UBERON:0007135!1.46e-47!57;UBERON:0002616!1.12e-43!59;UBERON:0000955!2.10e-40!69;UBERON:0006238!2.10e-40!69;UBERON:0003075!1.65e-39!86;UBERON:0007284!1.65e-39!86;UBERON:0002346!1.45e-37!90;UBERON:0002780!2.49e-34!41;UBERON:0001890!2.49e-34!41;UBERON:0006240!2.49e-34!41;UBERON:0003080!4.11e-33!42;UBERON:0003056!3.26e-31!61;UBERON:0007023!1.03e-30!115;UBERON:0002020!3.44e-30!34;UBERON:0003528!3.44e-30!34;UBERON:0001893!5.80e-30!34;UBERON:0004121!9.21e-30!169;UBERON:0002791!4.62e-29!33;UBERON:0000924!5.76e-29!173;UBERON:0006601!5.76e-29!173;UBERON:0000153!2.37e-28!129;UBERON:0007811!2.37e-28!129;UBERON:0000033!3.09e-28!123;UBERON:0001869!6.44e-28!32;UBERON:0002619!2.64e-22!22;UBERON:0000956!1.57e-21!25;UBERON:0000203!1.57e-21!25;UBERON:0001950!2.92e-20!20;UBERON:0003076!2.82e-15!15;UBERON:0003057!2.82e-15!15;UBERON:0004732!1.02e-12!13;UBERON:0000475!1.84e-12!365;UBERON:0004733!4.50e-12!12;UBERON:0002028!4.50e-12!12;UBERON:0007277!4.50e-12!12;UBERON:0000922!3.07e-11!612;UBERON:0000468!5.30e-11!659;UBERON:0000119!3.16e-10!312;UBERON:0002308!4.07e-10!9;UBERON:0000125!4.07e-10!9;UBERON:0002420!4.90e-10!9;UBERON:0007245!4.90e-10!9;UBERON:0010009!4.90e-10!9;UBERON:0010011!4.90e-10!9;UBERON:0000454!4.90e-10!9;UBERON:0000483!1.65e-09!309;UBERON:0000025!3.27e-09!194;UBERON:0002680!5.24e-09!9;UBERON:0001895!5.24e-09!9;UBERON:0010092!5.24e-09!9;UBERON:0002050!1.37e-08!605;UBERON:0005423!1.37e-08!605;UBERON:0000481!1.70e-08!347;UBERON:0001871!1.96e-08!7;UBERON:0000062!2.14e-08!511;UBERON:0000923!2.60e-08!604;UBERON:0005291!2.60e-08!604;UBERON:0006598!2.60e-08!604;UBERON:0002532!2.60e-08!604;UBERON:0009663!5.07e-08!7;UBERON:0000467!1.00e-07!625;UBERON:0000480!1.24e-07!626;UBERON:0000064!1.90e-07!219;UBERON:0002298!1.91e-07!8;UBERON:0000200!7.26e-07!6
 +
|tf_chipseq_enrich=SUZ12#23512;2:25.0578904555315:0.00232525671652061:0.0131839026176274
 
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}}
 
}}

Revision as of 04:45, 5 September 2012


Full id: C2121_spinal_epididymis_glioma_thalamus_locus_pineal_medulla



Phase1 CAGE Peaks

Hg19::chr11:24518492..24518510,+p5@LUZP2
Hg19::chr8:132053091..132053127,-p1@ADCY8
Hg19::chr8:132053777..132053790,-p@chr8:132053777..132053790
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Hg19::chr8:132053800..132053811,-p@chr8:132053800..132053811
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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:0008294calcium- and calmodulin-responsive adenylate cyclase activity0.00397386082656305
GO:0004016adenylate cyclase activity0.00647592134699164
GO:0006171cAMP biosynthetic process0.00647592134699164
GO:0046058cAMP metabolic process0.00647592134699164
GO:0016849phosphorus-oxygen lyase activity0.00647592134699164
GO:0009975cyclase activity0.00647592134699164
GO:0004289subtilase activity0.00647592134699164
GO:0009190cyclic nucleotide biosynthetic process0.00647592134699164
GO:0007611learning and/or memory0.00647592134699164
GO:0009187cyclic nucleotide metabolic process0.00662310137760509
GO:0009165nucleotide biosynthetic process0.0277434357706346
GO:0016829lyase activity0.0277434357706346
GO:0007610behavior0.0277434357706346
GO:0004252serine-type endopeptidase activity0.0277434357706346
GO:0009117nucleotide metabolic process0.0277434357706346
GO:0055086nucleobase, nucleoside and nucleotide metabolic process0.0277434357706346
GO:0008236serine-type peptidase activity0.0277434357706346
GO:0017171serine hydrolase activity0.0277434357706346
GO:0000287magnesium ion binding0.0311634349030471
GO:0005624membrane fraction0.0452357824090427



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
neuronal stem cell1.22e-078
Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.29e-5194
nervous system1.29e-5194
central nervous system1.41e-5182
neural tube1.46e-4757
neural rod1.46e-4757
future spinal cord1.46e-4757
neural keel1.46e-4757
regional part of brain1.12e-4359
brain2.10e-4069
future brain2.10e-4069
neural plate1.65e-3986
presumptive neural plate1.65e-3986
neurectoderm1.45e-3790
regional part of forebrain2.49e-3441
forebrain2.49e-3441
future forebrain2.49e-3441
anterior neural tube4.11e-3342
pre-chordal neural plate3.26e-3161
adult organism1.03e-30115
gray matter3.44e-3034
brain grey matter3.44e-3034
telencephalon5.80e-3034
ectoderm-derived structure9.21e-30169
regional part of telencephalon4.62e-2933
ectoderm5.76e-29173
presumptive ectoderm5.76e-29173
anterior region of body2.37e-28129
craniocervical region2.37e-28129
head3.09e-28123
cerebral hemisphere6.44e-2832
regional part of cerebral cortex2.64e-2222
cerebral cortex1.57e-2125
pallium1.57e-2125
neocortex2.92e-2020
posterior neural tube2.82e-1515
chordal neural plate2.82e-1515
segmental subdivision of nervous system1.02e-1213
organism subdivision1.84e-12365
segmental subdivision of hindbrain4.50e-1212
hindbrain4.50e-1212
presumptive hindbrain4.50e-1212
embryo3.07e-11612
multi-cellular organism5.30e-11659
cell layer3.16e-10312
nucleus of brain4.07e-109
neural nucleus4.07e-109
basal ganglion4.90e-109
nuclear complex of neuraxis4.90e-109
aggregate regional part of brain4.90e-109
collection of basal ganglia4.90e-109
cerebral subcortex4.90e-109
epithelium1.65e-09309
tube3.27e-09194
regional part of metencephalon5.24e-099
metencephalon5.24e-099
future metencephalon5.24e-099
embryonic structure1.37e-08605
developing anatomical structure1.37e-08605
multi-tissue structure1.70e-08347
temporal lobe1.96e-087
organ2.14e-08511
germ layer2.60e-08604
embryonic tissue2.60e-08604
presumptive structure2.60e-08604
epiblast (generic)2.60e-08604
telencephalic nucleus5.07e-087
anatomical system1.00e-07625
anatomical group1.24e-07626
organ part1.90e-07219
brainstem1.91e-078
gyrus7.26e-076


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)

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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
SUZ12#23512225.05789045553150.002325256716520610.0131839026176274



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.