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|ontology_enrichment_disease=DOID:0050687!1.31e-07!143;DOID:3095!7.90e-07!22;DOID:2994!7.90e-07!22
|ontology_enrichment_disease=DOID:0050687!1.31e-07!143;DOID:3095!7.90e-07!22;DOID:2994!7.90e-07!22
|ontology_enrichment_uberon=UBERON:0000073!3.69e-41!94;UBERON:0001016!3.69e-41!94;UBERON:0005743!2.77e-38!86;UBERON:0001017!2.34e-36!82;UBERON:0001049!1.17e-33!57;UBERON:0005068!1.17e-33!57;UBERON:0006241!1.17e-33!57;UBERON:0007135!1.17e-33!57;UBERON:0002346!2.41e-32!90;UBERON:0003075!7.49e-31!86;UBERON:0007284!7.49e-31!86;UBERON:0000955!1.75e-30!69;UBERON:0006238!1.75e-30!69;UBERON:0002616!4.18e-29!59;UBERON:0002780!6.78e-27!41;UBERON:0001890!6.78e-27!41;UBERON:0006240!6.78e-27!41;UBERON:0000924!5.73e-26!173;UBERON:0006601!5.73e-26!173;UBERON:0003080!1.22e-25!42;UBERON:0007023!2.87e-25!115;UBERON:0004121!1.41e-24!169;UBERON:0003056!4.37e-24!61;UBERON:0001893!2.74e-22!34;UBERON:0002020!3.32e-22!34;UBERON:0003528!3.32e-22!34;UBERON:0002791!1.57e-21!33;UBERON:0001869!1.90e-21!32;UBERON:0000153!1.26e-20!129;UBERON:0007811!1.26e-20!129;UBERON:0000033!1.28e-20!123;UBERON:0000956!6.05e-17!25;UBERON:0000203!6.05e-17!25;UBERON:0002619!2.04e-16!22;UBERON:0001950!3.29e-15!20;UBERON:0000025!4.80e-11!194;UBERON:0004111!8.52e-10!241;UBERON:0000119!1.78e-09!312;UBERON:0000483!2.27e-09!309;UBERON:0000481!4.31e-09!347;UBERON:0003076!4.51e-09!15;UBERON:0003057!4.51e-09!15;UBERON:0000475!6.08e-09!365;UBERON:0000064!1.84e-08!219;UBERON:0000477!1.96e-08!286;UBERON:0000062!6.31e-08!511;UBERON:0004732!6.75e-08!13;UBERON:0004733!1.29e-07!12;UBERON:0002028!1.29e-07!12;UBERON:0007277!1.29e-07!12;UBERON:0000922!3.25e-07!612;UBERON:0002420!9.25e-07!9;UBERON:0007245!9.25e-07!9;UBERON:0010009!9.25e-07!9;UBERON:0010011!9.25e-07!9;UBERON:0000454!9.25e-07!9
|ontology_enrichment_uberon=UBERON:0000073!3.69e-41!94;UBERON:0001016!3.69e-41!94;UBERON:0005743!2.77e-38!86;UBERON:0001017!2.34e-36!82;UBERON:0001049!1.17e-33!57;UBERON:0005068!1.17e-33!57;UBERON:0006241!1.17e-33!57;UBERON:0007135!1.17e-33!57;UBERON:0002346!2.41e-32!90;UBERON:0003075!7.49e-31!86;UBERON:0007284!7.49e-31!86;UBERON:0000955!1.75e-30!69;UBERON:0006238!1.75e-30!69;UBERON:0002616!4.18e-29!59;UBERON:0002780!6.78e-27!41;UBERON:0001890!6.78e-27!41;UBERON:0006240!6.78e-27!41;UBERON:0000924!5.73e-26!173;UBERON:0006601!5.73e-26!173;UBERON:0003080!1.22e-25!42;UBERON:0007023!2.87e-25!115;UBERON:0004121!1.41e-24!169;UBERON:0003056!4.37e-24!61;UBERON:0001893!2.74e-22!34;UBERON:0002020!3.32e-22!34;UBERON:0003528!3.32e-22!34;UBERON:0002791!1.57e-21!33;UBERON:0001869!1.90e-21!32;UBERON:0000153!1.26e-20!129;UBERON:0007811!1.26e-20!129;UBERON:0000033!1.28e-20!123;UBERON:0000956!6.05e-17!25;UBERON:0000203!6.05e-17!25;UBERON:0002619!2.04e-16!22;UBERON:0001950!3.29e-15!20;UBERON:0000025!4.80e-11!194;UBERON:0004111!8.52e-10!241;UBERON:0000119!1.78e-09!312;UBERON:0000483!2.27e-09!309;UBERON:0000481!4.31e-09!347;UBERON:0003076!4.51e-09!15;UBERON:0003057!4.51e-09!15;UBERON:0000475!6.08e-09!365;UBERON:0000064!1.84e-08!219;UBERON:0000477!1.96e-08!286;UBERON:0000062!6.31e-08!511;UBERON:0004732!6.75e-08!13;UBERON:0004733!1.29e-07!12;UBERON:0002028!1.29e-07!12;UBERON:0007277!1.29e-07!12;UBERON:0000922!3.25e-07!612;UBERON:0002420!9.25e-07!9;UBERON:0007245!9.25e-07!9;UBERON:0010009!9.25e-07!9;UBERON:0010011!9.25e-07!9;UBERON:0000454!9.25e-07!9
|tf_chipseq_enrich=ATF3#467;2:11.2315872630044:0.0111955903992222:0.0411159809305987
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}}
}}

Revision as of 13:36, 5 September 2012


Full id: C2063_Hepatocyte_pineal_occipital_postcentral_pons_temporal_liver



Phase1 CAGE Peaks

Hg19::chr10:50970322..50970381,-p1@OGDHL
Hg19::chr10:50970382..50970399,-p2@OGDHL
Hg19::chr3:10547333..10547371,-p4@ATP2B2
Hg19::chr3:10547397..10547418,-p5@ATP2B2


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:0004591oxoglutarate dehydrogenase (succinyl-transferring) activity0.0311332101046855
GO:0030976thiamin pyrophosphate binding0.0311332101046855
GO:0005388calcium-transporting ATPase activity0.0311332101046855
GO:0016624oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor0.0311332101046855
GO:0015085calcium ion transmembrane transporter activity0.0311332101046855



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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
regional part of nervous system3.69e-4194
nervous system3.69e-4194
central nervous system2.34e-3682
neural tube1.17e-3357
neural rod1.17e-3357
future spinal cord1.17e-3357
neural keel1.17e-3357
neurectoderm2.41e-3290
neural plate7.49e-3186
presumptive neural plate7.49e-3186
brain1.75e-3069
future brain1.75e-3069
regional part of brain4.18e-2959
regional part of forebrain6.78e-2741
forebrain6.78e-2741
future forebrain6.78e-2741
ectoderm5.73e-26173
presumptive ectoderm5.73e-26173
anterior neural tube1.22e-2542
adult organism2.87e-25115
ectoderm-derived structure1.41e-24169
pre-chordal neural plate4.37e-2461
telencephalon2.74e-2234
gray matter3.32e-2234
brain grey matter3.32e-2234
regional part of telencephalon1.57e-2133
cerebral hemisphere1.90e-2132
anterior region of body1.26e-20129
craniocervical region1.26e-20129
head1.28e-20123
cerebral cortex6.05e-1725
pallium6.05e-1725
regional part of cerebral cortex2.04e-1622
neocortex3.29e-1520
tube4.80e-11194
anatomical conduit8.52e-10241
cell layer1.78e-09312
epithelium2.27e-09309
multi-tissue structure4.31e-09347
posterior neural tube4.51e-0915
chordal neural plate4.51e-0915
organism subdivision6.08e-09365
organ part1.84e-08219
anatomical cluster1.96e-08286
organ6.31e-08511
segmental subdivision of nervous system6.75e-0813
segmental subdivision of hindbrain1.29e-0712
hindbrain1.29e-0712
presumptive hindbrain1.29e-0712
embryo3.25e-07612
basal ganglion9.25e-079
nuclear complex of neuraxis9.25e-079
aggregate regional part of brain9.25e-079
collection of basal ganglia9.25e-079
cerebral subcortex9.25e-079
Disease
Ontology termp-valuen
cell type cancer1.31e-07143
germ cell and embryonal cancer7.90e-0722
germ cell cancer7.90e-0722


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
ATF3#467211.23158726300440.01119559039922220.0411159809305987



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.