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Coexpression cluster:C4072: Difference between revisions

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|full_id=C4072_occipital_seminal_olfactory_parietal_Hepatocyte_locus_medial
|full_id=C4072_occipital_seminal_olfactory_parietal_Hepatocyte_locus_medial
|id=C4072
|id=C4072
|ontology_enrichment_celltype=CL:0000066!2.60e-09!254;CL:0002321!7.08e-07!248
|ontology_enrichment_celltype=CL:0000066!6.57e-08!253
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!5.86e-23!57;UBERON:0005068!5.86e-23!57;UBERON:0006241!5.86e-23!57;UBERON:0007135!5.86e-23!57;UBERON:0005743!2.42e-22!86;UBERON:0001017!7.16e-22!82;UBERON:0002616!1.03e-20!59;UBERON:0000073!4.96e-20!94;UBERON:0001016!4.96e-20!94;UBERON:0002346!6.31e-20!90;UBERON:0000468!9.19e-20!659;UBERON:0003080!1.11e-19!42;UBERON:0002780!2.04e-19!41;UBERON:0001890!2.04e-19!41;UBERON:0006240!2.04e-19!41;UBERON:0003075!2.39e-19!86;UBERON:0007284!2.39e-19!86;UBERON:0000955!3.19e-19!69;UBERON:0006238!3.19e-19!69;UBERON:0000924!2.44e-18!173;UBERON:0006601!2.44e-18!173;UBERON:0004121!1.09e-17!169;UBERON:0002020!1.63e-17!34;UBERON:0003528!1.63e-17!34;UBERON:0000033!2.81e-17!123;UBERON:0004111!3.29e-17!241;UBERON:0007023!4.56e-17!115;UBERON:0001893!5.96e-17!34;UBERON:0000467!1.23e-16!625;UBERON:0002791!1.41e-16!33;UBERON:0000477!1.47e-16!286;UBERON:0000480!2.83e-16!626;UBERON:0001869!3.39e-16!32;UBERON:0003056!4.31e-16!61;UBERON:0000153!9.80e-16!129;UBERON:0007811!9.80e-16!129;UBERON:0000922!1.43e-15!612;UBERON:0000483!2.42e-14!309;UBERON:0002050!4.15e-14!605;UBERON:0005423!4.15e-14!605;UBERON:0000923!7.21e-14!604;UBERON:0005291!7.21e-14!604;UBERON:0006598!7.21e-14!604;UBERON:0002532!7.21e-14!604;UBERON:0000119!1.02e-13!312;UBERON:0002619!5.14e-13!22;UBERON:0000025!6.43e-13!194;UBERON:0000956!6.51e-13!25;UBERON:0000203!6.51e-13!25;UBERON:0000475!5.33e-12!365;UBERON:0001950!9.86e-12!20;UBERON:0000062!1.22e-11!511;UBERON:0000481!1.24e-10!347;UBERON:0000064!1.95e-08!219
|ontology_enrichment_uberon=UBERON:0001049!5.82e-22!56;UBERON:0005068!5.82e-22!56;UBERON:0006241!5.82e-22!56;UBERON:0007135!5.82e-22!56;UBERON:0001017!4.71e-21!81;UBERON:0000073!2.29e-20!53;UBERON:0002616!2.29e-20!53;UBERON:0002780!2.04e-19!41;UBERON:0001890!2.04e-19!41;UBERON:0003080!2.04e-19!41;UBERON:0006240!2.04e-19!41;UBERON:0001016!1.75e-18!89;UBERON:0000955!2.11e-18!68;UBERON:0006238!2.11e-18!68;UBERON:0000477!2.88e-18!373;UBERON:0002346!5.32e-18!86;UBERON:0000468!8.35e-18!656;UBERON:0003075!2.36e-17!82;UBERON:0007284!2.36e-17!82;UBERON:0003528!4.80e-17!34;UBERON:0002020!4.80e-17!34;UBERON:0001893!9.31e-17!34;UBERON:0010371!1.67e-16!104;UBERON:0004121!1.97e-16!171;UBERON:0000924!1.97e-16!171;UBERON:0006601!1.97e-16!171;UBERON:0007023!2.49e-16!114;UBERON:0002791!3.24e-16!32;UBERON:0004111!3.25e-16!240;UBERON:0001869!5.61e-16!32;UBERON:0010314!1.04e-15!132;UBERON:0003056!3.20e-15!61;UBERON:0000467!1.67e-14!624;UBERON:0000480!3.46e-14!625;UBERON:0002619!1.38e-12!22;UBERON:0000956!1.39e-12!25;UBERON:0000203!1.39e-12!25;UBERON:0000922!2.97e-12!592;UBERON:0000025!8.29e-12!192;UBERON:0000483!9.97e-12!306;UBERON:0011216!2.29e-11!223;UBERON:0001950!2.35e-11!20;UBERON:0005423!4.13e-11!581;UBERON:0000119!4.13e-11!309;UBERON:0000062!1.63e-10!503;UBERON:0002050!2.46e-10!564;UBERON:0000481!4.72e-10!342;UBERON:0000923!1.44e-09!560;UBERON:0010316!1.44e-09!560;UBERON:0005291!1.44e-09!560;UBERON:0006598!1.44e-09!560;UBERON:0010317!1.44e-09!560;UBERON:0002532!1.44e-09!560;UBERON:0000064!4.44e-07!218
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}}
}}

Revision as of 15:39, 19 October 2012


Full id: C4072_occipital_seminal_olfactory_parietal_Hepatocyte_locus_medial



Phase1 CAGE Peaks

Hg19::chr21:27394286..27394319,-p17@APP
Hg19::chr21:27394320..27394368,-p8@APP
Hg19::chr21:27423401..27423412,-p23@APP


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

No GOStat results

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
epithelial cell6.57e-08253
Uber Anatomy
Ontology termp-valuen
neural tube5.82e-2256
neural rod5.82e-2256
future spinal cord5.82e-2256
neural keel5.82e-2256
central nervous system4.71e-2181
regional part of nervous system2.29e-2053
regional part of brain2.29e-2053
regional part of forebrain2.04e-1941
forebrain2.04e-1941
anterior neural tube2.04e-1941
future forebrain2.04e-1941
nervous system1.75e-1889
brain2.11e-1868
future brain2.11e-1868
anatomical cluster2.88e-18373
neurectoderm5.32e-1886
multi-cellular organism8.35e-18656
neural plate2.36e-1782
presumptive neural plate2.36e-1782
brain grey matter4.80e-1734
gray matter4.80e-1734
telencephalon9.31e-1734
ecto-epithelium1.67e-16104
ectoderm-derived structure1.97e-16171
ectoderm1.97e-16171
presumptive ectoderm1.97e-16171
adult organism2.49e-16114
regional part of telencephalon3.24e-1632
anatomical conduit3.25e-16240
cerebral hemisphere5.61e-1632
structure with developmental contribution from neural crest1.04e-15132
pre-chordal neural plate3.20e-1561
anatomical system1.67e-14624
anatomical group3.46e-14625
regional part of cerebral cortex1.38e-1222
cerebral cortex1.39e-1225
pallium1.39e-1225
embryo2.97e-12592
tube8.29e-12192
epithelium9.97e-12306
organ system subdivision2.29e-11223
neocortex2.35e-1120
developing anatomical structure4.13e-11581
cell layer4.13e-11309
organ1.63e-10503
embryonic structure2.46e-10564
multi-tissue structure4.72e-10342
germ layer1.44e-09560
germ layer / neural crest1.44e-09560
embryonic tissue1.44e-09560
presumptive structure1.44e-09560
germ layer / neural crest derived structure1.44e-09560
epiblast (generic)1.44e-09560
organ part4.44e-07218


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.

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