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Coexpression cluster:C4070: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!8.16e-46!115;UBERON:0000073!1.18e-31!94;UBERON:0001016!1.18e-31!94;UBERON:0001017!9.59e-31!82;UBERON:0005743!2.82e-30!86;UBERON:0001049!1.94e-28!57;UBERON:0005068!1.94e-28!57;UBERON:0006241!1.94e-28!57;UBERON:0007135!1.94e-28!57;UBERON:0003075!4.18e-28!86;UBERON:0007284!4.18e-28!86;UBERON:0002346!5.22e-26!90;UBERON:0000955!8.09e-25!69;UBERON:0006238!8.09e-25!69;UBERON:0002616!4.87e-24!59;UBERON:0004121!6.09e-22!169;UBERON:0003080!4.74e-21!42;UBERON:0000924!7.15e-21!173;UBERON:0006601!7.15e-21!173;UBERON:0002780!1.44e-20!41;UBERON:0001890!1.44e-20!41;UBERON:0006240!1.44e-20!41;UBERON:0000153!9.05e-20!129;UBERON:0007811!9.05e-20!129;UBERON:0003056!1.10e-19!61;UBERON:0000033!2.18e-19!123;UBERON:0001893!2.52e-17!34;UBERON:0002020!2.80e-17!34;UBERON:0003528!2.80e-17!34;UBERON:0002791!8.46e-17!33;UBERON:0001869!2.50e-16!32;UBERON:0000475!1.71e-13!365;UBERON:0000956!4.21e-13!25;UBERON:0000203!4.21e-13!25;UBERON:0002619!6.43e-12!22;UBERON:0001950!4.74e-11!20;UBERON:0000481!6.26e-09!347;UBERON:0003076!1.63e-08!15;UBERON:0003057!1.63e-08!15;UBERON:0000468!3.51e-08!659;UBERON:0000119!8.40e-08!312;UBERON:0000483!1.43e-07!309;UBERON:0000064!1.73e-07!219;UBERON:0004111!2.30e-07!241;UBERON:0000025!2.60e-07!194;UBERON:0004732!2.79e-07!13;UBERON:0000477!5.83e-07!286;UBERON:0000479!5.94e-07!787;UBERON:0004733!9.90e-07!12;UBERON:0002028!9.90e-07!12;UBERON:0007277!9.90e-07!12
|ontology_enrichment_uberon=UBERON:0007023!8.16e-46!115;UBERON:0000073!1.18e-31!94;UBERON:0001016!1.18e-31!94;UBERON:0001017!9.59e-31!82;UBERON:0005743!2.82e-30!86;UBERON:0001049!1.94e-28!57;UBERON:0005068!1.94e-28!57;UBERON:0006241!1.94e-28!57;UBERON:0007135!1.94e-28!57;UBERON:0003075!4.18e-28!86;UBERON:0007284!4.18e-28!86;UBERON:0002346!5.22e-26!90;UBERON:0000955!8.09e-25!69;UBERON:0006238!8.09e-25!69;UBERON:0002616!4.87e-24!59;UBERON:0004121!6.09e-22!169;UBERON:0003080!4.74e-21!42;UBERON:0000924!7.15e-21!173;UBERON:0006601!7.15e-21!173;UBERON:0002780!1.44e-20!41;UBERON:0001890!1.44e-20!41;UBERON:0006240!1.44e-20!41;UBERON:0000153!9.05e-20!129;UBERON:0007811!9.05e-20!129;UBERON:0003056!1.10e-19!61;UBERON:0000033!2.18e-19!123;UBERON:0001893!2.52e-17!34;UBERON:0002020!2.80e-17!34;UBERON:0003528!2.80e-17!34;UBERON:0002791!8.46e-17!33;UBERON:0001869!2.50e-16!32;UBERON:0000475!1.71e-13!365;UBERON:0000956!4.21e-13!25;UBERON:0000203!4.21e-13!25;UBERON:0002619!6.43e-12!22;UBERON:0001950!4.74e-11!20;UBERON:0000481!6.26e-09!347;UBERON:0003076!1.63e-08!15;UBERON:0003057!1.63e-08!15;UBERON:0000468!3.51e-08!659;UBERON:0000119!8.40e-08!312;UBERON:0000483!1.43e-07!309;UBERON:0000064!1.73e-07!219;UBERON:0004111!2.30e-07!241;UBERON:0000025!2.60e-07!194;UBERON:0004732!2.79e-07!13;UBERON:0000477!5.83e-07!286;UBERON:0000479!5.94e-07!787;UBERON:0004733!9.90e-07!12;UBERON:0002028!9.90e-07!12;UBERON:0007277!9.90e-07!12
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}}
}}

Revision as of 19:42, 8 August 2012


Full id: C4070_placenta_spinal_left_skeletal_lung_Skeletal_colon



Phase1 CAGE Peaks

Hg19::chr21:27011975..27012064,+p1@JAM2
Hg19::chr21:27012071..27012091,+p9@JAM2
Hg19::chr21:27012101..27012112,+p12@JAM2


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism8.16e-46115
regional part of nervous system1.18e-3194
nervous system1.18e-3194
central nervous system9.59e-3182
neural tube1.94e-2857
neural rod1.94e-2857
future spinal cord1.94e-2857
neural keel1.94e-2857
neural plate4.18e-2886
presumptive neural plate4.18e-2886
neurectoderm5.22e-2690
brain8.09e-2569
future brain8.09e-2569
regional part of brain4.87e-2459
ectoderm-derived structure6.09e-22169
anterior neural tube4.74e-2142
ectoderm7.15e-21173
presumptive ectoderm7.15e-21173
regional part of forebrain1.44e-2041
forebrain1.44e-2041
future forebrain1.44e-2041
anterior region of body9.05e-20129
craniocervical region9.05e-20129
pre-chordal neural plate1.10e-1961
head2.18e-19123
telencephalon2.52e-1734
gray matter2.80e-1734
brain grey matter2.80e-1734
regional part of telencephalon8.46e-1733
cerebral hemisphere2.50e-1632
organism subdivision1.71e-13365
cerebral cortex4.21e-1325
pallium4.21e-1325
regional part of cerebral cortex6.43e-1222
neocortex4.74e-1120
multi-tissue structure6.26e-09347
posterior neural tube1.63e-0815
chordal neural plate1.63e-0815
multi-cellular organism3.51e-08659
cell layer8.40e-08312
epithelium1.43e-07309
organ part1.73e-07219
anatomical conduit2.30e-07241
tube2.60e-07194
segmental subdivision of nervous system2.79e-0713
anatomical cluster5.83e-07286
tissue5.94e-07787
segmental subdivision of hindbrain9.90e-0712
hindbrain9.90e-0712
presumptive hindbrain9.90e-0712


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

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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