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Coexpression cluster:C4481: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001869!2.34e-18!32;UBERON:0002619!1.52e-17!22;UBERON:0002780!6.66e-17!41;UBERON:0001890!6.66e-17!41;UBERON:0003080!6.66e-17!41;UBERON:0006240!6.66e-17!41;UBERON:0001893!7.29e-17!34;UBERON:0002791!9.59e-17!32;UBERON:0003528!2.29e-15!34;UBERON:0002020!2.29e-15!34;UBERON:0001950!2.78e-15!20;UBERON:0000956!7.94e-15!25;UBERON:0000203!7.94e-15!25;UBERON:0002371!1.81e-14!76;UBERON:0002390!1.95e-14!98;UBERON:0003061!1.95e-14!98;UBERON:0001474!2.05e-14!82;UBERON:0002193!1.28e-12!108;UBERON:0001434!2.23e-12!100;UBERON:0001049!3.18e-12!56;UBERON:0005068!3.18e-12!56;UBERON:0006241!3.18e-12!56;UBERON:0007135!3.18e-12!56;UBERON:0000073!3.33e-12!53;UBERON:0002616!3.33e-12!53;UBERON:0004765!3.86e-12!90;UBERON:0002405!5.22e-12!93;UBERON:0003056!2.21e-10!61;UBERON:0001017!4.56e-10!81;UBERON:0007023!1.81e-09!114;UBERON:0000955!2.97e-09!68;UBERON:0006238!2.97e-09!68;UBERON:0001016!8.57e-09!89;UBERON:0003075!2.03e-08!82;UBERON:0007284!2.03e-08!82;UBERON:0002346!2.96e-08!86;UBERON:0000200!5.15e-08!6;UBERON:0001872!8.98e-07!5
|ontology_enrichment_uberon=UBERON:0001869!2.34e-18!32;UBERON:0002619!1.52e-17!22;UBERON:0002780!6.66e-17!41;UBERON:0001890!6.66e-17!41;UBERON:0003080!6.66e-17!41;UBERON:0006240!6.66e-17!41;UBERON:0001893!7.29e-17!34;UBERON:0002791!9.59e-17!32;UBERON:0003528!2.29e-15!34;UBERON:0002020!2.29e-15!34;UBERON:0001950!2.78e-15!20;UBERON:0000956!7.94e-15!25;UBERON:0000203!7.94e-15!25;UBERON:0002371!1.81e-14!76;UBERON:0002390!1.95e-14!98;UBERON:0003061!1.95e-14!98;UBERON:0001474!2.05e-14!82;UBERON:0002193!1.28e-12!108;UBERON:0001434!2.23e-12!100;UBERON:0001049!3.18e-12!56;UBERON:0005068!3.18e-12!56;UBERON:0006241!3.18e-12!56;UBERON:0007135!3.18e-12!56;UBERON:0000073!3.33e-12!53;UBERON:0002616!3.33e-12!53;UBERON:0004765!3.86e-12!90;UBERON:0002405!5.22e-12!93;UBERON:0003056!2.21e-10!61;UBERON:0001017!4.56e-10!81;UBERON:0007023!1.81e-09!114;UBERON:0000955!2.97e-09!68;UBERON:0006238!2.97e-09!68;UBERON:0001016!8.57e-09!89;UBERON:0003075!2.03e-08!82;UBERON:0007284!2.03e-08!82;UBERON:0002346!2.96e-08!86;UBERON:0000200!5.15e-08!6;UBERON:0001872!8.98e-07!5
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}}
}}

Revision as of 16:46, 26 November 2012


Full id: C4481_Mast_CD14_immature_Neutrophils_melanoma_medial_occipital



Phase1 CAGE Peaks

Hg19::chr5:158636727..158636752,+p1@ENST00000521204
Hg19::chr8:22548472..22548496,-p@chr8:22548472..22548496
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Hg19::chr8:22548707..22548737,-p@chr8:22548707..22548737
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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


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>


Uber Anatomy
Ontology termp-valuen
cerebral hemisphere2.34e-1832
regional part of cerebral cortex1.52e-1722
regional part of forebrain6.66e-1741
forebrain6.66e-1741
anterior neural tube6.66e-1741
future forebrain6.66e-1741
telencephalon7.29e-1734
regional part of telencephalon9.59e-1732
brain grey matter2.29e-1534
gray matter2.29e-1534
neocortex2.78e-1520
cerebral cortex7.94e-1525
pallium7.94e-1525
bone marrow1.81e-1476
hematopoietic system1.95e-1498
blood island1.95e-1498
bone element2.05e-1482
hemolymphoid system1.28e-12108
skeletal system2.23e-12100
neural tube3.18e-1256
neural rod3.18e-1256
future spinal cord3.18e-1256
neural keel3.18e-1256
regional part of nervous system3.33e-1253
regional part of brain3.33e-1253
skeletal element3.86e-1290
immune system5.22e-1293
pre-chordal neural plate2.21e-1061
central nervous system4.56e-1081
adult organism1.81e-09114
brain2.97e-0968
future brain2.97e-0968
nervous system8.57e-0989
neural plate2.03e-0882
presumptive neural plate2.03e-0882
neurectoderm2.96e-0886
gyrus5.15e-086
parietal lobe8.98e-075


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.