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|full_id=C2123_pituitary_thyroid_esophagus_kidney_tongue_salivary_throat
|full_id=C2123_pituitary_thyroid_esophagus_kidney_tongue_salivary_throat
|id=C2123
|id=C2123
|ontology_enrichment_celltype=CL:0002076!9.59e-09!43;CL:0000622!3.80e-07!5;CL:0002623!3.91e-07!3;CL:0000223!6.84e-07!59
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!5.13e-22!115;UBERON:0001049!6.06e-13!57;UBERON:0005068!6.06e-13!57;UBERON:0006241!6.06e-13!57;UBERON:0007135!6.06e-13!57;UBERON:0000153!1.01e-12!129;UBERON:0007811!1.01e-12!129;UBERON:0004121!8.47e-12!169;UBERON:0000924!2.96e-11!173;UBERON:0006601!2.96e-11!173;UBERON:0003075!1.09e-10!86;UBERON:0007284!1.09e-10!86;UBERON:0000475!1.83e-10!365;UBERON:0000033!3.06e-10!123;UBERON:0000062!3.08e-10!511;UBERON:0002346!6.96e-10!90;UBERON:0005743!2.19e-09!86;UBERON:0002616!7.59e-09!59;UBERON:0001017!1.85e-08!82;UBERON:0003076!2.13e-08!15;UBERON:0003057!2.13e-08!15;UBERON:0000955!3.33e-08!69;UBERON:0006238!3.33e-08!69;UBERON:0002020!6.80e-08!34;UBERON:0003528!6.80e-08!34;UBERON:0000073!7.24e-08!94;UBERON:0001016!7.24e-08!94;UBERON:0002298!1.47e-07!8;UBERON:0002780!2.85e-07!41;UBERON:0001890!2.85e-07!41;UBERON:0006240!2.85e-07!41;UBERON:0000064!3.09e-07!219;UBERON:0006947!4.88e-07!3;UBERON:0004054!4.88e-07!3;UBERON:0003080!5.12e-07!42
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Revision as of 14:20, 21 May 2012


Full id: C2123_pituitary_thyroid_esophagus_kidney_tongue_salivary_throat



Phase1 CAGE Peaks

Hg19::chr11:27062483..27062497,+p10@BBOX1
Hg19::chr11:27062502..27062512,+p13@BBOX1
Hg19::chr11:27062521..27062534,+p11@BBOX1
Hg19::chr11:27062537..27062557,+p9@BBOX1


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
endo-epithelial cell9.59e-0943
acinar cell3.80e-075
acinar cell of salivary gland3.91e-073
endodermal cell6.84e-0759
Uber Anatomy
Ontology termp-valuen
adult organism5.13e-22115
neural tube6.06e-1357
neural rod6.06e-1357
future spinal cord6.06e-1357
neural keel6.06e-1357
anterior region of body1.01e-12129
craniocervical region1.01e-12129
ectoderm-derived structure8.47e-12169
ectoderm2.96e-11173
presumptive ectoderm2.96e-11173
neural plate1.09e-1086
presumptive neural plate1.09e-1086
organism subdivision1.83e-10365
head3.06e-10123
organ3.08e-10511
neurectoderm6.96e-1090
regional part of brain7.59e-0959
central nervous system1.85e-0882
posterior neural tube2.13e-0815
chordal neural plate2.13e-0815
brain3.33e-0869
future brain3.33e-0869
gray matter6.80e-0834
brain grey matter6.80e-0834
regional part of nervous system7.24e-0894
nervous system7.24e-0894
brainstem1.47e-078
regional part of forebrain2.85e-0741
forebrain2.85e-0741
future forebrain2.85e-0741
organ part3.09e-07219
male genital duct4.88e-073
internal male genitalia4.88e-073
anterior neural tube5.12e-0742


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.