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Coexpression cluster:C1733: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000341!2.02e-14!2;UBERON:0000974!4.39e-11!10;UBERON:0009722!3.31e-10!11;UBERON:0007690!3.31e-10!11;UBERON:0001896!2.41e-09!3;UBERON:0005290!2.41e-09!3;UBERON:0010096!2.41e-09!3;UBERON:0004177!4.35e-09!7;UBERON:0005057!4.35e-09!7;UBERON:0002370!7.72e-08!4;UBERON:0005058!7.72e-08!4;UBERON:0009113!7.72e-08!4;UBERON:0003295!7.72e-08!4;UBERON:0005562!7.72e-08!4;UBERON:0002372!9.10e-08!1;UBERON:0001961!9.10e-08!1;UBERON:0001744!9.10e-08!1;UBERON:0001735!9.10e-08!1
|ontology_enrichment_uberon=UBERON:0000341!2.02e-14!2;UBERON:0000974!4.39e-11!10;UBERON:0009722!3.31e-10!11;UBERON:0007690!3.31e-10!11;UBERON:0001896!2.41e-09!3;UBERON:0005290!2.41e-09!3;UBERON:0010096!2.41e-09!3;UBERON:0004177!4.35e-09!7;UBERON:0005057!4.35e-09!7;UBERON:0002370!7.72e-08!4;UBERON:0005058!7.72e-08!4;UBERON:0009113!7.72e-08!4;UBERON:0003295!7.72e-08!4;UBERON:0005562!7.72e-08!4;UBERON:0002372!9.10e-08!1;UBERON:0001961!9.10e-08!1;UBERON:0001744!9.10e-08!1;UBERON:0001735!9.10e-08!1
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}}
}}

Revision as of 15:04, 26 November 2012


Full id: C1733_thymus_thyroid_throat_Hodgkin_CD4_vein_chronic



Phase1 CAGE Peaks

Hg19::chr14:81421324..81421348,+p2@TSHR
Hg19::chr14:81421355..81421379,+p3@TSHR
Hg19::chr14:81421710..81421757,+p4@TSHR
Hg19::chr14:81423399..81423412,+p@chr14:81423399..81423412
+
Hg19::chr14:81423432..81423444,+p@chr14:81423432..81423444
+


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
throat2.02e-142
neck4.39e-1110
entire pharyngeal arch endoderm3.31e-1011
early pharyngeal endoderm3.31e-1011
medulla oblongata2.41e-093
myelencephalon2.41e-093
future myelencephalon2.41e-093
hemopoietic organ4.35e-097
immune organ4.35e-097
thymus7.72e-084
hemolymphoid system gland7.72e-084
thymic region7.72e-084
pharyngeal gland7.72e-084
thymus primordium7.72e-084
tonsil9.10e-081
mucosa-associated lymphoid tissue9.10e-081
lymphoid tissue9.10e-081
tonsillar ring9.10e-081
Disease
Ontology termp-valuen
non-Hodgkin lymphoma6.52e-081
cutaneous T cell lymphoma6.52e-081
mycosis fungoides6.52e-081
bone marrow cancer7.45e-081
myeloma7.45e-081


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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