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Coexpression cluster:C717: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001154!1.23e-66!1;UBERON:0001153!1.23e-66!1;UBERON:0001045!1.23e-66!1;UBERON:0002372!2.39e-66!1;UBERON:0001961!2.39e-66!1;UBERON:0001744!2.39e-66!1;UBERON:0001735!2.39e-66!1;UBERON:0000160!9.05e-16!17;UBERON:0004907!1.40e-14!5;UBERON:0002108!1.83e-14!4;UBERON:0005409!2.77e-11!25;UBERON:0001155!1.04e-08!9;UBERON:0002465!6.13e-08!10;UBERON:0001042!6.13e-08!10;UBERON:0009145!6.13e-08!10;UBERON:0000059!2.32e-07!11;UBERON:0006562!2.47e-07!11
|ontology_enrichment_uberon=UBERON:0001154!1.23e-66!1;UBERON:0001153!1.23e-66!1;UBERON:0001045!1.23e-66!1;UBERON:0002372!2.39e-66!1;UBERON:0001961!2.39e-66!1;UBERON:0001744!2.39e-66!1;UBERON:0001735!2.39e-66!1;UBERON:0000160!9.05e-16!17;UBERON:0004907!1.40e-14!5;UBERON:0002108!1.83e-14!4;UBERON:0005409!2.77e-11!25;UBERON:0001155!1.04e-08!9;UBERON:0002465!6.13e-08!10;UBERON:0001042!6.13e-08!10;UBERON:0009145!6.13e-08!10;UBERON:0000059!2.32e-07!11;UBERON:0006562!2.47e-07!11
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}}
}}

Revision as of 14:25, 26 November 2012


Full id: C717_appendix_tonsil_colon_small_plasma_submaxillary_vein



Phase1 CAGE Peaks

Hg19::chr10:101292921..101292931,+p4@NKX2-3
Hg19::chr15:36739580..36739587,-p@chr15:36739580..36739587
-
Hg19::chr16:23489788..23489792,-p@chr16:23489788..23489792
-
Hg19::chr18:43195438..43195446,+p2@SLC14A2
Hg19::chr1:157567826..157567835,-p2@FCRL4
Hg19::chr1:157567868..157567880,-p1@FCRL4
Hg19::chr1:207143802..207143832,-p1@FCAMR
Hg19::chr20:36694117..36694150,+p24@RPRD1B
Hg19::chr20:36694529..36694537,+p30@RPRD1B
Hg19::chr3:164875937..164875960,-p1@ENST00000472120
Hg19::chr6:45748006..45748023,+p@chr6:45748006..45748023
+


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

GO IDGO nameFDR corrected p-value
GO:0042887amide transporter activity0.0102998729232835
GO:0015204urea transmembrane transporter activity0.0102998729232835
GO:0015840urea transport0.0102998729232835
GO:0042886amide transport0.0102998729232835



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
vermiform appendix1.23e-661
caecum1.23e-661
midgut1.23e-661
tonsil2.39e-661
mucosa-associated lymphoid tissue2.39e-661
lymphoid tissue2.39e-661
tonsillar ring2.39e-661
intestine9.05e-1617
lower digestive tract1.40e-145
small intestine1.83e-144
gastrointestinal system2.77e-1125
colon1.04e-089
lymphoid system6.13e-0810
chordate pharynx6.13e-0810
pharyngeal region of foregut6.13e-0810
large intestine2.32e-0711
pharynx2.47e-0711


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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