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Coexpression cluster:C4370: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000476!1.71e-28!3;UBERON:0000920!1.71e-28!3;UBERON:0000473!6.15e-19!8;UBERON:0002323!6.09e-15!46;UBERON:0004458!5.98e-14!49;UBERON:0003135!7.75e-14!11;UBERON:0003124!1.45e-12!7;UBERON:0003886!1.53e-12!54;UBERON:0000991!4.79e-11!21;UBERON:0009196!4.79e-11!21;UBERON:0009117!4.79e-11!21;UBERON:0005564!4.79e-11!21;UBERON:0002553!5.88e-11!61;UBERON:0004911!7.40e-11!1;UBERON:0004176!1.55e-10!22;UBERON:0004645!3.96e-10!1;UBERON:0001256!3.96e-10!1;UBERON:0001259!3.96e-10!1;UBERON:0002372!4.75e-10!1;UBERON:0001961!4.75e-10!1;UBERON:0001744!4.75e-10!1;UBERON:0001735!4.75e-10!1;UBERON:0003133!1.13e-08!48;UBERON:0002075!3.06e-08!18;UBERON:0003101!5.43e-07!22;UBERON:0000079!5.43e-07!22;UBERON:0005156!6.47e-07!59;UBERON:0000990!6.47e-07!59;UBERON:0000002!8.22e-07!6;UBERON:0001560!8.22e-07!6
|ontology_enrichment_uberon=UBERON:0000476!1.71e-28!3;UBERON:0000920!1.71e-28!3;UBERON:0000473!6.15e-19!8;UBERON:0002323!6.09e-15!46;UBERON:0004458!5.98e-14!49;UBERON:0003135!7.75e-14!11;UBERON:0003124!1.45e-12!7;UBERON:0003886!1.53e-12!54;UBERON:0000991!4.79e-11!21;UBERON:0009196!4.79e-11!21;UBERON:0009117!4.79e-11!21;UBERON:0005564!4.79e-11!21;UBERON:0002553!5.88e-11!61;UBERON:0004911!7.40e-11!1;UBERON:0004176!1.55e-10!22;UBERON:0004645!3.96e-10!1;UBERON:0001256!3.96e-10!1;UBERON:0001259!3.96e-10!1;UBERON:0002372!4.75e-10!1;UBERON:0001961!4.75e-10!1;UBERON:0001744!4.75e-10!1;UBERON:0001735!4.75e-10!1;UBERON:0003133!1.13e-08!48;UBERON:0002075!3.06e-08!18;UBERON:0003101!5.43e-07!22;UBERON:0000079!5.43e-07!22;UBERON:0005156!6.47e-07!59;UBERON:0000990!6.47e-07!59;UBERON:0000002!8.22e-07!6;UBERON:0001560!8.22e-07!6
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}}
}}

Revision as of 16:42, 26 November 2012


Full id: C4370_testicular_serous_chorionic_retinoblastoma_endometrial_gall_pancreatic



Phase1 CAGE Peaks

Hg19::chr4:135548764..135548775,+p@chr4:135548764..135548775
+
Hg19::chr9:119601015..119601029,+p1@uc004bjy.2
Hg19::chr9:119601047..119601058,+p2@uc004bjy.2


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
acellular anatomical structure1.71e-283
egg chorion1.71e-283
testis6.15e-198
body cavity6.09e-1546
body cavity or lining5.98e-1449
male reproductive organ7.75e-1411
chorion1.45e-127
body cavity precursor1.53e-1254
gonad4.79e-1121
indifferent external genitalia4.79e-1121
indifferent gonad4.79e-1121
gonad primordium4.79e-1121
anatomical cavity5.88e-1161
epithelium of female gonad7.40e-111
external genitalia1.55e-1022
urinary bladder urothelium3.96e-101
wall of urinary bladder3.96e-101
mucosa of urinary bladder3.96e-101
tonsil4.75e-101
mucosa-associated lymphoid tissue4.75e-101
lymphoid tissue4.75e-101
tonsillar ring4.75e-101
reproductive organ1.13e-0848
viscus3.06e-0818
male organism5.43e-0722
male reproductive system5.43e-0722
reproductive structure6.47e-0759
reproductive system6.47e-0759
uterine cervix8.22e-076
neck of organ8.22e-076


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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