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Coexpression cluster:C1507: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000468!1.23e-18!659;UBERON:0000477!3.08e-18!286;UBERON:0004111!2.66e-17!241;UBERON:0000467!3.47e-17!625;UBERON:0000480!4.92e-17!626;UBERON:0007023!2.92e-15!115;UBERON:0000483!8.13e-14!309;UBERON:0000062!1.89e-13!511;UBERON:0000119!4.60e-13!312;UBERON:0000481!4.34e-12!347;UBERON:0002050!1.02e-11!605;UBERON:0005423!1.02e-11!605;UBERON:0000475!1.33e-11!365;UBERON:0000923!1.53e-11!604;UBERON:0005291!1.53e-11!604;UBERON:0006598!1.53e-11!604;UBERON:0002532!1.53e-11!604;UBERON:0000922!4.02e-11!612;UBERON:0004119!4.83e-11!169;UBERON:0000925!4.83e-11!169;UBERON:0006595!4.83e-11!169;UBERON:0000025!2.20e-10!194;UBERON:0003914!3.05e-09!118;UBERON:0000064!3.75e-09!219;UBERON:0001007!1.24e-08!155;UBERON:0001555!1.24e-08!155;UBERON:0007026!1.24e-08!155;UBERON:0002100!7.64e-08!216;UBERON:0002530!9.23e-08!59;UBERON:0004872!4.64e-07!84;UBERON:0003103!4.78e-07!69;UBERON:0004921!4.79e-07!129;UBERON:0004185!4.79e-07!129;UBERON:0009569!6.68e-07!113;UBERON:0005911!8.38e-07!82
|ontology_enrichment_uberon=UBERON:0000468!1.23e-18!659;UBERON:0000477!3.08e-18!286;UBERON:0004111!2.66e-17!241;UBERON:0000467!3.47e-17!625;UBERON:0000480!4.92e-17!626;UBERON:0007023!2.92e-15!115;UBERON:0000483!8.13e-14!309;UBERON:0000062!1.89e-13!511;UBERON:0000119!4.60e-13!312;UBERON:0000481!4.34e-12!347;UBERON:0002050!1.02e-11!605;UBERON:0005423!1.02e-11!605;UBERON:0000475!1.33e-11!365;UBERON:0000923!1.53e-11!604;UBERON:0005291!1.53e-11!604;UBERON:0006598!1.53e-11!604;UBERON:0002532!1.53e-11!604;UBERON:0000922!4.02e-11!612;UBERON:0004119!4.83e-11!169;UBERON:0000925!4.83e-11!169;UBERON:0006595!4.83e-11!169;UBERON:0000025!2.20e-10!194;UBERON:0003914!3.05e-09!118;UBERON:0000064!3.75e-09!219;UBERON:0001007!1.24e-08!155;UBERON:0001555!1.24e-08!155;UBERON:0007026!1.24e-08!155;UBERON:0002100!7.64e-08!216;UBERON:0002530!9.23e-08!59;UBERON:0004872!4.64e-07!84;UBERON:0003103!4.78e-07!69;UBERON:0004921!4.79e-07!129;UBERON:0004185!4.79e-07!129;UBERON:0009569!6.68e-07!113;UBERON:0005911!8.38e-07!82
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}}
}}

Revision as of 17:22, 8 August 2012


Full id: C1507_lung_chorionic_liver_adipose_placenta_amniotic_breast



Phase1 CAGE Peaks

Hg19::chr2:46524865..46524870,+p9@EPAS1
Hg19::chr2:46588018..46588031,+p@chr2:46588018..46588031
+
Hg19::chr2:46588040..46588071,+p@chr2:46588040..46588071
+
Hg19::chr2:46588084..46588107,+p@chr2:46588084..46588107
+
Hg19::chr2:46588140..46588166,+p@chr2:46588140..46588166
+
Hg19::chr2:46607455..46607495,+p@chr2:46607455..46607495
+


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
epithelial cell4.53e-08254
meso-epithelial cell1.48e-0744
endothelial cell1.59e-0735
lining cell1.82e-0757
barrier cell1.82e-0757
Uber Anatomy
Ontology termp-valuen
multi-cellular organism1.23e-18659
anatomical cluster3.08e-18286
anatomical conduit2.66e-17241
anatomical system3.47e-17625
anatomical group4.92e-17626
adult organism2.92e-15115
epithelium8.13e-14309
organ1.89e-13511
cell layer4.60e-13312
multi-tissue structure4.34e-12347
embryonic structure1.02e-11605
developing anatomical structure1.02e-11605
organism subdivision1.33e-11365
germ layer1.53e-11604
embryonic tissue1.53e-11604
presumptive structure1.53e-11604
epiblast (generic)1.53e-11604
embryo4.02e-11612
endoderm-derived structure4.83e-11169
endoderm4.83e-11169
presumptive endoderm4.83e-11169
tube2.20e-10194
epithelial tube3.05e-09118
organ part3.75e-09219
digestive system1.24e-08155
digestive tract1.24e-08155
primitive gut1.24e-08155
trunk7.64e-08216
gland9.23e-0859
splanchnic layer of lateral plate mesoderm4.64e-0784
compound organ4.78e-0769
subdivision of digestive tract4.79e-07129
endodermal part of digestive tract4.79e-07129
subdivision of trunk6.68e-07113
endo-epithelium8.38e-0782


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.