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Coexpression cluster:C2351: Difference between revisions

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|full_id=C2351_Small_Keratinocyte_Bronchial_Sebocyte_mesothelioma_salivary_Tracheal
|full_id=C2351_Small_Keratinocyte_Bronchial_Sebocyte_mesothelioma_salivary_Tracheal
|id=C2351
|id=C2351
|ontology_enrichment_celltype=CL:0000220!1.49e-28!246;CL:0002321!9.88e-28!248;CL:0000222!2.91e-25!119;CL:0000076!3.60e-21!62;CL:0000055!9.11e-19!180;CL:0000680!9.55e-13!57;CL:0000056!9.55e-13!57;CL:0000355!9.55e-13!57;CL:0000183!1.32e-12!59;CL:0000144!4.52e-12!625;CL:0000187!4.82e-12!54;CL:0000213!5.18e-12!57;CL:0000215!5.18e-12!57;CL:0000066!8.87e-12!254;CL:0000393!2.02e-10!60;CL:0000211!2.02e-10!60;CL:0000057!2.32e-10!75;CL:0000548!3.47e-10!679;CL:0000004!3.47e-10!679;CL:0000255!3.47e-10!679;CL:0000192!4.63e-10!42;CL:0000514!4.63e-10!42;CL:0002371!1.18e-09!591;CL:0000012!1.21e-09!682;CL:0000359!6.74e-09!32;CL:0000077!2.14e-08!19;CL:0002078!9.30e-08!44;CL:0002076!4.56e-07!43
|ontology_enrichment_celltype=CL:0002321!3.11e-27!250;CL:0000076!1.64e-22!63;CL:0000222!2.12e-21!121;CL:0000066!2.23e-14!253;CL:0000548!7.28e-13!679;CL:0000255!7.28e-13!679;CL:0000213!6.43e-11!58;CL:0000215!6.43e-11!58;CL:0000680!2.63e-10!58;CL:0000056!2.63e-10!58;CL:0000355!2.63e-10!58;CL:0002371!1.21e-09!588;CL:0000077!1.31e-09!19;CL:0000187!1.75e-09!55;CL:0002076!1.77e-09!42;CL:0000183!3.21e-09!59;CL:0000057!1.34e-08!76;CL:0000393!3.12e-08!61;CL:0000211!3.12e-08!61;CL:0002368!1.15e-07!13;CL:1000449!1.96e-07!15;CL:0000192!3.53e-07!43;CL:0000514!3.53e-07!43;CL:0000359!3.82e-07!32;CL:0000003!4.70e-07!722;CL:0000055!9.99e-07!106
|ontology_enrichment_disease=
|ontology_enrichment_disease=DOID:1749!3.74e-07!14
|ontology_enrichment_uberon=UBERON:0000486!2.03e-18!82;UBERON:0000914!2.57e-18!83;UBERON:0002329!2.57e-18!83;UBERON:0003077!2.57e-18!83;UBERON:0003059!2.57e-18!83;UBERON:0007282!2.57e-18!83;UBERON:0009618!2.57e-18!83;UBERON:0007285!2.57e-18!83;UBERON:0005256!1.05e-16!143;UBERON:0003102!1.15e-15!95;UBERON:0000483!1.97e-15!309;UBERON:0000119!2.92e-15!312;UBERON:0004290!3.34e-15!70;UBERON:0000475!1.36e-13!365;UBERON:0002049!2.17e-12!79;UBERON:0007798!2.17e-12!79;UBERON:0001134!2.37e-12!61;UBERON:0002036!2.37e-12!61;UBERON:0003082!2.37e-12!61;UBERON:0002385!5.02e-12!63;UBERON:0001015!5.02e-12!63;UBERON:0000383!5.02e-12!63;UBERON:0000490!5.46e-12!138;UBERON:0000481!8.75e-12!347;UBERON:0002100!1.01e-11!216;UBERON:0003914!1.55e-11!118;UBERON:0000055!1.78e-11!69;UBERON:0001981!2.00e-11!60;UBERON:0007500!2.00e-11!60;UBERON:0004537!2.00e-11!60;UBERON:0006965!2.00e-11!60;UBERON:0003104!6.74e-11!238;UBERON:0009142!6.74e-11!238;UBERON:0004872!1.08e-10!84;UBERON:0001444!2.84e-10!48;UBERON:0001637!1.26e-09!42;UBERON:0003509!1.26e-09!42;UBERON:0004572!1.26e-09!42;UBERON:0002199!9.22e-09!45;UBERON:0002416!9.22e-09!45;UBERON:0002097!1.51e-08!40;UBERON:0000468!2.29e-08!659;UBERON:0004535!2.41e-08!110;UBERON:0001009!5.61e-08!113;UBERON:0000165!1.05e-07!28;UBERON:0000930!1.05e-07!28;UBERON:0005085!1.36e-07!29;UBERON:0004573!1.59e-07!33;UBERON:0004571!1.59e-07!33;UBERON:0006555!4.87e-07!17;UBERON:0005103!4.87e-07!17;UBERON:0000083!4.87e-07!17;UBERON:0009201!4.87e-07!17;UBERON:0004819!4.87e-07!17;UBERON:0006553!4.87e-07!17;UBERON:0003074!4.87e-07!17;UBERON:0003060!4.87e-07!17;UBERON:0000467!6.48e-07!625;UBERON:0000480!9.01e-07!626
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}}
}}

Revision as of 13:55, 19 October 2012


Full id: C2351_Small_Keratinocyte_Bronchial_Sebocyte_mesothelioma_salivary_Tracheal



Phase1 CAGE Peaks

Hg19::chr15:83953373..83953386,-p2@BNC1
Hg19::chr15:83953397..83953425,-p1@BNC1
Hg19::chr15:83953474..83953483,-p3@BNC1
Hg19::chr15:83953694..83953708,-p4@BNC1


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
organism subdivision3.24e-16264
multilaminar epithelium1.70e-1483
surface structure1.92e-1499
epithelial vesicle3.37e-1378
cell layer1.41e-11309
epithelium1.48e-11306
somite2.63e-1171
presomitic mesoderm2.63e-1171
presumptive segmental plate2.63e-1171
dermomyotome2.63e-1171
trunk paraxial mesoderm2.63e-1171
unilaminar epithelium3.50e-11148
paraxial mesoderm6.44e-1172
presumptive paraxial mesoderm6.44e-1172
dense mesenchyme tissue1.53e-1073
epithelial tube3.73e-10117
trunk mesenchyme1.52e-09122
skeletal muscle tissue1.66e-0962
striated muscle tissue1.66e-0962
myotome1.66e-0962
trunk4.55e-09199
mesenchyme5.25e-09160
entire embryonic mesenchyme5.25e-09160
muscle tissue8.89e-0964
musculature8.89e-0964
musculature of body8.89e-0964
epithelial tube open at both ends9.74e-0959
blood vessel9.74e-0959
blood vasculature9.74e-0959
vascular cord9.74e-0959
multi-tissue structure1.70e-08342
artery3.42e-0842
arterial blood vessel3.42e-0842
arterial system3.42e-0842
head4.11e-0856
vasculature4.70e-0878
vascular system4.70e-0878
excretory tube7.32e-0816
kidney epithelium7.32e-0816
mouth1.14e-0729
stomodeum1.14e-0729
vessel1.28e-0768
anterior region of body1.37e-0762
craniocervical region1.37e-0762
nephron epithelium1.96e-0715
renal tubule1.96e-0715
nephron tubule1.96e-0715
nephron1.96e-0715
uriniferous tubule1.96e-0715
nephrogenic mesenchyme1.96e-0715
subdivision of head1.97e-0749
splanchnic layer of lateral plate mesoderm4.59e-0783
skin of body7.06e-0741
Disease
Ontology termp-valuen
squamous cell carcinoma3.74e-0714


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.