Personal tools

Coexpression cluster:C4282: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{Coexpression_clusters |full_id=C4282_Mallassezderived_Small_Gingival_Urothelial_papillotubular_Sebocyte_transitionalcell |id=C4282 }}")
 
No edit summary
Line 2: Line 2:
|full_id=C4282_Mallassezderived_Small_Gingival_Urothelial_papillotubular_Sebocyte_transitionalcell
|full_id=C4282_Mallassezderived_Small_Gingival_Urothelial_papillotubular_Sebocyte_transitionalcell
|id=C4282
|id=C4282
|ontology_enrichment_celltype=CL:0000066!3.80e-47!254;CL:0000076!4.16e-19!62;CL:0002076!9.80e-19!43;CL:0000220!7.36e-16!246;CL:0002321!2.05e-15!248;CL:0000223!3.22e-11!59;CL:0002139!2.53e-09!24;CL:0002368!5.54e-09!13;CL:0000213!1.70e-08!57;CL:0000215!1.70e-08!57;CL:0002078!7.50e-07!44;CL:0002251!8.91e-07!21
|ontology_enrichment_disease=DOID:305!1.87e-11!106;DOID:0050687!2.36e-08!143;DOID:1749!2.99e-08!14
|ontology_enrichment_uberon=UBERON:0001004!1.29e-09!72;UBERON:0000064!1.58e-09!219;UBERON:0000065!4.69e-09!53;UBERON:0000467!6.10e-09!625;UBERON:0000480!8.03e-09!626;UBERON:0000464!1.28e-08!104;UBERON:0004119!1.38e-08!169;UBERON:0000925!1.38e-08!169;UBERON:0006595!1.38e-08!169;UBERON:0000468!2.13e-08!659;UBERON:0003100!3.80e-08!41;UBERON:0005631!1.10e-07!14;UBERON:0000158!1.10e-07!14;UBERON:0005795!1.62e-07!22;UBERON:0008947!2.66e-07!38;UBERON:0003258!2.66e-07!38;UBERON:0000995!3.54e-07!21;UBERON:0000483!3.89e-07!309;UBERON:0005156!4.51e-07!59;UBERON:0000990!4.51e-07!59;UBERON:0003133!5.41e-07!48;UBERON:0003134!5.81e-07!37;UBERON:0000474!5.81e-07!37;UBERON:0000119!8.86e-07!312
}}
}}

Revision as of 14:46, 21 May 2012


Full id: C4282_Mallassezderived_Small_Gingival_Urothelial_papillotubular_Sebocyte_transitionalcell



Phase1 CAGE Peaks

Hg19::chr3:129513355..129513392,-p6@TMCC1
Hg19::chr3:129513407..129513425,-p10@TMCC1
Hg19::chr3:129513434..129513460,-p8@TMCC1


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
respiratory system1.29e-0972
organ part1.58e-09219
respiratory tract4.69e-0953
anatomical system6.10e-09625
anatomical group8.03e-09626
anatomical space1.28e-08104
endoderm-derived structure1.38e-08169
endoderm1.38e-08169
presumptive endoderm1.38e-08169
multi-cellular organism2.13e-08659
female organism3.80e-0841
extraembryonic membrane1.10e-0714
membranous layer1.10e-0714
embryonic uterus1.62e-0722
respiratory primordium2.66e-0738
endoderm of foregut2.66e-0738
uterus3.54e-0721
epithelium3.89e-07309
reproductive structure4.51e-0759
reproductive system4.51e-0759
reproductive organ5.41e-0748
female reproductive organ5.81e-0737
female reproductive system5.81e-0737
cell layer8.86e-07312
Disease
Ontology termp-valuen
carcinoma1.87e-11106
cell type cancer2.36e-08143
squamous cell carcinoma2.99e-0814


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.