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Coexpression cluster:C3978: Difference between revisions

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|full_id=C3978_smallcell_somatostatinoma_small_merkel_Hep2_carcinoid_gastrointestinal
|full_id=C3978_smallcell_somatostatinoma_small_merkel_Hep2_carcinoid_gastrointestinal
|id=C3978
|id=C3978
|ontology_enrichment_celltype=CL:0000066!1.11e-08!254
|ontology_enrichment_celltype=CL:0000066!3.94e-09!253
|ontology_enrichment_disease=DOID:162!6.46e-43!235;DOID:14566!1.78e-41!239;DOID:0050687!2.26e-34!143;DOID:305!1.11e-31!106;DOID:0050686!1.10e-16!137;DOID:7!1.42e-07!39;DOID:299!1.70e-07!25;DOID:2531!6.46e-07!51;DOID:0060083!6.46e-07!51
|ontology_enrichment_disease=DOID:162!5.07e-43!235;DOID:14566!1.69e-41!239;DOID:0050687!1.49e-34!143;DOID:305!4.57e-32!106;DOID:0050686!1.02e-16!137;DOID:299!4.67e-08!25;DOID:7!1.07e-07!39
|ontology_enrichment_uberon=UBERON:0001017!8.83e-17!82;UBERON:0005743!8.21e-16!86;UBERON:0000073!3.25e-15!94;UBERON:0001016!3.25e-15!94;UBERON:0001049!8.85e-14!57;UBERON:0005068!8.85e-14!57;UBERON:0006241!8.85e-14!57;UBERON:0007135!8.85e-14!57;UBERON:0000955!1.20e-13!69;UBERON:0006238!1.20e-13!69;UBERON:0007023!6.47e-13!115;UBERON:0002780!1.72e-11!41;UBERON:0001890!1.72e-11!41;UBERON:0006240!1.72e-11!41;UBERON:0003080!2.46e-11!42;UBERON:0002616!2.64e-10!59;UBERON:0001893!5.76e-09!34;UBERON:0002020!8.70e-09!34;UBERON:0003528!8.70e-09!34;UBERON:0001869!9.94e-09!32;UBERON:0002791!1.36e-08!33;UBERON:0004921!2.01e-08!129;UBERON:0004185!2.01e-08!129;UBERON:0002346!2.23e-08!90;UBERON:0002619!2.69e-08!22;UBERON:0003075!2.83e-08!86;UBERON:0007284!2.83e-08!86;UBERON:0001950!6.10e-08!20;UBERON:0001041!7.75e-08!98;UBERON:0000924!1.80e-07!173;UBERON:0006601!1.80e-07!173;UBERON:0001737!1.84e-07!9;UBERON:0004121!2.61e-07!169;UBERON:0001007!3.50e-07!155;UBERON:0001555!3.50e-07!155;UBERON:0007026!3.50e-07!155
|ontology_enrichment_uberon=UBERON:0011216!6.81e-17!223;UBERON:0001017!1.11e-16!81;UBERON:0001016!7.67e-16!89;UBERON:0000955!1.52e-13!68;UBERON:0006238!1.52e-13!68;UBERON:0001049!2.20e-13!56;UBERON:0005068!2.20e-13!56;UBERON:0006241!2.20e-13!56;UBERON:0007135!2.20e-13!56;UBERON:0000073!6.35e-13!53;UBERON:0002616!6.35e-13!53;UBERON:0007023!3.09e-12!114;UBERON:0002780!2.68e-11!41;UBERON:0001890!2.68e-11!41;UBERON:0003080!2.68e-11!41;UBERON:0006240!2.68e-11!41;UBERON:0001893!7.67e-09!34;UBERON:0003528!1.12e-08!34;UBERON:0002020!1.12e-08!34;UBERON:0001869!1.23e-08!32;UBERON:0002791!2.98e-08!32;UBERON:0002619!4.38e-08!22;UBERON:0001950!9.85e-08!20;UBERON:0001737!1.62e-07!9;UBERON:0002346!1.62e-07!86;UBERON:0003075!1.99e-07!82;UBERON:0007284!1.99e-07!82
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0325700065858367!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0322598396057431!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0462784532385057!ESR1#2099;2:20.5124021974363:0.00309974157709518:0.0163131222257618!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.015425191660084!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294833092483211!REST#5978;3:9.65002871612802:0.00111263624711459:0.00768281765371244!SUZ12#23512;3:50.1157809110629:7.93834897779404e-06:0.000222689559197376!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190497470364275!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109531507836175
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0325700065858367!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0322598396057431!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0462784532385057!ESR1#2099;2:20.5124021974363:0.00309974157709518:0.0163131222257618!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.015425191660084!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294833092483211!REST#5978;3:9.65002871612802:0.00111263624711459:0.00768281765371244!SUZ12#23512;3:50.1157809110629:7.93834897779404e-06:0.000222689559197376!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190497470364275!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109531507836175
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}}
}}

Revision as of 15:33, 19 October 2012


Full id: C3978_smallcell_somatostatinoma_small_merkel_Hep2_carcinoid_gastrointestinal



Phase1 CAGE Peaks

Hg19::chr1:38259459..38259532,+p2@MANEAL
Hg19::chr1:38259540..38259569,+p3@MANEAL
Hg19::chr1:38259727..38259807,+p1@MANEAL


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>


Cell Type
Ontology termp-valuen
epithelial cell3.94e-09253
Uber Anatomy
Ontology termp-valuen
organ system subdivision6.81e-17223
central nervous system1.11e-1681
nervous system7.67e-1689
brain1.52e-1368
future brain1.52e-1368
neural tube2.20e-1356
neural rod2.20e-1356
future spinal cord2.20e-1356
neural keel2.20e-1356
regional part of nervous system6.35e-1353
regional part of brain6.35e-1353
adult organism3.09e-12114
regional part of forebrain2.68e-1141
forebrain2.68e-1141
anterior neural tube2.68e-1141
future forebrain2.68e-1141
telencephalon7.67e-0934
brain grey matter1.12e-0834
gray matter1.12e-0834
cerebral hemisphere1.23e-0832
regional part of telencephalon2.98e-0832
regional part of cerebral cortex4.38e-0822
neocortex9.85e-0820
larynx1.62e-079
neurectoderm1.62e-0786
neural plate1.99e-0782
presumptive neural plate1.99e-0782
Disease
Ontology termp-valuen
cancer5.07e-43235
disease of cellular proliferation1.69e-41239
cell type cancer1.49e-34143
carcinoma4.57e-32106
organ system cancer1.02e-16137
adenocarcinoma4.67e-0825
disease of anatomical entity1.07e-0739


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
E2F1#186934.907389214879320.008460985347239390.0325700065858367
E2F6#187635.017155731697390.00791769806886330.0322598396057431
ELF1#199734.258097958807540.01295179875054610.0462784532385057
ESR1#2099220.51240219743630.003099741577095180.0163131222257618
GABPB1#255337.067683836182170.002832212825417420.015425191660084
MYC#460935.22228187160940.007020843755740150.0294833092483211
REST#597839.650028716128020.001112636247114590.00768281765371244
SUZ12#23512350.11578091106297.93834897779404e-060.000222689559197376
USF1#739136.361499277207960.00388404057290560.0190497470364275
ZNF263#1012738.221841637010680.001799043925565870.0109531507836175



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.