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Coexpression cluster:C1992: Difference between revisions

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|full_id=C1992_Mesothelial_glioma_Smooth_Basophils_mesenchymal_Neutrophils_gastric
|full_id=C1992_Mesothelial_glioma_Smooth_Basophils_mesenchymal_Neutrophils_gastric
|id=C1992
|id=C1992
|ontology_enrichment_celltype=CL:0002057!2.25e-10!42;CL:0000860!1.67e-09!45;CL:0002334!2.27e-09!12
|ontology_enrichment_celltype=CL:0002334!2.32e-11!12
|ontology_enrichment_disease=DOID:2394!1.01e-07!14
|ontology_enrichment_disease=DOID:2394!5.86e-08!14
|ontology_enrichment_uberon=UBERON:0009569!9.94e-09!113;UBERON:0000489!2.94e-07!32
|ontology_enrichment_uberon=UBERON:0009569!1.30e-07!112
|tf_chipseq_enrich=BHLHE40#8553;5:44.8718135469774:5.48404023694134e-09:4.38215515153723e-07!CEBPB#1051;5:7.97114762582482:3.10621793420244e-05:0.000629189865845943!CTCF#10664;5:5.36025637307503:0.000225927829993709:0.00250272344470863!EP300#2033;5:6.7739417262232:7.00901578206049e-05:0.00111029061013592!HEY1#23462;5:4.04011104310571:0.000928885220517799:0.00674958905904532!MAX#4149;5:6.45255550900712:8.93743970843928e-05:0.00130822321753285!MXI1#4601;5:9.9615716287593:1.01894348670516e-05:0.000266777234414641!MYC#4609;5:5.2222818716094:0.000257394484885061:0.00276763333747667!RAD21#5885;4:8.28402711636506:0.000401162263912245:0.00386967633515572!RXRA#6256;3:12.04477028348:0.00114526216283683:0.00783711407577749!SMARCB1#6598;5:18.2527157811574:4.93125075403021e-07:2.31779881863259e-05!SMC3#9126;5:15.0449328449328:1.29633924985553e-06:5.17144289211848e-05!SRF#6722;5:13.7971782621678:1.9987012616697e-06:7.32686420033421e-05!STAT3#6774;5:10.5194649971542:7.759040745861e-06:0.000220802849170838!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135557287056428!TBP#6908;5:3.70677068709639:0.00142875510672112:0.00920358691117296!USF1#7391;5:6.36149927720796:9.59569864925045e-05:0.00137095098663347!USF2#7392;5:12.9921973850696:2.69963551658264e-06:9.44230521488193e-05
|tf_chipseq_enrich=BHLHE40#8553;5:44.8718135469774:5.48404023694134e-09:4.38215515153723e-07!CEBPB#1051;5:7.97114762582482:3.10621793420244e-05:0.000629189865845943!CTCF#10664;5:5.36025637307503:0.000225927829993709:0.00250272344470863!EP300#2033;5:6.7739417262232:7.00901578206049e-05:0.00111029061013592!HEY1#23462;5:4.04011104310571:0.000928885220517799:0.00674958905904532!MAX#4149;5:6.45255550900712:8.93743970843928e-05:0.00130822321753285!MXI1#4601;5:9.9615716287593:1.01894348670516e-05:0.000266777234414641!MYC#4609;5:5.2222818716094:0.000257394484885061:0.00276763333747667!RAD21#5885;4:8.28402711636506:0.000401162263912245:0.00386967633515572!RXRA#6256;3:12.04477028348:0.00114526216283683:0.00783711407577749!SMARCB1#6598;5:18.2527157811574:4.93125075403021e-07:2.31779881863259e-05!SMC3#9126;5:15.0449328449328:1.29633924985553e-06:5.17144289211848e-05!SRF#6722;5:13.7971782621678:1.9987012616697e-06:7.32686420033421e-05!STAT3#6774;5:10.5194649971542:7.759040745861e-06:0.000220802849170838!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135557287056428!TBP#6908;5:3.70677068709639:0.00142875510672112:0.00920358691117296!USF1#7391;5:6.36149927720796:9.59569864925045e-05:0.00137095098663347!USF2#7392;5:12.9921973850696:2.69963551658264e-06:9.44230521488193e-05
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}}
}}

Revision as of 11:55, 19 October 2012


Full id: C1992_Mesothelial_glioma_Smooth_Basophils_mesenchymal_Neutrophils_gastric



Phase1 CAGE Peaks

Hg19::chr7:27183095..27183108,-p7@HOXA5
Hg19::chr7:27183114..27183138,-p3@HOXA5
Hg19::chr7:27183141..27183152,-p6@HOXA5
Hg19::chr7:27183156..27183167,-p8@HOXA5
Hg19::chr7:27183191..27183214,-p4@HOXA5


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
preadipocyte2.32e-1112
Uber Anatomy
Ontology termp-valuen
subdivision of trunk1.30e-07112
Disease
Ontology termp-valuen
ovarian cancer5.86e-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

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

TF#promotersEnrichmentp-valueq-value
BHLHE40#8553544.87181354697745.48404023694134e-094.38215515153723e-07
CEBPB#105157.971147625824823.10621793420244e-050.000629189865845943
CTCF#1066455.360256373075030.0002259278299937090.00250272344470863
EP300#203356.77394172622327.00901578206049e-050.00111029061013592
HEY1#2346254.040111043105710.0009288852205177990.00674958905904532
MAX#414956.452555509007128.93743970843928e-050.00130822321753285
MXI1#460159.96157162875931.01894348670516e-050.000266777234414641
MYC#460955.22228187160940.0002573944848850610.00276763333747667
RAD21#588548.284027116365060.0004011622639122450.00386967633515572
RXRA#6256312.044770283480.001145262162836830.00783711407577749
SMARCB1#6598518.25271578115744.93125075403021e-072.31779881863259e-05
SMC3#9126515.04493284493281.29633924985553e-065.17144289211848e-05
SRF#6722513.79717826216781.9987012616697e-067.32686420033421e-05
STAT3#6774510.51946499715427.759040745861e-060.000220802849170838
TAF1#687253.343046285745290.002394600090870310.0135557287056428
TBP#690853.706770687096390.001428755106721120.00920358691117296
USF1#739156.361499277207969.59569864925045e-050.00137095098663347
USF2#7392512.99219738506962.69963551658264e-069.44230521488193e-05



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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