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Coexpression cluster:C1359: Difference between revisions

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|ontology_enrichment_disease=DOID:1749!2.82e-07!14
|ontology_enrichment_disease=DOID:1749!2.82e-07!14
|ontology_enrichment_uberon=UBERON:0000475!9.07e-13!365;UBERON:0004111!1.34e-11!241;UBERON:0000468!1.26e-10!659;UBERON:0000467!1.66e-10!625;UBERON:0000477!2.67e-10!286;UBERON:0000480!2.71e-10!626;UBERON:0000033!4.13e-10!123;UBERON:0004121!8.03e-10!169;UBERON:0000924!1.05e-09!173;UBERON:0006601!1.05e-09!173;UBERON:0000153!3.12e-09!129;UBERON:0007811!3.12e-09!129;UBERON:0000483!7.21e-09!309;UBERON:0002050!2.07e-08!605;UBERON:0005423!2.07e-08!605;UBERON:0000922!2.09e-08!612;UBERON:0004119!2.19e-08!169;UBERON:0000925!2.19e-08!169;UBERON:0006595!2.19e-08!169;UBERON:0000119!2.22e-08!312;UBERON:0000481!2.71e-08!347;UBERON:0000923!3.14e-08!604;UBERON:0005291!3.14e-08!604;UBERON:0006598!3.14e-08!604;UBERON:0002532!3.14e-08!604;UBERON:0001637!3.24e-08!42;UBERON:0003509!3.24e-08!42;UBERON:0004572!3.24e-08!42;UBERON:0000025!9.59e-08!194;UBERON:0000161!1.59e-07!35;UBERON:0003102!1.84e-07!95;UBERON:0001004!3.59e-07!72;UBERON:0003100!4.23e-07!41;UBERON:0004573!8.08e-07!33;UBERON:0004571!8.08e-07!33;UBERON:0005156!8.22e-07!59;UBERON:0000990!8.22e-07!59;UBERON:0000064!8.68e-07!219
|ontology_enrichment_uberon=UBERON:0000475!9.07e-13!365;UBERON:0004111!1.34e-11!241;UBERON:0000468!1.26e-10!659;UBERON:0000467!1.66e-10!625;UBERON:0000477!2.67e-10!286;UBERON:0000480!2.71e-10!626;UBERON:0000033!4.13e-10!123;UBERON:0004121!8.03e-10!169;UBERON:0000924!1.05e-09!173;UBERON:0006601!1.05e-09!173;UBERON:0000153!3.12e-09!129;UBERON:0007811!3.12e-09!129;UBERON:0000483!7.21e-09!309;UBERON:0002050!2.07e-08!605;UBERON:0005423!2.07e-08!605;UBERON:0000922!2.09e-08!612;UBERON:0004119!2.19e-08!169;UBERON:0000925!2.19e-08!169;UBERON:0006595!2.19e-08!169;UBERON:0000119!2.22e-08!312;UBERON:0000481!2.71e-08!347;UBERON:0000923!3.14e-08!604;UBERON:0005291!3.14e-08!604;UBERON:0006598!3.14e-08!604;UBERON:0002532!3.14e-08!604;UBERON:0001637!3.24e-08!42;UBERON:0003509!3.24e-08!42;UBERON:0004572!3.24e-08!42;UBERON:0000025!9.59e-08!194;UBERON:0000161!1.59e-07!35;UBERON:0003102!1.84e-07!95;UBERON:0001004!3.59e-07!72;UBERON:0003100!4.23e-07!41;UBERON:0004573!8.08e-07!33;UBERON:0004571!8.08e-07!33;UBERON:0005156!8.22e-07!59;UBERON:0000990!8.22e-07!59;UBERON:0000064!8.68e-07!219
|tf_chipseq_enrich=CCNT2#905;4:4.22413438464176:0.00710980547887581:0.0296068969062325!CTCF#10664;5:4.46688031089586:0.00114484834617236:0.00783530907115956!RAD21#5885;4:6.90335593030422:0.0011108515162536:0.00771230615608656!SUZ12#23512;5:41.7631507592191:1.86145137032345e-08:1.33430418438717e-06!TCF12#6938;4:7.08964326812428:0.00100299157265771:0.00718706256307363!ZBTB7A#51341;4:4.90127287191726:0.00407962811884375:0.0194838248172637
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}}
}}

Revision as of 13:15, 5 September 2012


Full id: C1359_acantholytic_Mallassezderived_maxillary_renal_gastric_amniotic_Prostate



Phase1 CAGE Peaks

Hg19::chr12:28123016..28123029,-p4@PTHLH
Hg19::chr12:28123126..28123133,-p5@PTHLH
Hg19::chr12:28123174..28123181,-p7@PTHLH
Hg19::chr12:28123206..28123229,-p3@PTHLH
Hg19::chr12:28123422..28123440,-p8@PTHLH
Hg19::chr12:28124161..28124192,-p9@PTHLH


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 cell5.90e-12254
endo-epithelial cell1.59e-0943
squamous epithelial cell8.37e-0962
embryonic cell1.15e-08248
respiratory epithelial cell9.37e-0813
Uber Anatomy
Ontology termp-valuen
organism subdivision9.07e-13365
anatomical conduit1.34e-11241
multi-cellular organism1.26e-10659
anatomical system1.66e-10625
anatomical cluster2.67e-10286
anatomical group2.71e-10626
head4.13e-10123
ectoderm-derived structure8.03e-10169
ectoderm1.05e-09173
presumptive ectoderm1.05e-09173
anterior region of body3.12e-09129
craniocervical region3.12e-09129
epithelium7.21e-09309
embryonic structure2.07e-08605
developing anatomical structure2.07e-08605
embryo2.09e-08612
endoderm-derived structure2.19e-08169
endoderm2.19e-08169
presumptive endoderm2.19e-08169
cell layer2.22e-08312
multi-tissue structure2.71e-08347
germ layer3.14e-08604
embryonic tissue3.14e-08604
presumptive structure3.14e-08604
epiblast (generic)3.14e-08604
artery3.24e-0842
arterial blood vessel3.24e-0842
arterial system3.24e-0842
tube9.59e-08194
orifice1.59e-0735
surface structure1.84e-0795
respiratory system3.59e-0772
female organism4.23e-0741
systemic artery8.08e-0733
systemic arterial system8.08e-0733
reproductive structure8.22e-0759
reproductive system8.22e-0759
organ part8.68e-07219
Disease
Ontology termp-valuen
squamous cell carcinoma2.82e-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

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

TF#promotersEnrichmentp-valueq-value
CCNT2#90544.224134384641760.007109805478875810.0296068969062325
CTCF#1066454.466880310895860.001144848346172360.00783530907115956
RAD21#588546.903355930304220.00111085151625360.00771230615608656
SUZ12#23512541.76315075921911.86145137032345e-081.33430418438717e-06
TCF12#693847.089643268124280.001002991572657710.00718706256307363
ZBTB7A#5134144.901272871917260.004079628118843750.0194838248172637



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C1359&oldid=2132075"