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Coexpression cluster:C744: Difference between revisions

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|full_id=C744_breast_salivary_parotid_submaxillary_seminal_small_ductus
|full_id=C744_breast_salivary_parotid_submaxillary_seminal_small_ductus
|id=C744
|id=C744
|ontology_enrichment_celltype=CL:0000066!2.53e-08!254
|ontology_enrichment_celltype=
|ontology_enrichment_disease=DOID:305!1.33e-25!106;DOID:0050687!6.17e-21!143;DOID:162!4.56e-16!235;DOID:14566!6.81e-15!239;DOID:299!8.75e-09!25
|ontology_enrichment_disease=DOID:305!1.60e-10!106;DOID:5093!1.97e-08!4;DOID:1612!1.97e-08!4;DOID:0050687!6.89e-08!143;DOID:299!9.43e-07!25
|ontology_enrichment_uberon=UBERON:0004921!7.07e-17!129;UBERON:0004185!7.07e-17!129;UBERON:0007023!1.64e-15!115;UBERON:0001007!1.75e-13!155;UBERON:0001555!1.75e-13!155;UBERON:0007026!1.75e-13!155;UBERON:0001041!4.89e-13!98;UBERON:0000077!5.38e-13!130;UBERON:0004119!2.62e-12!169;UBERON:0000925!2.62e-12!169;UBERON:0006595!2.62e-12!169;UBERON:0005409!9.55e-09!35;UBERON:0005743!7.20e-08!86;UBERON:0000073!1.44e-07!94;UBERON:0001016!1.44e-07!94;UBERON:0005177!1.55e-07!107;UBERON:0000065!2.02e-07!53;UBERON:0008947!2.26e-07!38;UBERON:0003258!2.26e-07!38;UBERON:0001017!2.37e-07!82;UBERON:0001004!6.21e-07!72
|ontology_enrichment_uberon=UBERON:0004921!1.05e-15!118;UBERON:0000466!5.46e-15!117;UBERON:0001007!1.68e-13!145;UBERON:0001555!1.68e-13!145;UBERON:0007026!1.68e-13!145;UBERON:0001041!3.60e-13!87;UBERON:0000464!4.56e-13!95;UBERON:0007023!4.75e-13!114;UBERON:0004119!1.64e-11!160;UBERON:0000925!1.64e-11!160;UBERON:0006595!1.64e-11!160;UBERON:0006947!6.62e-11!3;UBERON:0004054!6.62e-11!3;UBERON:0000475!7.03e-11!264;UBERON:0000915!1.80e-10!52;UBERON:0005177!3.01e-10!101;UBERON:0009569!5.67e-10!112;UBERON:0005178!4.71e-09!34;UBERON:0002224!4.71e-09!34;UBERON:0005181!9.95e-09!35;UBERON:0001004!1.70e-08!74;UBERON:0005904!2.90e-08!4;UBERON:0005153!3.51e-08!37;UBERON:0001829!4.33e-08!2;UBERON:0002048!6.14e-08!22;UBERON:0000117!6.14e-08!22;UBERON:0000171!6.14e-08!22;UBERON:0000170!6.14e-08!22;UBERON:0005597!6.14e-08!22;UBERON:0000118!6.14e-08!22;UBERON:0003127!7.62e-08!2;UBERON:0005911!9.33e-08!82;UBERON:0000341!1.28e-07!2;UBERON:0002100!2.57e-07!199;UBERON:0000065!4.55e-07!54
|tf_chipseq_enrich=CTCF#10664;6:2.92377620349547:0.0082120479432594:0.0324133815247947!E2F1#1869;6:2.67675775357054:0.0127881671753266:0.04601493166663!EP300#2033;6:3.69487730521265:0.00244128806655223:0.0137470040644119!FOXA1#3169;5:5.03700897699339:0.00173389791582009:0.0106722397707646!GATA3#2625;5:12.3802347078209:2.5558774340898e-05:0.000553114967548496!MYC#4609;7:3.32327028193326:0.00150133599624924:0.00959126682849731!NR3C1#2908;4:5.4447357567902:0.00448160080404692:0.0212038555030288!SUZ12#23512;3:13.6679402484717:0.0011615972136501:0.00794161111523978
|tf_chipseq_enrich=CTCF#10664;6:2.92377620349547:0.0082120479432594:0.0324133815247947!E2F1#1869;6:2.67675775357054:0.0127881671753266:0.04601493166663!EP300#2033;6:3.69487730521265:0.00244128806655223:0.0137470040644119!FOXA1#3169;5:5.03700897699339:0.00173389791582009:0.0106722397707646!GATA3#2625;5:12.3802347078209:2.5558774340898e-05:0.000553114967548496!MYC#4609;7:3.32327028193326:0.00150133599624924:0.00959126682849731!NR3C1#2908;4:5.4447357567902:0.00448160080404692:0.0212038555030288!SUZ12#23512;3:13.6679402484717:0.0011615972136501:0.00794161111523978
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}}
}}

Revision as of 16:39, 19 October 2012


Full id: C744_breast_salivary_parotid_submaxillary_seminal_small_ductus



Phase1 CAGE Peaks

Hg19::chr11:826136..826180,+p2@EFCAB4A
Hg19::chr13:34922173..34922187,+p@chr13:34922173..34922187
+
Hg19::chr15:41069078..41069092,-p2@DNAJC17
Hg19::chr17:36763272..36763286,-p@chr17:36763272..36763286
-
Hg19::chr18:20911089..20911104,-p4@TMEM241
Hg19::chr18:20911109..20911117,-p5@TMEM241
Hg19::chr22:31739395..31739404,-p24@PATZ1
Hg19::chr7:94138905..94138932,+p3@CASD1
Hg19::chr9:140063847..140063858,-p2@MIR3621
Hg19::chr9:140063873..140063890,-p1@MIR3621
Hg19::chr9:140064092..140064112,-p3@MIR3621


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><br>uberon_data<br>disease_data<br>


Uber Anatomy
Ontology termp-valuen
subdivision of digestive tract1.05e-15118
immaterial anatomical entity5.46e-15117
digestive system1.68e-13145
digestive tract1.68e-13145
primitive gut1.68e-13145
foregut3.60e-1387
anatomical space4.56e-1395
adult organism4.75e-13114
endoderm-derived structure1.64e-11160
endoderm1.64e-11160
presumptive endoderm1.64e-11160
male genital duct6.62e-113
internal male genitalia6.62e-113
organism subdivision7.03e-11264
thoracic segment of trunk1.80e-1052
trunk region element3.01e-10101
subdivision of trunk5.67e-10112
thoracic cavity element4.71e-0934
thoracic cavity4.71e-0934
thoracic segment organ9.95e-0935
respiratory system1.70e-0874
duct of male reproductive system2.90e-084
epithelial bud3.51e-0837
major salivary gland4.33e-082
lung6.14e-0822
respiratory tube6.14e-0822
respiration organ6.14e-0822
pair of lungs6.14e-0822
lung primordium6.14e-0822
lung bud6.14e-0822
open tracheal system trachea7.62e-082
endo-epithelium9.33e-0882
throat1.28e-072
trunk2.57e-07199
respiratory tract4.55e-0754
Disease
Ontology termp-valuen
carcinoma1.60e-10106
thoracic cancer1.97e-084
breast cancer1.97e-084
cell type cancer6.89e-08143
adenocarcinoma9.43e-0725


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
CTCF#1066462.923776203495470.00821204794325940.0324133815247947
E2F1#186962.676757753570540.01278816717532660.04601493166663
EP300#203363.694877305212650.002441288066552230.0137470040644119
FOXA1#316955.037008976993390.001733897915820090.0106722397707646
GATA3#2625512.38023470782092.5558774340898e-050.000553114967548496
MYC#460973.323270281933260.001501335996249240.00959126682849731
NR3C1#290845.44473575679020.004481600804046920.0212038555030288
SUZ12#23512313.66794024847170.00116159721365010.00794161111523978



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.