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Coexpression cluster:C688: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001004!8.93e-22!74;UBERON:0000166!1.59e-20!22;UBERON:0000161!3.48e-20!36;UBERON:0004119!2.27e-18!160;UBERON:0000925!2.27e-18!160;UBERON:0006595!2.27e-18!160;UBERON:0003729!2.07e-17!13;UBERON:0003102!2.15e-17!99;UBERON:0000165!2.18e-17!29;UBERON:0000930!2.18e-17!29;UBERON:0000365!5.92e-16!5;UBERON:0000344!7.15e-16!20;UBERON:0000033!2.64e-15!56;UBERON:0000153!6.15e-15!62;UBERON:0007811!6.15e-15!62;UBERON:0005910!3.08e-13!6;UBERON:0007196!5.82e-13!15;UBERON:0001558!5.82e-13!15;UBERON:0001444!3.16e-12!49;UBERON:0003343!7.74e-12!4;UBERON:0004785!7.74e-12!4;UBERON:0001007!2.26e-11!145;UBERON:0001555!2.26e-11!145;UBERON:0007026!2.26e-11!145;UBERON:0004815!3.22e-11!3;UBERON:0002031!3.22e-11!3;UBERON:0000065!4.65e-11!54;UBERON:0001949!1.08e-10!3;UBERON:0005178!3.24e-09!34;UBERON:0002224!3.24e-09!34;UBERON:0005181!6.94e-09!35;UBERON:0005157!1.41e-08!47;UBERON:0001708!3.77e-08!4;UBERON:0008895!3.77e-08!4;UBERON:0005153!3.99e-08!37;UBERON:0001911!7.30e-08!4;UBERON:0005333!7.30e-08!4;UBERON:0008425!7.30e-08!4;UBERON:0005311!7.30e-08!4;UBERON:0003126!9.60e-08!7;UBERON:0001005!9.60e-08!7;UBERON:0002419!3.78e-07!2;UBERON:0007771!3.78e-07!2;UBERON:0003297!3.78e-07!2;UBERON:0001821!3.78e-07!2;UBERON:0003487!3.78e-07!2;UBERON:0001820!3.78e-07!2;UBERON:0005089!3.78e-07!2;UBERON:0005088!3.78e-07!2;UBERON:0004921!3.89e-07!118;UBERON:0000072!4.29e-07!47;UBERON:0000974!4.98e-07!10;UBERON:0002185!7.44e-07!5
|ontology_enrichment_uberon=UBERON:0001004!8.93e-22!74;UBERON:0000166!1.59e-20!22;UBERON:0000161!3.48e-20!36;UBERON:0004119!2.27e-18!160;UBERON:0000925!2.27e-18!160;UBERON:0006595!2.27e-18!160;UBERON:0003729!2.07e-17!13;UBERON:0003102!2.15e-17!99;UBERON:0000165!2.18e-17!29;UBERON:0000930!2.18e-17!29;UBERON:0000365!5.92e-16!5;UBERON:0000344!7.15e-16!20;UBERON:0000033!2.64e-15!56;UBERON:0000153!6.15e-15!62;UBERON:0007811!6.15e-15!62;UBERON:0005910!3.08e-13!6;UBERON:0007196!5.82e-13!15;UBERON:0001558!5.82e-13!15;UBERON:0001444!3.16e-12!49;UBERON:0003343!7.74e-12!4;UBERON:0004785!7.74e-12!4;UBERON:0001007!2.26e-11!145;UBERON:0001555!2.26e-11!145;UBERON:0007026!2.26e-11!145;UBERON:0004815!3.22e-11!3;UBERON:0002031!3.22e-11!3;UBERON:0000065!4.65e-11!54;UBERON:0001949!1.08e-10!3;UBERON:0005178!3.24e-09!34;UBERON:0002224!3.24e-09!34;UBERON:0005181!6.94e-09!35;UBERON:0005157!1.41e-08!47;UBERON:0001708!3.77e-08!4;UBERON:0008895!3.77e-08!4;UBERON:0005153!3.99e-08!37;UBERON:0001911!7.30e-08!4;UBERON:0005333!7.30e-08!4;UBERON:0008425!7.30e-08!4;UBERON:0005311!7.30e-08!4;UBERON:0003126!9.60e-08!7;UBERON:0001005!9.60e-08!7;UBERON:0002419!3.78e-07!2;UBERON:0007771!3.78e-07!2;UBERON:0003297!3.78e-07!2;UBERON:0001821!3.78e-07!2;UBERON:0003487!3.78e-07!2;UBERON:0001820!3.78e-07!2;UBERON:0005089!3.78e-07!2;UBERON:0005088!3.78e-07!2;UBERON:0004921!3.89e-07!118;UBERON:0000072!4.29e-07!47;UBERON:0000974!4.98e-07!10;UBERON:0002185!7.44e-07!5
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|tfbs_overrepresentation_for_novel_motifs=0.22923,0.243897,0.223258,0.345441,0.556358,0.344001,0.411652,0.340819,0.336485,0.0552668,0.317729,0.451026,0.0765797,0.401301,1.05539,1.12766,0.617549,0.890765,0.0839658,1.22708,1.18892,1.24247,0.337221,1.04387,0.260754,0.471832,0.858875,0.335332,1.06915,1.20435,0.298956,0.65246,0.396376,1.43308,0.163884,0.376499,0.161511,0.345014,0.443749,1.05941,0.48973,0.285097,0.20746,0.187953,0.653532,0.24831,0.412635,0.308385,0.0729507,0.192687,0.484909,0.423285,0.347648,0.725869,0.873575,0.403938,0.570319,0.374657,0.20655,0.373762,0.691524,0.414771,1.67357,0.591384,0.43102,0.559038,0.959746,1.32257,0.642589,1.16217,0.273995,0.350755,0.0373297,0.871629,0.0739759,1.31915,0.472331,0.575479,0.639503,0.255642,1.52117,0.590372,0.4307,0.345708,0.821696,0.328031,0.0287315,0.440676,0.508983,1.42111,1.05129,0.795567,0.66846,0.409242,0.190761,0.140087,0.9978,0.709167,0.51326,0.701432,0.145361,0.663075,0.703825,1.50526,0.54826,0.313822,0.606045,0.398205,0.260543,0.177931,1.2234,0.701175,1.17167,0.869962,1.00416,2.14736,0.0362329,0.807094,0.556847,1.92798,0.863578,0.506732,0.341589,0.44095,1.11293,0.576194,0.405934,0.673222,0.905059,0.434621,0.796235,0.814941,0.919079,0.437919,1.06395,1.13627,0.293853,0.335825,1.02226,1.87395,1.47317,0.985665,1.85021,0.70579,1.35552,0.367151,0.534339,1.71519,1.40937,0.403378,1.75094,0.0163338,0.796604,1.62429,1.06491,1.19239,0.494,0.530398,0.260802,0.237047,0.984474,0.778717,0.638755,0.239672,0.564971,0.429983,0.381825,0.410452,0.13471
}}
}}

Revision as of 14:24, 26 November 2012


Full id: C688_Bronchial_Tracheal_Corneal_Prostate_Urothelial_Mallassezderived_Sebocyte



Phase1 CAGE Peaks

Hg19::chr11:66673469..66673482,-p@chr11:66673469..66673482
-
Hg19::chr13:61507880..61507904,-p@chr13:61507880..61507904
-
Hg19::chr1:153533922..153533941,-p@chr1:153533922..153533941
-
Hg19::chr1:153534013..153534025,+p@chr1:153534013..153534025
+
Hg19::chr1:153534027..153534037,+p@chr1:153534027..153534037
+
Hg19::chr1:153536209..153536258,+p@chr1:153536209..153536258
+
Hg19::chr1:153536234..153536259,-p9@S100A2
Hg19::chr1:153536265..153536284,-p11@S100A2
Hg19::chr1:153536308..153536350,-p6@S100A2
Hg19::chr1:153538011..153538030,-p1@S100A2
Hg19::chr1:153538047..153538062,-p2@S100A2
Hg19::chr2:113830230..113830233,-p@chr2:113830230..113830233
-


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
endo-epithelial cell2.53e-4842
endodermal cell6.35e-3358
respiratory epithelial cell1.23e-2813
epithelial cell5.75e-28253
epithelial cell of alimentary canal2.91e-2320
epithelial cell of tracheobronchial tree9.61e-189
epithelial cell of lower respiratory tract9.61e-189
general ecto-epithelial cell1.30e-1714
acinar cell1.29e-155
transitional epithelial cell1.42e-134
urothelial cell1.42e-134
protein secreting cell5.84e-136
squamous epithelial cell1.32e-1263
bronchial epithelial cell3.22e-113
duct epithelial cell4.33e-113
branched duct epithelial cell4.33e-113
tracheal epithelial cell4.33e-113
tracheoblast4.33e-113
epithelial cell of Malassez9.46e-113
gingival epithelial cell1.08e-103
acinar cell of salivary gland3.71e-103
embryonic cell1.73e-09250
ecto-epithelial cell2.96e-0934
glandular epithelial cell1.60e-089
mammary gland epithelial cell7.30e-084
corneal epithelial cell1.02e-072
sebum secreting cell3.78e-072
epithelial cell of sweat gland3.78e-072
epithelial cell of skin gland3.78e-072
acinar cell of sebaceous gland3.78e-072
Uber Anatomy
Ontology termp-valuen
respiratory system8.93e-2274
oral opening1.59e-2022
orifice3.48e-2036
endoderm-derived structure2.27e-18160
endoderm2.27e-18160
presumptive endoderm2.27e-18160
mouth mucosa2.07e-1713
surface structure2.15e-1799
mouth2.18e-1729
stomodeum2.18e-1729
urothelium5.92e-165
mucosa7.15e-1620
head2.64e-1556
anterior region of body6.15e-1562
craniocervical region6.15e-1562
transitional epithelium3.08e-136
tracheobronchial tree5.82e-1315
lower respiratory tract5.82e-1315
subdivision of head3.16e-1249
mucosa of oral region7.74e-124
respiratory system mucosa7.74e-124
digestive system2.26e-11145
digestive tract2.26e-11145
primitive gut2.26e-11145
lower respiratory tract epithelium3.22e-113
epithelium of bronchus3.22e-113
respiratory tract4.65e-1154
gingival epithelium1.08e-103
thoracic cavity element3.24e-0934
thoracic cavity3.24e-0934
thoracic segment organ6.94e-0935
epithelial fold1.41e-0847
jaw skeleton3.77e-084
splanchnocranium3.77e-084
epithelial bud3.99e-0837
mammary gland7.30e-084
mammary bud7.30e-084
mammary ridge7.30e-084
mammary placode7.30e-084
trachea9.60e-087
respiratory airway9.60e-087
skin gland3.78e-072
epidermis gland3.78e-072
gland of integumental system3.78e-072
sebaceous gland3.78e-072
skin sebaceous gland3.78e-072
sweat gland3.78e-072
sweat gland placode3.78e-072
sebaceous gland placode3.78e-072
subdivision of digestive tract3.89e-07118
segment of respiratory tract4.29e-0747
neck4.98e-0710
bronchus7.44e-075
Disease
Ontology termp-valuen
squamous cell carcinoma1.93e-2714


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.

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