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Coexpression cluster:C594: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0005631!5.18e-24!14;UBERON:0000158!5.18e-24!14;UBERON:0003124!3.21e-20!7;UBERON:0000166!9.07e-17!22;UBERON:0004119!6.94e-16!160;UBERON:0000925!6.94e-16!160;UBERON:0006595!6.94e-16!160;UBERON:0001004!2.02e-15!74;UBERON:0000165!3.03e-14!29;UBERON:0000930!3.03e-14!29;UBERON:0003102!1.24e-13!99;UBERON:0000161!5.66e-13!36;UBERON:0000478!5.74e-13!24;UBERON:0000033!1.29e-12!56;UBERON:0000153!2.40e-12!62;UBERON:0007811!2.40e-12!62;UBERON:0001987!4.52e-12!4;UBERON:0004340!4.52e-12!4;UBERON:0004923!2.10e-11!66;UBERON:0004815!1.55e-10!3;UBERON:0002031!1.55e-10!3;UBERON:0001949!1.70e-10!3;UBERON:0003729!3.58e-10!13;UBERON:0001444!4.51e-10!49;UBERON:0000476!7.18e-10!3;UBERON:0000920!7.18e-10!3;UBERON:0000365!1.00e-09!5;UBERON:0007196!4.13e-09!15;UBERON:0001558!4.13e-09!15;UBERON:0005910!4.18e-08!6;UBERON:0000344!4.91e-08!20;UBERON:0000065!8.79e-08!54;UBERON:0001911!2.39e-07!4;UBERON:0005333!2.39e-07!4;UBERON:0008425!2.39e-07!4;UBERON:0005311!2.39e-07!4;UBERON:0000305!2.85e-07!7;UBERON:0001708!3.69e-07!4;UBERON:0008895!3.69e-07!4;UBERON:0002419!4.01e-07!2;UBERON:0007771!4.01e-07!2;UBERON:0003297!4.01e-07!2;UBERON:0001821!4.01e-07!2;UBERON:0003487!4.01e-07!2;UBERON:0001820!4.01e-07!2;UBERON:0005089!4.01e-07!2;UBERON:0005088!4.01e-07!2;UBERON:0003126!7.32e-07!7;UBERON:0001005!7.32e-07!7
|ontology_enrichment_uberon=UBERON:0005631!5.18e-24!14;UBERON:0000158!5.18e-24!14;UBERON:0003124!3.21e-20!7;UBERON:0000166!9.07e-17!22;UBERON:0004119!6.94e-16!160;UBERON:0000925!6.94e-16!160;UBERON:0006595!6.94e-16!160;UBERON:0001004!2.02e-15!74;UBERON:0000165!3.03e-14!29;UBERON:0000930!3.03e-14!29;UBERON:0003102!1.24e-13!99;UBERON:0000161!5.66e-13!36;UBERON:0000478!5.74e-13!24;UBERON:0000033!1.29e-12!56;UBERON:0000153!2.40e-12!62;UBERON:0007811!2.40e-12!62;UBERON:0001987!4.52e-12!4;UBERON:0004340!4.52e-12!4;UBERON:0004923!2.10e-11!66;UBERON:0004815!1.55e-10!3;UBERON:0002031!1.55e-10!3;UBERON:0001949!1.70e-10!3;UBERON:0003729!3.58e-10!13;UBERON:0001444!4.51e-10!49;UBERON:0000476!7.18e-10!3;UBERON:0000920!7.18e-10!3;UBERON:0000365!1.00e-09!5;UBERON:0007196!4.13e-09!15;UBERON:0001558!4.13e-09!15;UBERON:0005910!4.18e-08!6;UBERON:0000344!4.91e-08!20;UBERON:0000065!8.79e-08!54;UBERON:0001911!2.39e-07!4;UBERON:0005333!2.39e-07!4;UBERON:0008425!2.39e-07!4;UBERON:0005311!2.39e-07!4;UBERON:0000305!2.85e-07!7;UBERON:0001708!3.69e-07!4;UBERON:0008895!3.69e-07!4;UBERON:0002419!4.01e-07!2;UBERON:0007771!4.01e-07!2;UBERON:0003297!4.01e-07!2;UBERON:0001821!4.01e-07!2;UBERON:0003487!4.01e-07!2;UBERON:0001820!4.01e-07!2;UBERON:0005089!4.01e-07!2;UBERON:0005088!4.01e-07!2;UBERON:0003126!7.32e-07!7;UBERON:0001005!7.32e-07!7
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|tfbs_overrepresentation_for_novel_motifs=0.172755,4.95726,0.167518,0.277483,0.429786,0.276158,0.338925,1.33368,0.875714,0.746147,0.252096,1.74161,0.177832,0.329255,0.843993,0.467196,0.534852,1.68137,0.19463,1.62766,0.501333,1.17624,0.743358,0.135481,0.200668,0.395548,0.9801,0.268197,0.140919,0.568017,0.235027,0.568576,1.01289,0.405736,0.749865,1.79116,0.114552,0.759737,0.100329,0.212026,0.115672,0.222502,0.118046,1.3579,0.565712,0.189598,0.339845,0.243586,0.394038,1.38293,0.407934,0.349819,0.428224,0.639823,0.784252,0.331716,0.442382,0.304469,0.896459,0.303639,0.606437,0.341844,2.41189,0.509653,0.357077,0.478604,0.869007,1.22829,0.559029,1.06908,0.212516,0.908623,0.420444,0.782342,0.171892,0.357608,0.0348214,0.494371,1.36852,0.196113,0.774709,0.50868,0.356776,0.0697103,0.733386,0.00154893,0.0669348,0.550078,0.430803,1.32629,0.95934,0.70782,0.584068,1.04207,1.37276,2.20567,0.427968,0.623577,0.434875,0.789337,0.10113,0.578851,0.618385,0.538198,1.18153,0.248535,0.523764,0.326366,0.20048,0.128402,0.520729,0.61581,0.49168,0.259545,4.9646,1.76541,0.117386,0.660476,0.476505,1.55923,1.82408,0.428661,0.273941,0.366411,1.02031,0.495057,0.33358,0.588683,0.815183,0.0973529,0.708473,0.237246,0.828971,0.363559,2.22871,0.836754,0.651842,0.268649,0.930667,1.77777,1.3781,0.894557,0.335034,0.620293,2.06075,0.297516,2.98737,1.61933,0.219968,0.0873523,0.0167889,0.00708394,0.708834,0.489782,0.904639,1.09904,0.41656,0.129698,0.200711,0.179634,0.893382,0.691354,1.36699,0.536459,0.48429,0.356103,0.275921,0.337803,0.0505796
}}
}}

Revision as of 14:20, 26 November 2012


Full id: C594_Keratinocyte_Placental_amniotic_Esophageal_tongue_Corneal_Prostate



Phase1 CAGE Peaks

Hg19::chr12:52867616..52867640,-p2@KRT6C
Hg19::chr12:52881014..52881084,-p@chr12:52881014..52881084
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Hg19::chr12:52881094..52881129,-p@chr12:52881094..52881129
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Hg19::chr12:52881151..52881162,-p@chr12:52881151..52881162
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Hg19::chr12:52881340..52881386,-p@chr12:52881340..52881386
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Hg19::chr12:52881401..52881421,-p@chr12:52881401..52881421
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Hg19::chr12:52881422..52881438,-p@chr12:52881422..52881438
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Hg19::chr12:52881440..52881469,-p@chr12:52881440..52881469
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Hg19::chr12:52881475..52881528,-p@chr12:52881475..52881528
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Hg19::chr12:52884399..52884420,-p7@KRT6A
Hg19::chr12:52885340..52885349,-p10@KRT6A
Hg19::chr12:52885355..52885376,-p2@KRT6A
Hg19::chr12:52886485..52886506,-p6@KRT6A
Hg19::chr12:52886515..52886548,-p4@KRT6A
Hg19::chr12:52887034..52887049,-p1@KRT6A


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

GO IDGO nameFDR corrected p-value
GO:0045111intermediate filament cytoskeleton0.00086501357605482
GO:0005882intermediate filament0.00086501357605482
GO:0044430cytoskeletal part0.00875313881962261
GO:0005856cytoskeleton0.0156475434545066
GO:0005200structural constituent of cytoskeleton0.0359851262584485
GO:0043232intracellular non-membrane-bound organelle0.037983235872607
GO:0043228non-membrane-bound organelle0.037983235872607
GO:0007398ectoderm development0.0385963645451909
GO:0008284positive regulation of cell proliferation0.0483587763804884
GO:0044446intracellular organelle part0.0483587763804884
GO:0044422organelle part0.0483587763804884



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 cell3.00e-3242
respiratory epithelial cell4.93e-2213
endodermal cell1.31e-2158
epithelial cell1.27e-20253
general ecto-epithelial cell5.19e-2014
epithelial cell of alimentary canal1.20e-1520
acinar cell6.02e-155
extraembryonic cell3.08e-1419
protein secreting cell2.12e-126
transitional epithelial cell3.79e-124
urothelial cell3.79e-124
epithelial cell of tracheobronchial tree5.02e-129
epithelial cell of lower respiratory tract5.02e-129
bronchial epithelial cell1.55e-103
gingival epithelial cell1.70e-103
ecto-epithelial cell2.96e-1034
chorionic membrane mesenchymal stem cell7.18e-103
placental epithelial cell7.63e-103
duct epithelial cell1.31e-093
branched duct epithelial cell1.31e-093
tracheal epithelial cell1.31e-093
tracheoblast1.31e-093
acinar cell of salivary gland1.66e-093
epithelial cell of Malassez2.03e-093
epidermal cell1.90e-089
stratified squamous epithelial cell2.13e-086
keratin accumulating cell2.13e-086
stratified epithelial cell2.13e-086
keratinizing barrier epithelial cell2.13e-086
epithelial fate stem cell2.13e-086
stratified epithelial stem cell2.13e-086
surface ectodermal cell2.13e-086
glandular epithelial cell3.81e-089
corneal epithelial cell2.23e-072
mammary gland epithelial cell2.39e-074
sebum secreting cell4.01e-072
epithelial cell of sweat gland4.01e-072
epithelial cell of skin gland4.01e-072
acinar cell of sebaceous gland4.01e-072
squamous epithelial cell7.69e-0763
Uber Anatomy
Ontology termp-valuen
extraembryonic membrane5.18e-2414
membranous layer5.18e-2414
chorion3.21e-207
oral opening9.07e-1722
endoderm-derived structure6.94e-16160
endoderm6.94e-16160
presumptive endoderm6.94e-16160
respiratory system2.02e-1574
mouth3.03e-1429
stomodeum3.03e-1429
surface structure1.24e-1399
orifice5.66e-1336
extraembryonic structure5.74e-1324
head1.29e-1256
anterior region of body2.40e-1262
craniocervical region2.40e-1262
placenta4.52e-124
allantois4.52e-124
organ component layer2.10e-1166
lower respiratory tract epithelium1.55e-103
epithelium of bronchus1.55e-103
gingival epithelium1.70e-103
mouth mucosa3.58e-1013
subdivision of head4.51e-1049
acellular anatomical structure7.18e-103
egg chorion7.18e-103
urothelium1.00e-095
tracheobronchial tree4.13e-0915
lower respiratory tract4.13e-0915
transitional epithelium4.18e-086
mucosa4.91e-0820
respiratory tract8.79e-0854
mammary gland2.39e-074
mammary bud2.39e-074
mammary ridge2.39e-074
mammary placode2.39e-074
amnion2.85e-077
jaw skeleton3.69e-074
splanchnocranium3.69e-074
skin gland4.01e-072
epidermis gland4.01e-072
gland of integumental system4.01e-072
sebaceous gland4.01e-072
skin sebaceous gland4.01e-072
sweat gland4.01e-072
sweat gland placode4.01e-072
sebaceous gland placode4.01e-072
trachea7.32e-077
respiratory airway7.32e-077
Disease
Ontology termp-valuen
squamous cell carcinoma1.49e-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

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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