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Coexpression cluster:C544: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;8:2.52247358732942:0.00710763553513563:0.0296309415477419!GATA2#2624;5:3.74850933339823:0.00825039453437635:0.0325131293779991!STAT3#6774;6:3.71275235193679:0.00361806375137964:0.0183119437911479
|tf_chipseq_enrich=CTCF#10664;8:2.52247358732942:0.00710763553513563:0.0296309415477419!GATA2#2624;5:3.74850933339823:0.00825039453437635:0.0325131293779991!STAT3#6774;6:3.71275235193679:0.00361806375137964:0.0183119437911479
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|tfbs_overrepresentation_for_novel_motifs=0.871638,11.7168,0.139625,0.241986,0.364884,0.240734,1.47509,1.61621,1.1367,1.08989,0.218065,0.335828,0.920897,1.44167,0.362746,1.29616,1.22781,0.590721,0.983369,2.18443,0.431825,2.39602,0.234854,0.110606,0.978664,0.354732,2.09166,1.22676,0.115495,2.43859,0.202067,0.522822,0.235149,0.326663,0.311809,1.41681,0.307024,0.241614,1.99589,0.04349,0.0929322,0.190375,0.178207,0.111922,1.29926,0.482397,0.301272,0.21008,0.702528,0.745498,0.366671,0.836154,0.56057,0.592653,1.74242,0.293507,0.118135,0.267557,2.43733,0.736109,0.559896,0.303183,0.423107,0.465305,0.317765,0.4351,0.818746,1.17567,0.513487,1.01727,0.181085,1.65366,0.0128276,0.73304,0.0326098,1.21133,0.479497,0.450429,0.510572,0.165891,1.00731,0.464358,0.317477,0.0530449,0.684728,0.00542149,0.127301,0.44194,0.38876,1.27332,0.90828,0.659533,0.537982,0.0697368,0.114084,0.558858,0.0381258,2.41233,0.392699,2.20467,0.0801198,0.532876,0.571612,0.493139,0.425079,0.214722,0.479058,0.288402,0.169928,0.340143,0.146911,0.569087,0.136085,0.225069,0.862131,0.091073,0.0757057,2.4509,0.433061,1.36396,0.725237,0.386689,0.23864,1.56927,0.968805,0.451097,0.80111,0.542501,0.765493,0.0768182,0.660176,0.204142,0.779127,0.323981,2.12431,0.419578,0.19775,0.233646,0.879842,1.7239,1.32497,0.844052,0.296675,0.573485,0.426604,0.260955,0.412168,1.56567,1.05096,1.33225,0.766653,0.00407349,0.660531,1.54803,0.818076,1.04704,0.374997,0.343221,0.170141,0.459614,0.842888,0.643319,0.509866,0.152845,0.440625,3.22414,0.486038,0.810238,0.341372
}}
}}

Revision as of 14:17, 26 November 2012


Full id: C544_nasal_Keratinocyte_Esophageal_Urothelial_Placental_Corneal_Prostate



Phase1 CAGE Peaks

Hg19::chr17:39775781..39775811,-p@chr17:39775781..39775811
-
Hg19::chr17:39775857..39775872,-p@chr17:39775857..39775872
-
Hg19::chr17:39776987..39777014,-p@chr17:39776987..39777014
-
Hg19::chr17:39777017..39777027,+p@chr17:39777017..39777027
+
Hg19::chr17:39777054..39777079,-p5@KRT17
Hg19::chr17:39777082..39777104,-p6@KRT17
Hg19::chr17:39777267..39777358,-p1@EF608070
Hg19::chr17:39777878..39777913,+p@chr17:39777878..39777913
+
Hg19::chr17:39777922..39777964,-p@chr17:39777922..39777964
-
Hg19::chr17:39777995..39778013,-p@chr17:39777995..39778013
-
Hg19::chr17:39779227..39779270,-p3@KRT17
Hg19::chr17:39780328..39780347,+p@chr17:39780328..39780347
+
Hg19::chr17:39780497..39780517,+p@chr17:39780497..39780517
+
Hg19::chr17:39780530..39780549,-p2@KRT17
Hg19::chr17:39780624..39780631,-p8@KRT17
Hg19::chr17:39780634..39780644,-p4@KRT17
Hg19::chr17:39780819..39780835,-p1@KRT17


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:0005200structural constituent of cytoskeleton0.0347344872247733
GO:0008544epidermis development0.0347344872247733
GO:0007398ectoderm development0.0347344872247733
GO:0045111intermediate filament cytoskeleton0.0347344872247733
GO:0005882intermediate filament0.0347344872247733
GO:0009888tissue development0.0374082577809176



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 cell2.05e-3242
epithelial cell5.99e-32253
endodermal cell4.49e-2358
respiratory epithelial cell4.67e-2213
general ecto-epithelial cell5.84e-1614
epithelial cell of alimentary canal4.21e-1420
epithelial cell of tracheobronchial tree2.93e-139
epithelial cell of lower respiratory tract2.93e-139
transitional epithelial cell1.89e-104
urothelial cell1.89e-104
extraembryonic cell3.24e-1019
bronchial epithelial cell6.40e-093
duct epithelial cell1.70e-083
branched duct epithelial cell1.70e-083
tracheal epithelial cell1.70e-083
tracheoblast1.70e-083
placental epithelial cell2.11e-083
acinar cell3.55e-085
ecto-epithelial cell6.86e-0834
epithelial cell of Malassez1.09e-073
gingival epithelial cell1.12e-073
stratified squamous epithelial cell5.89e-076
keratin accumulating cell5.89e-076
stratified epithelial cell5.89e-076
keratinizing barrier epithelial cell5.89e-076
epithelial fate stem cell5.89e-076
stratified epithelial stem cell5.89e-076
surface ectodermal cell5.89e-076
epidermal cell7.41e-079
protein secreting cell8.51e-076
Uber Anatomy
Ontology termp-valuen
respiratory system1.30e-2574
respiratory tract1.35e-2254
endoderm-derived structure2.78e-22160
endoderm2.78e-22160
presumptive endoderm2.78e-22160
larynx5.76e-199
segment of respiratory tract4.10e-1847
upper respiratory tract6.48e-1719
respiratory primordium1.35e-1538
endoderm of foregut1.35e-1538
extraembryonic membrane1.22e-1414
membranous layer1.22e-1414
digestive system1.38e-12145
digestive tract1.38e-12145
primitive gut1.38e-12145
foregut3.86e-1287
urothelium4.27e-125
organ part1.37e-11218
subdivision of digestive tract2.10e-10118
transitional epithelium5.26e-106
tracheobronchial tree2.33e-0915
lower respiratory tract2.33e-0915
surface structure3.02e-0999
lower respiratory tract epithelium6.40e-093
epithelium of bronchus6.40e-093
oral opening2.04e-0822
chorion2.49e-087
amnion6.21e-087
orifice6.47e-0836
mouth mucosa9.92e-0813
gingival epithelium1.12e-073
extraembryonic structure1.18e-0724
organ segment1.88e-0798
mouth2.81e-0729
stomodeum2.81e-0729
tongue3.05e-073
gustatory system3.05e-073
future tongue3.05e-073
embryonic structure4.03e-07564
somatic layer of lateral plate mesoderm6.81e-078
head9.29e-0756
Disease
Ontology termp-valuen
squamous cell carcinoma5.60e-0914
carcinoma5.89e-08106


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#1066482.522473587329420.007107635535135630.0296309415477419
GATA2#262453.748509333398230.008250394534376350.0325131293779991
STAT3#677463.712752351936790.003618063751379640.0183119437911479



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.