Personal tools

Coexpression cluster:C689: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0.0724992894770213,0.042127323255851,0,0,0,0,0,0,0,0.856491707063834,1.74644970483262,0.50302948658008,0.657405884776523,0,0,0,0,0,0,0,0,0,0,0,0.0256809761409315,0,0,0,0,0,0,0.896909805419262,0.643442433824134,0.595010285899821,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.066999117963169,0,0.459845357397929,0,0,0.0392295810357272,0.544854213062532,0.422529769381778,0.027549189648299,0,0.136969166919767,0,0,0,0,0,0,0.0393665576067778,0,0.219672789380753,0.194599788733868,0.390814988305917,0.62721505149791,0.237625718238676,0.0499122467204788,0,0,0.256635648918622,0.122789903474634,0.0474210224034912,0.135979123430744,0.974442620142268,0,0,0,0,0,0.104318881509615,0,0,0.498369919101481,0.0876068315883375,0.0517815087208527,0,0,0.131832994540557,0.259963295066464,0.315443408671468,0.317501257906926,0,0.0548851394659095,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0466637702013911,0.133148912944135,0.084060318828564,0,0.056986891976762,0,0.214591368372661,0.074127477864629,0.126310890838218,0.175385447870597,0.0488773853372077,0,0,0,0.0416895219742318,0.068022726550833,0.479335725161584,0,0.196896883446942,0,0,0.0477396614475454,0,0,0,0,0.107850623000567,0,0,0,0.541996267543568,0.652238758182793,0.561478013548184,0.670148475077397,0.681402360394857,0.53663195985979,0.526193378239061,0.498632361433045,0.567406366261856,0,0,0.149703653910611,0,0,0,0,0,0,0.203627521222391,0.332777351830361,0,0,0.0561198889326417,0,0,0.488776012972257,0,0.131049308664644,0,0.0826200127416755,0,0,0,0,0,0,0,0.0966155181422749,0.0287902832834152,0.256189536348066,0.438353026499584,0.51560264211527,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.490721392993681,0.272197595679984,1.05007848118756,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.424168535411478,0.233938840156098,0.212403275340347,0.0481081524026529,0,0,0,0,0,0,0,0,0,0,0,0.450058936364808,0.425591991369837,0.449376834911192,0.0481260500124022,0.16446763709968,0.380808071780009,0.0990858576492829,0,0.168441447192827,0.395183177140817,0,0,0,0,0,0,1.15053395748371,0.53560237182587,0.0684883245749248,0,0,0.363601659769023,0.263082373017921,0,0.195590414110735,0.101326563843197,0,0.0682206429897042,0.0849035433286077,0,0,0,0.356863288375568,0.589571578454396,0.160693426449034,0,0,0.139477774314491,0.890136850361422,0.536114973851412,0.0813768443325499,0,0,0,0.28962519419462,0,0,0,0,0,0,0,0,0,0.561644942994249,0.703474091745823,0.365128926412535,0.458029175950908,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.11721277736131,0,0,0.0203504163566182,0,0,0,0,0,0,0.125777638903371,0.558668719869382,0.655660899559718,0.0749215657724743,0.457186815895515,0.835364850731378,0.367410057325623,0.126997852997145,0,0,0,0,0,0,0,0,0,0,0.488607994576353,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.138075567776705,0,0,0,0,0.363614307653431,0.202469070812448,0.162159494019219,0,0,0,0,0.265879043943754,0.0394544993028877,0,0,0,0,0,0.65229473894443,0.532272350340448,0,0.0408567533019575,0,0,0,0,0,0,0.115736199425214,0,0,0.533141750877929,0.495195809741345,0,0,0,0,0,0,0,0,0,0.20364026719403,0,0,0,0,0.335828723562909,0.0650945893050404,0.601080750939192,0.511056444914176,1.10126243212683,0,0,0,0,0,0,0,0,0,0.296532874566658,0,0,0,0,0,0,0,0,0,0,0,0,0.225821697000685,0,0.0722224018548135,0,0,0,0,0,0,0.220626815433903,0.118573193298914,0,0.231876585133011,0,0.327638476076582,0,0.335334233093074,0.0349684140344003,0,0.352090688837915,0.238270264445636,0.329490236928856,0,0,0.0442418239009707,0,0,0,0.615826173178679,0.158457778539378,0.154395360924333,0.716952975013758,0.109976833388356,0,0,0.109952815588116,0,0.619812894960929,0,0,0,0,0,0,0,0.212334095534857,0,0,0,0,0.25496259830806,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0778639055112537,0,0.0435981622194311,0,0.369847608197732,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.247438606465559,0.11583863179761,0.153250317994279,0.0634100406668813,0.150522826464445,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0921527833256962,0,0.0626808480570541,0,0,0.182341901105911,0.0607951148206197,0.288406800485004,0.258575382110128,0,0.242685017699519,0,0,0,0,0,0,0,0.4656975136876,0.519567898567975,1.3318952101731,0.783608870413655,0.851354323258103,0.876416024455346,0.699395523187481,0.857866273159477,0.127686160120224,1.09945143458074,0.568110546001944,0,0.064430608766392,0.572260327223744,0,0,0,0,0,0.596517365589807,0.443752472664903,0,0,0,0,0,0.21164269262322,0.333691421496995,0,0,0,0,0,0,0,0,0.290927460291345,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.80595832276446,0,0,0,0,0,0,0.0505136221569435,0.55706090578371,0.450882104087609,0,0,0,0,0,0.321498084569989,0,0,0,0,0,0,0,0.284833564819988,0,0,0,0,0.442935400151253,0.261650899053765,0.032817368032432,0,0,0,0,0,0,0,0,0,0,0.180269448356156,0,0,0.155405081403798,0,0,0.430324751605904,0.669108642238077,0.0586698558795205,0.291266468109506,0.36156440012121,0.224168339771827,0,0,0,0,0,0,0,0,0,0,0.0610613035651264,0,0,0.335066156333804,0,0,0,0,0,0.282788418069102,0,0,0,0,0,0.21483565429053,0,0.282725988318231,0,0,0,0,0,0,0,0,0,0,0,0.0421771923324582,0,0.0381808373167472,0,0,0,0,0,0.0839445661171913,0.092743246865863,0,0,0.729849758078913,0.275719197973553,0.417793352497445,0,0,0.0141538448872959,0.132489128796425,0.124719478691449,0.228256120657282,0.170059447469222,0,0,0,0,0,0,0,0
|full_id=C689_Alveolar_mesothelioma_Retinal_Mesothelial_Prostate_bile_Tracheal
|full_id=C689_Alveolar_mesothelioma_Retinal_Mesothelial_Prostate_bile_Tracheal
|id=C689
|id=C689

Revision as of 18:21, 12 September 2012


Full id: C689_Alveolar_mesothelioma_Retinal_Mesothelial_Prostate_bile_Tracheal



Phase1 CAGE Peaks

Hg19::chr11:67232723..67232762,-p2@TMEM134
Hg19::chr12:52627019..52627037,+p1@KRT7
Hg19::chr12:52628993..52629014,+p@chr12:52628993..52629014
+
Hg19::chr12:52629037..52629072,+p@chr12:52629037..52629072
+
Hg19::chr12:52629080..52629112,+p@chr12:52629080..52629112
+
Hg19::chr12:52629130..52629159,-p@chr12:52629130..52629159
-
Hg19::chr12:52635300..52635325,+p9@KRT7
Hg19::chr12:52636796..52636807,+p26@KRT7
Hg19::chr12:52636827..52636840,+p3@KRT7
Hg19::chr12:52639223..52639262,+p6@KRT7
Hg19::chr12:52642466..52642508,+p@chr12:52642466..52642508
+
Hg19::chr12:52642530..52642567,+p@chr12:52642530..52642567
+


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 cell3.84e-45254
squamous epithelial cell5.84e-1462
embryonic cell8.44e-14248
lining cell2.12e-1257
barrier cell2.12e-1257
mesothelial cell1.68e-0919
endo-epithelial cell8.84e-0943
mesodermal cell3.87e-08119
meso-epithelial cell1.91e-0744
respiratory epithelial cell3.45e-0713
endodermal cell3.97e-0759
Uber Anatomy
Ontology termp-valuen
primordium1.37e-18168
endoderm-derived structure2.97e-18169
endoderm2.97e-18169
presumptive endoderm2.97e-18169
immaterial anatomical entity4.27e-16126
anatomical space9.67e-16104
mixed endoderm/mesoderm-derived structure1.28e-15130
mesenchyme6.27e-14238
entire embryonic mesenchyme6.27e-14238
digestive system2.45e-13155
digestive tract2.45e-13155
primitive gut2.45e-13155
subdivision of digestive tract4.27e-12129
endodermal part of digestive tract4.27e-12129
foregut4.34e-1298
respiratory tract6.44e-1153
trunk1.16e-10216
anatomical cavity1.42e-1070
respiratory system2.01e-1072
subdivision of trunk3.28e-10113
respiratory primordium6.91e-1038
endoderm of foregut6.91e-1038
anatomical cluster8.13e-10286
multi-tissue structure8.22e-10347
epithelial tube2.12e-09118
body cavity precursor2.63e-0963
multi-cellular organism2.86e-09659
endo-epithelium5.08e-0982
cell layer6.30e-09312
epithelium9.03e-09309
trunk region element1.04e-08107
intermediate mesoderm1.24e-0837
organ segment1.66e-0897
segment of respiratory tract2.47e-0846
duct4.40e-0826
anatomical system4.97e-08625
anatomical group7.80e-08626
organ part1.20e-07219
extraembryonic membrane2.12e-0714
membranous layer2.12e-0714
epithelial bud2.76e-0737
thoracic segment of trunk3.34e-0752
renal system3.36e-0745
mesoderm4.49e-07448
mesoderm-derived structure4.49e-07448
presumptive mesoderm4.49e-07448
urinary system structure4.76e-0744
ectodermal placode6.73e-0729
larynx7.22e-079
unilaminar epithelium7.76e-07138
urogenital ridge9.17e-0720
Disease
Ontology termp-valuen
carcinoma9.69e-09106


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.