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Coexpression cluster:C3209: Difference between revisions

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|full_id=C3209_renal_anaplastic_Fibroblast_mesenchymal_clear_mucinous_glioblastoma
|full_id=C3209_renal_anaplastic_Fibroblast_mesenchymal_clear_mucinous_glioblastoma
|id=C3209
|id=C3209
|ontology_enrichment_celltype=CL:0000055!4.10e-29!180;CL:0000680!2.58e-13!57;CL:0000056!2.58e-13!57;CL:0000355!2.58e-13!57;CL:0000393!3.25e-13!60;CL:0000211!3.25e-13!60;CL:0000187!2.51e-12!54;CL:0000183!1.22e-10!59;CL:0002620!1.82e-09!23;CL:0000057!2.06e-09!75;CL:0000192!1.07e-08!42;CL:0000514!1.07e-08!42;CL:0000359!5.18e-08!32
|ontology_enrichment_celltype=CL:0000055!3.46e-17!106;CL:0000680!1.17e-14!58;CL:0000056!1.17e-14!58;CL:0000355!1.17e-14!58;CL:0000393!2.49e-14!61;CL:0000211!2.49e-14!61;CL:0000187!1.47e-13!55;CL:0000183!1.33e-12!59;CL:0000192!2.17e-09!43;CL:0000514!2.17e-09!43;CL:0000057!3.24e-09!76;CL:0002620!3.74e-09!23;CL:0000359!4.75e-09!32
|ontology_enrichment_disease=DOID:120!1.57e-07!27;DOID:193!2.31e-07!29
|ontology_enrichment_disease=DOID:120!4.81e-08!27;DOID:193!5.06e-08!29
|ontology_enrichment_uberon=UBERON:0000475!6.61e-27!365;UBERON:0005743!3.12e-18!86;UBERON:0000483!3.40e-18!309;UBERON:0000119!1.39e-17!312;UBERON:0001017!1.78e-17!82;UBERON:0000073!8.33e-17!94;UBERON:0001016!8.33e-17!94;UBERON:0000914!6.50e-16!83;UBERON:0002329!6.50e-16!83;UBERON:0003077!6.50e-16!83;UBERON:0003059!6.50e-16!83;UBERON:0007282!6.50e-16!83;UBERON:0009618!6.50e-16!83;UBERON:0007285!6.50e-16!83;UBERON:0000481!3.55e-15!347;UBERON:0004290!4.93e-15!70;UBERON:0001049!1.68e-14!57;UBERON:0005068!1.68e-14!57;UBERON:0006241!1.68e-14!57;UBERON:0007135!1.68e-14!57;UBERON:0002385!4.76e-14!63;UBERON:0001015!4.76e-14!63;UBERON:0000383!4.76e-14!63;UBERON:0003075!4.88e-14!86;UBERON:0007284!4.88e-14!86;UBERON:0001134!8.29e-14!61;UBERON:0002036!8.29e-14!61;UBERON:0003082!8.29e-14!61;UBERON:0000955!1.06e-13!69;UBERON:0006238!1.06e-13!69;UBERON:0002616!3.82e-13!59;UBERON:0005256!3.97e-13!143;UBERON:0002346!3.31e-12!90;UBERON:0007023!3.58e-12!115;UBERON:0001893!8.46e-12!34;UBERON:0000486!8.92e-12!82;UBERON:0002020!1.36e-11!34;UBERON:0003528!1.36e-11!34;UBERON:0001869!1.64e-11!32;UBERON:0000025!3.01e-11!194;UBERON:0002791!3.12e-11!33;UBERON:0000468!3.33e-11!659;UBERON:0004121!4.23e-11!169;UBERON:0002780!9.94e-11!41;UBERON:0001890!9.94e-11!41;UBERON:0006240!9.94e-11!41;UBERON:0000033!1.10e-10!123;UBERON:0000467!1.42e-10!625;UBERON:0000153!1.96e-10!129;UBERON:0007811!1.96e-10!129;UBERON:0004111!2.05e-10!241;UBERON:0000480!2.15e-10!626;UBERON:0000477!2.69e-10!286;UBERON:0003080!4.15e-10!42;UBERON:0000924!5.04e-10!173;UBERON:0006601!5.04e-10!173;UBERON:0000956!8.04e-10!25;UBERON:0000203!8.04e-10!25;UBERON:0002100!2.09e-09!216;UBERON:0003056!7.09e-09!61;UBERON:0002619!1.83e-08!22;UBERON:0001950!7.20e-08!20;UBERON:0002097!4.79e-07!40;UBERON:0002199!7.73e-07!45;UBERON:0002416!7.73e-07!45
|ontology_enrichment_uberon=UBERON:0000483!7.53e-17!306;UBERON:0000119!3.83e-16!309;UBERON:0000481!7.99e-16!342;UBERON:0003077!3.21e-15!72;UBERON:0007285!3.21e-15!72;UBERON:0002385!3.96e-15!64;UBERON:0001015!3.96e-15!64;UBERON:0000383!3.96e-15!64;UBERON:0001017!5.99e-15!81;UBERON:0001134!9.32e-15!62;UBERON:0002036!9.32e-15!62;UBERON:0003082!9.32e-15!62;UBERON:0007524!1.05e-14!73;UBERON:0002329!1.07e-14!71;UBERON:0003059!1.07e-14!71;UBERON:0007282!1.07e-14!71;UBERON:0004290!1.07e-14!71;UBERON:0009618!1.07e-14!71;UBERON:0010314!1.16e-14!132;UBERON:0001016!4.71e-14!89;UBERON:0001049!2.16e-12!56;UBERON:0005068!2.16e-12!56;UBERON:0006241!2.16e-12!56;UBERON:0007135!2.16e-12!56;UBERON:0000477!4.45e-12!373;UBERON:0007503!5.13e-12!78;UBERON:0000955!1.04e-11!68;UBERON:0006238!1.04e-11!68;UBERON:0000486!1.10e-11!83;UBERON:0001869!1.15e-11!32;UBERON:0000025!1.26e-11!192;UBERON:0001893!1.34e-11!34;UBERON:0000073!1.79e-11!53;UBERON:0002616!1.79e-11!53;UBERON:0000467!2.19e-11!624;UBERON:0000480!3.17e-11!625;UBERON:0003528!3.87e-11!34;UBERON:0002020!3.87e-11!34;UBERON:0000468!4.04e-11!656;UBERON:0003075!4.24e-11!82;UBERON:0007284!4.24e-11!82;UBERON:0003104!4.68e-11!160;UBERON:0009142!4.68e-11!160;UBERON:0002791!5.50e-11!32;UBERON:0000956!6.81e-11!25;UBERON:0000203!6.81e-11!25;UBERON:0005256!7.84e-11!122;UBERON:0002780!1.69e-10!41;UBERON:0001890!1.69e-10!41;UBERON:0003080!1.69e-10!41;UBERON:0006240!1.69e-10!41;UBERON:0004111!2.34e-10!240;UBERON:0007023!3.94e-10!114;UBERON:0002619!6.88e-10!22;UBERON:0002346!1.14e-09!86;UBERON:0004121!2.94e-09!171;UBERON:0000924!2.94e-09!171;UBERON:0006601!2.94e-09!171;UBERON:0001950!3.83e-09!20;UBERON:0010371!1.30e-08!104;UBERON:0003056!3.39e-08!61;UBERON:0000475!8.67e-08!264;UBERON:0002100!1.47e-07!199;UBERON:0011216!2.81e-07!223;UBERON:0000490!5.51e-07!148;UBERON:0002097!6.26e-07!41
|tf_chipseq_enrich=EP300#2033;3:6.7739417262232:0.00321688050010379:0.0166990298996143!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00443230777618575!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156257142924983!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.0064161779784854!USF1#7391;3:6.36149927720796:0.0038840405729056:0.018963363722766
|tf_chipseq_enrich=EP300#2033;3:6.7739417262232:0.00321688050010379:0.0166990298996143!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00443230777618575!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156257142924983!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.0064161779784854!USF1#7391;3:6.36149927720796:0.0038840405729056:0.018963363722766
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2233,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,2.49047e-05,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.00796449,0.0906475,0.0558058,0.28262,0.517717,0.137332,0.0145999,0.00220694,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.0199999,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.00102636,0.370421,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.26144,0.0286025,0.549354,0.144567,0.038848,0.0874516,0.0550279,0.000558597,0.00335855,0.217069,0.190048,0.131088,0.394069,0.237101,0.286988,0.0761239,0.0158143,0.0818785,0.00117737,0.0637246,0.147698,0.141463,0.0148418,0.140622,0.0889592,0.309588,0.0458479,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.131452,0.687347,0.448776,0.051838,0.00511251,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.739716,0.655293,0.21727,0.289306,0.119215,0.192475,0.0168693,0.547859,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.00824114,0.175094,0.911304,0.936279,0.206454,0.000125718,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.0227848,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,6.6846e-06,0.057168,0.234298,0.0759837,0.286863,0.152372,0.194941,0.218271,0.101607,0.327067,0.172982,0.340936,0.0121199,0.0626744,0.191335,0.148574,0.504592,0.155821,0.0718905,0.000138924,3.81507e-05,0.0109522,0.15063,0.0973823,0.15503,0.170295,0.0200941,0.00987736,0.228144,0.251466,0.288096,0.11903,0.0838874,0.00806892,0.113145,0.112651,2.64043e-06,0.174776,0.0948451,0.264079,0.0339656,0.140533,0.0997756,0.257598,5.47758e-06,0.113069,0.025556,0.16791,0.09066,0.585505,0.166967,0.0013029,0.0813902,0.184948,0.156261,0.000604034,0.511859,0.0590944,0.247324,0.0169521,0.218229,0.231073,0.407281,0.619906,0.0360851,0.412187,0.131093,1.02888e-11,0.133616,0.418146,0.0115948,0.449036,0.000211816,0.0291288,0.544776,0.115047,0.0789454,0.42622,3.73344e-05,0.197484,0.396996,0.36145,0.406019,0.381071,0.00201312,0.276075,0.00272579,0.138468,0.390366,0.0305485,0.00559336,0.117158,0.522904,0.875915,0.871256,0.227104,0.166658,0.617852,0.38649,0.0450114,0.156746,0.55194,0.729153,0.0465139,0.164197,0.0252589,0.287881,0.574635,0.138768,0.336276,0.468444,0.258219,0.119142,0.032364,0.777351,0.390974,0.73485,0.683217,0.161598,0.405056,0.644754,8.02175e-05,0.799185,0.000126599,0.78509,0.477353,0.78384,0.746954,0.0629574,0.20342,0.200493,0.20558,0.300504,0.25656,0.0189087,0.349197,0.00154995,0.156104,0.000526011,0.411941,0.0961477,0.314438,0.354789,0.163828,0.230581,0.00753552,0.28424,0.562405,0.314429,0.181415,0.282286,0.0192486,0.616388,0.000215097,0.0374737,0.0073454,0.28903,0.33942,0.0156581,0.0871388,0.00694606,0.802166,0.0433137,0.222037,0.0175112,0.10205,0.128937,0.734551,0.579431,0.204817,0.000401229,0.00049814,0.00583733,0.166905,0.19783,0.0833851,0.316453,0.140384,0.175199,0.332919,0.00137548,0.00101302,0.0164118,0.00124345,0.00780726,0.39088,0.363192,0.236011,0.203486,1.12188e-06,0.375787,0.4466,0.00977892,0.275347,0.000640194,0.305885,0.0317395,6.15454e-07,0.30666,0.303709,0.495883,0.0867777,0.508064,0.250964,0.383276,0.125961,9.18584e-05,0.220231,0.00608438,0.196976,0.191517,0.0254647,0.0145214,0.307334,2.96818e-07,0.283463,0.563586,0.0272975,0.0151656,0.00427533,0.00128492,0.275089,0.0133102,0.47795,7.38448e-06,0.00876091,0.197805,5.57217e-05,0.387069,0.332774,0.52832,0.000506965,0.634365,0.205413,0.17639,0.0779009,0.00446098,0.205298,0.0337138,0.0192444,0.258854,0.00129444,0.0719199,0.264884,0.00081525,0.0195357,0.163057,6.3286e-06,0.000102347,0.0900729,0.0953646,0.166124,0.252184,1.06858e-05,0.255516,0.20753,0.0224033,0.179412,0.193601,0.220904,0.00221755,0.341681,0.310674,0.0257082,0.0211771,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.00899848,0.00178627,0.0335483,0.222339,0.0673329,0.00178902,0.0391817,0.0066506,0.145701,0.0285999,0.00080862,0.228955,0.0151141,0.000750623,0.0660995,0.0521984,0.0455518,0.0398662,0.00160819,0.350452,2.9262e-05,0.120196,0.0986735,0.108462,0.0595618,0.00200124,0.158479,0.220319,0.195218,0.124213,0.259632,0.000570717,0.180606,0.0135229,0.257294,0.0119784,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.00176424,0.141867,0.193031,0.249101,0.115972,7.17934e-06,0.246105,0.173026,0.200432,0.139785,3.5411e-06,0.0315594,3.04938e-05,0.13108,0.256963,0.222798,0.172134,0.0166394,0.0969345,0.202137,0.310405,0.00467879,0.0257454,2.11007e-06,0.202065,0.106739,2.67472e-05,0.0537737,0.0120432,0.078016,0.0407233,0.0537355,0.0577193,0.00371523,5.15979e-06,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,1.34631e-05,0.109171,0.04411,0.066952,0.00414049,0.0367455,0.13497,0.204393,0.295769,0.0457063,0.347036,0.141729,0.0381402,0.0359756,0.200105,0.227491,0.2983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}}
}}

Revision as of 14:54, 19 October 2012


Full id: C3209_renal_anaplastic_Fibroblast_mesenchymal_clear_mucinous_glioblastoma



Phase1 CAGE Peaks

Hg19::chr11:85430088..85430151,-p2@SYTL2
Hg19::chr11:85430163..85430200,-p3@SYTL2
Hg19::chr11:85430204..85430243,-p5@SYTL2


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>

Uber Anatomy
Ontology termp-valuen
epithelium7.53e-17306
cell layer3.83e-16309
multi-tissue structure7.99e-16342
paraxial mesoderm3.21e-1572
presumptive paraxial mesoderm3.21e-1572
muscle tissue3.96e-1564
musculature3.96e-1564
musculature of body3.96e-1564
central nervous system5.99e-1581
skeletal muscle tissue9.32e-1562
striated muscle tissue9.32e-1562
myotome9.32e-1562
dense mesenchyme tissue1.05e-1473
somite1.07e-1471
presomitic mesoderm1.07e-1471
presumptive segmental plate1.07e-1471
dermomyotome1.07e-1471
trunk paraxial mesoderm1.07e-1471
structure with developmental contribution from neural crest1.16e-14132
nervous system4.71e-1489
neural tube2.16e-1256
neural rod2.16e-1256
future spinal cord2.16e-1256
neural keel2.16e-1256
anatomical cluster4.45e-12373
epithelial vesicle5.13e-1278
brain1.04e-1168
future brain1.04e-1168
multilaminar epithelium1.10e-1183
cerebral hemisphere1.15e-1132
tube1.26e-11192
telencephalon1.34e-1134
regional part of nervous system1.79e-1153
regional part of brain1.79e-1153
anatomical system2.19e-11624
anatomical group3.17e-11625
brain grey matter3.87e-1134
gray matter3.87e-1134
multi-cellular organism4.04e-11656
neural plate4.24e-1182
presumptive neural plate4.24e-1182
mesenchyme4.68e-11160
entire embryonic mesenchyme4.68e-11160
regional part of telencephalon5.50e-1132
cerebral cortex6.81e-1125
pallium6.81e-1125
trunk mesenchyme7.84e-11122
regional part of forebrain1.69e-1041
forebrain1.69e-1041
anterior neural tube1.69e-1041
future forebrain1.69e-1041
anatomical conduit2.34e-10240
adult organism3.94e-10114
regional part of cerebral cortex6.88e-1022
neurectoderm1.14e-0986
ectoderm-derived structure2.94e-09171
ectoderm2.94e-09171
presumptive ectoderm2.94e-09171
neocortex3.83e-0920
ecto-epithelium1.30e-08104
pre-chordal neural plate3.39e-0861
organism subdivision8.67e-08264
trunk1.47e-07199
organ system subdivision2.81e-07223
unilaminar epithelium5.51e-07148
skin of body6.26e-0741
Disease
Ontology termp-valuen
female reproductive organ cancer4.81e-0827
reproductive organ cancer5.06e-0829


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
EP300#203336.77394172622320.003216880500103790.0166990298996143
JUN#3725312.51282919233630.0005103313992726250.00443230777618575
JUND#372736.994663941871030.002921845042734990.0156257142924983
STAT3#6774310.51946499715420.0008589184530415310.0064161779784854
USF1#739136.361499277207960.00388404057290560.018963363722766



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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