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Coexpression cluster:C3291: Difference between revisions

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|ontology_enrichment_disease=DOID:305!2.90e-11!106;DOID:0050687!1.68e-09!143;DOID:14566!1.06e-07!239;DOID:162!1.46e-07!235
|ontology_enrichment_disease=DOID:305!2.90e-11!106;DOID:0050687!1.68e-09!143;DOID:14566!1.06e-07!239;DOID:162!1.46e-07!235
|ontology_enrichment_uberon=UBERON:0003914!5.10e-23!118;UBERON:0000490!3.30e-20!138;UBERON:0003104!2.29e-18!238;UBERON:0009142!2.29e-18!238;UBERON:0001048!1.47e-17!168;UBERON:0002049!2.37e-17!79;UBERON:0007798!2.37e-17!79;UBERON:0002100!4.70e-16!216;UBERON:0000466!5.59e-15!126;UBERON:0000481!8.95e-15!347;UBERON:0004119!3.15e-14!169;UBERON:0000925!3.15e-14!169;UBERON:0006595!3.15e-14!169;UBERON:0004872!1.81e-13!84;UBERON:0000477!6.05e-13!286;UBERON:0000055!7.93e-13!69;UBERON:0005177!1.22e-12!107;UBERON:0000119!1.33e-12!312;UBERON:0004535!1.83e-12!110;UBERON:0000483!5.78e-12!309;UBERON:0005256!6.98e-12!143;UBERON:0004921!1.13e-11!129;UBERON:0004185!1.13e-11!129;UBERON:0001007!1.32e-11!155;UBERON:0001555!1.32e-11!155;UBERON:0007026!1.32e-11!155;UBERON:0001009!2.08e-11!113;UBERON:0001981!3.60e-11!60;UBERON:0007500!3.60e-11!60;UBERON:0004537!3.60e-11!60;UBERON:0006965!3.60e-11!60;UBERON:0009569!1.12e-10!113;UBERON:0000464!1.30e-10!104;UBERON:0000077!2.02e-10!130;UBERON:0004111!2.16e-10!241;UBERON:0005911!2.23e-10!82;UBERON:0000487!5.82e-10!22;UBERON:0001041!8.03e-10!98;UBERON:0000926!1.93e-09!448;UBERON:0004120!1.93e-09!448;UBERON:0006603!1.93e-09!448;UBERON:0006554!6.96e-09!44;UBERON:0001986!7.05e-09!18;UBERON:0004638!7.05e-09!18;UBERON:0004852!7.05e-09!18;UBERON:0000475!1.07e-08!365;UBERON:0001008!1.12e-08!45;UBERON:0005172!1.48e-08!55;UBERON:0005173!1.48e-08!55;UBERON:0000468!2.52e-08!659;UBERON:0000058!3.60e-08!26;UBERON:0002417!4.19e-08!61;UBERON:0000916!4.19e-08!61;UBERON:0006914!3.16e-07!25;UBERON:0002553!3.42e-07!70;UBERON:0001637!3.45e-07!42;UBERON:0003509!3.45e-07!42;UBERON:0004572!3.45e-07!42;UBERON:0000025!3.94e-07!194;UBERON:0003929!5.40e-07!54;UBERON:0000467!6.08e-07!625;UBERON:0003886!7.14e-07!63;UBERON:0000063!9.57e-07!97
|ontology_enrichment_uberon=UBERON:0003914!5.10e-23!118;UBERON:0000490!3.30e-20!138;UBERON:0003104!2.29e-18!238;UBERON:0009142!2.29e-18!238;UBERON:0001048!1.47e-17!168;UBERON:0002049!2.37e-17!79;UBERON:0007798!2.37e-17!79;UBERON:0002100!4.70e-16!216;UBERON:0000466!5.59e-15!126;UBERON:0000481!8.95e-15!347;UBERON:0004119!3.15e-14!169;UBERON:0000925!3.15e-14!169;UBERON:0006595!3.15e-14!169;UBERON:0004872!1.81e-13!84;UBERON:0000477!6.05e-13!286;UBERON:0000055!7.93e-13!69;UBERON:0005177!1.22e-12!107;UBERON:0000119!1.33e-12!312;UBERON:0004535!1.83e-12!110;UBERON:0000483!5.78e-12!309;UBERON:0005256!6.98e-12!143;UBERON:0004921!1.13e-11!129;UBERON:0004185!1.13e-11!129;UBERON:0001007!1.32e-11!155;UBERON:0001555!1.32e-11!155;UBERON:0007026!1.32e-11!155;UBERON:0001009!2.08e-11!113;UBERON:0001981!3.60e-11!60;UBERON:0007500!3.60e-11!60;UBERON:0004537!3.60e-11!60;UBERON:0006965!3.60e-11!60;UBERON:0009569!1.12e-10!113;UBERON:0000464!1.30e-10!104;UBERON:0000077!2.02e-10!130;UBERON:0004111!2.16e-10!241;UBERON:0005911!2.23e-10!82;UBERON:0000487!5.82e-10!22;UBERON:0001041!8.03e-10!98;UBERON:0000926!1.93e-09!448;UBERON:0004120!1.93e-09!448;UBERON:0006603!1.93e-09!448;UBERON:0006554!6.96e-09!44;UBERON:0001986!7.05e-09!18;UBERON:0004638!7.05e-09!18;UBERON:0004852!7.05e-09!18;UBERON:0000475!1.07e-08!365;UBERON:0001008!1.12e-08!45;UBERON:0005172!1.48e-08!55;UBERON:0005173!1.48e-08!55;UBERON:0000468!2.52e-08!659;UBERON:0000058!3.60e-08!26;UBERON:0002417!4.19e-08!61;UBERON:0000916!4.19e-08!61;UBERON:0006914!3.16e-07!25;UBERON:0002553!3.42e-07!70;UBERON:0001637!3.45e-07!42;UBERON:0003509!3.45e-07!42;UBERON:0004572!3.45e-07!42;UBERON:0000025!3.94e-07!194;UBERON:0003929!5.40e-07!54;UBERON:0000467!6.08e-07!625;UBERON:0003886!7.14e-07!63;UBERON:0000063!9.57e-07!97
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517717,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.26144,0.0286025,0.549354,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.237101,0.00501606,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.131452,0.687347,0.448776,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.739716,0.0926491,0.21727,0.289306,0.119215,0.192475,0.177967,0.547859,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.911304,0.76084,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.0277579,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.0298844,0.0759837,0.286863,0.152372,0.194941,0.218271,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.504592,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.0597157,0.166967,0.188651,0.0813902,0.184948,0.156261,0.0546539,0.511859,0.0590944,0.247324,0.178389,0.218229,0.0290303,0.407281,0.619906,0.0360851,0.412187,0.131093,0.0434602,0.133616,0.0177337,0.0785808,0.00328135,0.0973145,0.231447,0.544776,0.43956,0.37006,0.10748,0.448797,0.197484,0.396996,0.36145,0.406019,0.381071,0.580441,0.643768,0.432035,0.138468,0.390366,0.145312,0.50058,0.443185,0.522904,0.875915,0.871256,0.227104,0.518585,0.0734371,0.38649,0.284625,0.504757,0.55194,0.729153,0.28907,0.00084117,0.0252589,0.00506733,0.574635,0.478174,0.336276,0.00403041,0.258219,0.446557,0.243383,0.777351,0.390974,0.0458848,0.319063,0.161598,0.0527155,0.644754,0.496032,0.0239796,0.0805771,0.78509,0.477353,0.78384,0.746954,0.771991,0.20342,0.200493,0.20558,0.300504,0.25656,0.0189087,0.349197,0.383291,0.156104,0.141318,0.0168417,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.562405,0.314429,0.181415,0.282286,0.0674279,0.616388,0.0978616,0.516511,0.322213,0.656109,0.33942,0.61031,0.387276,0.169614,0.221908,0.0433137,0.222037,0.416621,0.416292,0.128937,0.734551,0.215157,0.204817,0.452428,0.138871,0.673493,0.166905,0.19783,0.0833851,0.316453,0.48065,0.175199,0.332919,0.00137548,0.170369,0.0980968,0.365487,0.0425451,0.0889149,0.0758087,0.236011,0.203486,0.273398,0.375787,0.4466,8.80437e-05,0.0419637,0.637444,0.305885,0.0317395,0.0118241,0.30666,0.303709,0.495883,0.00161207,0.035296,0.250964,0.383276,0.00360665,0.504711,0.220231,0.509064,0.196976,0.191517,0.463751,0.0663581,0.307334,0.459728,0.283463,0.563586,0.00422311,0.399569,0.273281,0.368095,0.275089,0.384593,0.47795,0.359231,0.339729,0.197805,0.24107,0.387069,0.332774,0.52832,0.299887,0.634365,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.0192444,0.258854,0.188263,0.0719199,0.264884,0.0139948,0.19104,0.163057,0.219428,0.0233135,0.0900729,0.0953646,0.166124,0.252184,0.0828367,0.255516,0.20753,0.119514,0.179412,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.0213665,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.00394192,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.0218443,0.350452,0.0126763,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.0204324,0.124213,0.259632,0.30793,0.0173907,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.0367308,0.261744,0.203781,0.21382,0.0232077,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.036274,0.222798,0.172134,0.176789,0.0969345,0.202137,0.0541163,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.00312563,0.0407233,0.0537355,0.0577193,0.261724,0.0240944,0.187731,0.233626,0.189559,0.00339727,0.0981146,0.064145,0.0077532,0.0638699,0.0056723,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.0497481,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.0229018,0.19924,0.28689,0.236464,0.325148,0.00698179,0.218052,0.223831,0.11528,0.194982,0.0195259,0.281727,0.000393044,0.0342254,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.0228361,0.361435
}}
}}

Revision as of 13:45, 5 September 2012


Full id: C3291_large_Fibroblast_Mesenchymal_anaplastic_Renal_cervical_Pericytes



Phase1 CAGE Peaks

Hg19::chr12:53343573..53343584,-p6@KRT8
Hg19::chr12:53343602..53343631,-p3@KRT8
Hg19::chr12:53343633..53343696,-p2@KRT8


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 cell1.02e-34254
embryonic cell4.44e-19248
mesodermal cell2.68e-17119
animal cell4.11e-12679
eukaryotic cell4.11e-12679
squamous epithelial cell3.07e-1162
contractile cell1.85e-1059
endothelial cell of vascular tree3.85e-1024
lining cell4.29e-1057
barrier cell4.29e-1057
endothelial cell8.78e-1035
blood vessel endothelial cell7.05e-0918
embryonic blood vessel endothelial progenitor cell7.05e-0918
muscle cell1.85e-0854
smooth muscle cell2.38e-0842
smooth muscle myoblast2.38e-0842
meso-epithelial cell3.83e-0844
kidney cell2.51e-0718
kidney epithelial cell2.51e-0718
muscle precursor cell3.10e-0757
myoblast3.10e-0757
multi-potent skeletal muscle stem cell3.10e-0757
electrically responsive cell5.15e-0760
electrically active cell5.15e-0760
endodermal cell5.65e-0759
non-terminally differentiated cell6.10e-07180
Uber Anatomy
Ontology termp-valuen
epithelial tube5.10e-23118
unilaminar epithelium3.30e-20138
mesenchyme2.29e-18238
entire embryonic mesenchyme2.29e-18238
primordium1.47e-17168
vasculature2.37e-1779
vascular system2.37e-1779
trunk4.70e-16216
immaterial anatomical entity5.59e-15126
multi-tissue structure8.95e-15347
endoderm-derived structure3.15e-14169
endoderm3.15e-14169
presumptive endoderm3.15e-14169
splanchnic layer of lateral plate mesoderm1.81e-1384
anatomical cluster6.05e-13286
vessel7.93e-1369
trunk region element1.22e-12107
cell layer1.33e-12312
cardiovascular system1.83e-12110
epithelium5.78e-12309
trunk mesenchyme6.98e-12143
subdivision of digestive tract1.13e-11129
endodermal part of digestive tract1.13e-11129
digestive system1.32e-11155
digestive tract1.32e-11155
primitive gut1.32e-11155
circulatory system2.08e-11113
blood vessel3.60e-1160
epithelial tube open at both ends3.60e-1160
blood vasculature3.60e-1160
vascular cord3.60e-1160
subdivision of trunk1.12e-10113
anatomical space1.30e-10104
mixed endoderm/mesoderm-derived structure2.02e-10130
anatomical conduit2.16e-10241
endo-epithelium2.23e-1082
simple squamous epithelium5.82e-1022
foregut8.03e-1098
mesoderm1.93e-09448
mesoderm-derived structure1.93e-09448
presumptive mesoderm1.93e-09448
urinary system structure6.96e-0944
endothelium7.05e-0918
blood vessel endothelium7.05e-0918
cardiovascular system endothelium7.05e-0918
organism subdivision1.07e-08365
renal system1.12e-0845
abdomen element1.48e-0855
abdominal segment element1.48e-0855
multi-cellular organism2.52e-08659
duct3.60e-0826
abdominal segment of trunk4.19e-0861
abdomen4.19e-0861
squamous epithelium3.16e-0725
anatomical cavity3.42e-0770
artery3.45e-0742
arterial blood vessel3.45e-0742
arterial system3.45e-0742
tube3.94e-07194
gut epithelium5.40e-0754
anatomical system6.08e-07625
body cavity precursor7.14e-0763
organ segment9.57e-0797
Disease
Ontology termp-valuen
carcinoma2.90e-11106
cell type cancer1.68e-09143
disease of cellular proliferation1.06e-07239
cancer1.46e-07235


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
CCNT2#90536.336201576962630.003930750035764890.0189443287025957
CHD2#1106310.34402283411690.0009033701102746880.00658986316595503
CTCF#1066435.360256373075030.0064925092527670.0278663203817751
ELF1#199734.258097958807540.01295179875054610.0460609837473451
ELK4#2005316.2356816584680.0002336043955745990.00255229725592798
EP300#203336.77394172622320.003216880500103790.0167031809958407
ETS1#211339.728760922202340.001085840092584840.0076064158179266
FOS#235338.99795530889440.001372499272417130.00895386666949669
FOSL1#8061339.7135797163731.59554825631833e-050.000370387784711337
FOSL2#2355316.93020060456170.0002060162053171620.00242489873403799
FOXA1#3169311.08141974938550.000734755275698670.0057993580893813
FOXA2#3170324.63046375266526.68983856509345e-050.00107077402283494
GABPB1#255337.067683836182170.002832212825417420.0153722833007884
GATA2#2624312.7449317335540.0004829527704283790.00436248956848032
GTF2F1#2962312.73966087675770.0004835525047438590.00432971022316049
HDAC2#3066313.41562023662630.0004140761399857210.00390163280259552
HNF4A#3172323.13229036295378.07584663437677e-050.00122556429329799
IRF1#365937.63716375356390.002244692747297240.0127749695294522
JUN#3725312.51282919233630.0005103313992726250.00443341382537296
JUNB#3726330.61063265982113.4847716247536e-050.000679637840742561
JUND#372736.994663941871030.002921845042734990.0156313172020387
MAFK#7975327.10073313782995.02195559325033e-050.00085630697176077
MAX#414936.452555509007120.003721913834265510.0186022664116029
MXI1#460139.96157162875930.001011470541259020.0071891228976828
MYC#460935.22228187160940.007020843755740150.0293523037911111
RAD21#5885310.35503389545630.0009004912073565420.00662438551842712
REST#597839.650028716128020.001112636247114590.00765901773084634
RFX5#5993312.04791082719510.0005717246050312580.00483484583197243
RXRA#6256320.07461713913330.0001235730348432220.00164909841374793
SMARCA4#65973156.7659033078882.58908533335753e-071.33928421560439e-05
SMARCB1#6598318.25271578115740.000164397760679890.00202662154481197
SMC3#9126315.04493284493280.0002935825420371870.00308372393722435
SP1#666735.69838137814090.005403962701712170.0245683641217185
SPI1#668838.204323508522730.001810593189410520.0108895215726372
TAF7#6879311.43306940492390.0006690181981945830.00541262619887242
TFAP2A#7020316.5186343730450.0002218033880766340.00247594314315258
TFAP2C#7022310.80922860986020.0007916746575753130.00613821154881278
TRIM28#10155318.59052504526250.0001555969297255280.00196640703577013
YY1#752834.911170749853860.008441455341808260.0328324577105286
ZNF263#1012738.221841637010680.001799043925565870.0109035717584827



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.