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Coexpression cluster:C1085: Difference between revisions

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|full_id=C1085_liposarcoma_placenta_Olfactory_amniotic_Hair_mesothelioma_Smooth
|full_id=C1085_liposarcoma_placenta_Olfactory_amniotic_Hair_mesothelioma_Smooth
|id=C1085
|id=C1085
|ontology_enrichment_celltype=CL:0000055!1.39e-24!180;CL:0000680!1.85e-15!57;CL:0000056!1.85e-15!57;CL:0000355!1.85e-15!57;CL:0000187!1.54e-14!54;CL:0000183!2.39e-13!59;CL:0000393!3.44e-12!60;CL:0000211!3.44e-12!60;CL:0000192!1.05e-11!42;CL:0000514!1.05e-11!42;CL:0000057!4.16e-11!75;CL:0000359!2.97e-08!32;CL:0000222!1.22e-07!119;CL:0000136!3.85e-07!15
|ontology_enrichment_celltype=CL:0000680!4.59e-16!58;CL:0000056!4.59e-16!58;CL:0000355!4.59e-16!58;CL:0000187!2.82e-15!55;CL:0000183!2.54e-14!59;CL:0000055!3.42e-13!106;CL:0000393!3.49e-13!61;CL:0000211!3.49e-13!61;CL:0000192!2.30e-12!43;CL:0000514!2.30e-12!43;CL:0000057!1.72e-11!76;CL:0000359!2.37e-08!32;CL:0000222!3.86e-08!121;CL:0000136!3.20e-07!15
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!1.92e-24!365;UBERON:0000481!1.69e-19!347;UBERON:0000119!3.26e-17!312;UBERON:0000483!6.07e-17!309;UBERON:0000477!1.55e-16!286;UBERON:0001134!2.72e-15!61;UBERON:0002036!2.72e-15!61;UBERON:0003082!2.72e-15!61;UBERON:0000914!6.32e-15!83;UBERON:0002329!6.32e-15!83;UBERON:0003077!6.32e-15!83;UBERON:0003059!6.32e-15!83;UBERON:0007282!6.32e-15!83;UBERON:0009618!6.32e-15!83;UBERON:0007285!6.32e-15!83;UBERON:0002385!8.84e-15!63;UBERON:0001015!8.84e-15!63;UBERON:0000383!8.84e-15!63;UBERON:0004111!2.77e-14!241;UBERON:0004290!5.71e-14!70;UBERON:0000468!1.18e-13!659;UBERON:0000025!1.54e-13!194;UBERON:0005256!2.00e-13!143;UBERON:0005743!1.10e-12!86;UBERON:0000073!1.27e-12!94;UBERON:0001016!1.27e-12!94;UBERON:0000033!8.22e-12!123;UBERON:0000955!1.45e-11!69;UBERON:0006238!1.45e-11!69;UBERON:0001017!1.59e-11!82;UBERON:0002616!4.46e-11!59;UBERON:0000467!1.75e-10!625;UBERON:0000153!2.01e-10!129;UBERON:0007811!2.01e-10!129;UBERON:0002100!2.06e-10!216;UBERON:0003075!2.25e-10!86;UBERON:0007284!2.25e-10!86;UBERON:0004121!2.53e-10!169;UBERON:0000480!2.62e-10!626;UBERON:0000486!4.08e-10!82;UBERON:0000490!4.33e-10!138;UBERON:0001049!4.48e-10!57;UBERON:0005068!4.48e-10!57;UBERON:0006241!4.48e-10!57;UBERON:0007135!4.48e-10!57;UBERON:0000924!1.13e-09!173;UBERON:0006601!1.13e-09!173;UBERON:0002346!2.20e-09!90;UBERON:0002050!8.32e-09!605;UBERON:0005423!8.32e-09!605;UBERON:0000923!8.67e-09!604;UBERON:0005291!8.67e-09!604;UBERON:0006598!8.67e-09!604;UBERON:0002532!8.67e-09!604;UBERON:0003056!1.46e-08!61;UBERON:0000922!2.27e-08!612;UBERON:0002780!4.33e-08!41;UBERON:0001890!4.33e-08!41;UBERON:0006240!4.33e-08!41;UBERON:0000064!4.98e-08!219;UBERON:0003080!5.59e-08!42;UBERON:0001893!1.62e-07!34;UBERON:0004872!1.89e-07!84;UBERON:0002791!2.82e-07!33;UBERON:0002020!3.07e-07!34;UBERON:0003528!3.07e-07!34;UBERON:0003914!3.34e-07!118;UBERON:0000062!6.71e-07!511;UBERON:0003104!7.37e-07!238;UBERON:0009142!7.37e-07!238;UBERON:0001869!7.48e-07!32
|ontology_enrichment_uberon=UBERON:0000481!1.03e-21!342;UBERON:0000477!7.23e-19!373;UBERON:0000119!9.17e-18!309;UBERON:0000483!1.85e-17!306;UBERON:0001134!8.77e-16!62;UBERON:0002036!8.77e-16!62;UBERON:0003082!8.77e-16!62;UBERON:0010314!1.62e-15!132;UBERON:0007524!2.20e-15!73;UBERON:0002385!2.45e-15!64;UBERON:0001015!2.45e-15!64;UBERON:0000383!2.45e-15!64;UBERON:0003077!6.67e-15!72;UBERON:0007285!6.67e-15!72;UBERON:0002329!1.39e-14!71;UBERON:0003059!1.39e-14!71;UBERON:0007282!1.39e-14!71;UBERON:0004290!1.39e-14!71;UBERON:0009618!1.39e-14!71;UBERON:0004111!3.42e-14!240;UBERON:0005256!1.53e-13!122;UBERON:0007503!3.28e-13!78;UBERON:0000025!4.27e-13!192;UBERON:0000468!1.22e-12!656;UBERON:0003104!1.37e-12!160;UBERON:0009142!1.37e-12!160;UBERON:0001017!5.65e-12!81;UBERON:0001016!8.41e-12!89;UBERON:0000955!9.04e-12!68;UBERON:0006238!9.04e-12!68;UBERON:0003075!5.93e-11!82;UBERON:0007284!5.93e-11!82;UBERON:0004121!1.00e-10!171;UBERON:0000924!1.00e-10!171;UBERON:0006601!1.00e-10!171;UBERON:0011216!1.28e-10!223;UBERON:0000486!1.35e-10!83;UBERON:0000467!1.67e-10!624;UBERON:0000475!1.99e-10!264;UBERON:0000480!2.36e-10!625;UBERON:0001049!3.47e-10!56;UBERON:0005068!3.47e-10!56;UBERON:0006241!3.47e-10!56;UBERON:0007135!3.47e-10!56;UBERON:0000490!4.96e-10!148;UBERON:0002346!8.48e-10!86;UBERON:0000073!1.57e-09!53;UBERON:0002616!1.57e-09!53;UBERON:0000923!2.90e-09!560;UBERON:0010316!2.90e-09!560;UBERON:0005291!2.90e-09!560;UBERON:0006598!2.90e-09!560;UBERON:0010317!2.90e-09!560;UBERON:0002532!2.90e-09!560;UBERON:0002050!9.79e-09!564;UBERON:0003056!1.25e-08!61;UBERON:0002100!1.29e-08!199;UBERON:0002780!4.00e-08!41;UBERON:0001890!4.00e-08!41;UBERON:0003080!4.00e-08!41;UBERON:0006240!4.00e-08!41;UBERON:0005423!7.11e-08!581;UBERON:0000064!1.78e-07!218;UBERON:0001893!2.49e-07!34;UBERON:0004872!2.66e-07!83;UBERON:0000922!4.82e-07!592;UBERON:0003528!5.04e-07!34;UBERON:0002020!5.04e-07!34;UBERON:0010371!8.37e-07!104;UBERON:0003914!8.75e-07!117
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93,0.19465,0.142897,0.10753,0.0894806,0.100334,0.543343,0.392173,0.450361,0.125132,0.401145,0.0367824,0.0857811,0.316921,0.48369,0.101821,0.151258,0.0162861,0.294186,0.264629,0.267153,2.21143e-05,0.0744668,0.166208,0.00883442,0.10027,0.216542,0.140095,0.339551,0.541739,0.479289,0.429978,0.312506,0.385866,0.514064,0.594251,0.190339,0.39643,0.203718,0.416086,0.66316,0.346997,0.33418,0.386217,0.332439,0.219989,0.0182559,0.594435,0.121222,0.233436,0.792498,0.316293,0.193405,0.00388424,0.307168,0.313275,0.0142231,0.0772098,0.132332,0.243599,0.127929,0.1565,0.188908,0.230656,0.339566,0.0881682,0.18579,0.579058,0.695352,0.941584,0.479647,0.597758,0.28717,0.434522,0.407023,1.5389e-11,0.146252,0.12193,0.735829,0.154198,0.401916,6.20494e-05,0.179067,0.491271,0.600481,0.0920973,0.300879,0.40148,1.47632e-05,7.38465e-18,0.460251,0.48128,0.263319,0.169668,0.264355,0.126386,0.235621,0.45894,0.189069,0.117159,0.267581,0.1766,0.495277,0.00114095,0.0973803,0.315733,0.115553,0.13739,0.276387,0.229078,0.396303,0.255961,0.487366,0.145278,0.509288,0.190011,0.0631125,0.356502,0.000333868,0.481419,0.248532,0.652258,0.397384,0.671042,0.354931,0.158525,0.43239,0.0010031,0.288995,0.36346,0.180408,0.226687,0.152678,0.00878757,0.35297,0.239072,0.0752133,0.0142235,0.436719,0.325366,0.498702,0.538083,0.595929,0.28677,0.208355,0.658265,0.273994,0.272914,0.423557,0.400864,0.233355,0.558548,0.534095,0.332254,0.24444,0.548105,0.253118,0.273827,0.0667061,0.387479,0.223866,0.904489,0.0134323,0.427353,0.202588,0.420356,0.364345,0.0796865,3.21318e-05,0.149927,0.531236,0.407834,0.481345,0.503758,0.000608922,0.0475485,0.0933565,0.757541,0.312516,0.111737,0.317827,0.76404,0.00852646,0.471691,0.752206,0.504402,0.877369,0.786493,0.708393,0.772671,0.795749,0.443827,0.74047,0.697643,1.53288e-05,0.721788,0.901346,0.297506,0.193296,0.967131,0.147454,0.832307,0.842996,0.790157,0.861021,0.11122,0.000187192,0.496897,0.85764,0.0465187,0.728237,0.590655,0.846474,0.882448,4.0293e-06,0.597402,0.380163,0.809189,0.595604,0.897663,0.823504,0.0981855,0.814591,2.01867e-05,0.793528,0.524662,0.762739,0.733501,0.147704,0.810414,0.375011,0.716143,0.520922,0.839155,0.425885,0.712705,0.776199,0.822762,0.387693,3.04336e-05,0.753324,3.53007e-06,0.44937,0.458665,0.614438,0.0460778,0.00418229,0.681923,0.724441,0.364029,0.333879,0.757271,0.0304198,0.0815395,0.689159,0.379433,0.502911,0.289349,0.590067,0.0250957,0.634568,0.413633,0.587076,0.767364,0.470215,0.753368,0.856,0.645528,0.941952,0.100734,0.918981,0.729164,0.0501415,4.72133e-05,0.87196,0.488054,0.762387,0.76203,0.809211,0.0105107,0.900712,0.457276,0.799317,0.328805,0.573398,0.385504,0.444467,0.207197,0.637438,0.825729,0.401684,0.660264,0.71269,0.861581,0.753866,0.702714,0.870027,0.733391,0.0340674,0.512211,0.45485,0.573299,0.715409,0.79357,0.684354,0.576345,0.000509237,0.622298,0.520881,0.710061,0.62342,0.619131,3.58237e-06,0.0107617,0.849193,0.537256,0.724424,0.804607,0.846436,0.484879,0.850008,0.442887,0.432731,0.810194,0.914222,0.624396,0.00681138,0.588879,0.890421,0.818739,0.743413,0.573115,0.705962,0.575942,0.72599,0.823302,0.332631,0.669433,0.44442,0.455825,0.72892,0.660067,0.00111012,0.613531,0.00183486,0.45836,0.403985,0.194485,0.578712,0.458152,0.0873966,0.42925,0.047253,0.426623,0.180477,0.559835,0.376936,0.431837,0.377907,0.483463,0.463074,0.222529,0.234528,0.383967,0.539263,0.718529,0.544718,0.462199,0.794152,0.000219518,0.436622,0.486064,0.489702,0.672033,0.629206,0.480957,0.445913,0.42387,3.31708e-05,0.447485,0.0845698,0.229886,0.297555,0.410714,0.49649,0.581581,0.212206,2.79508e-06,0.463718,0.531673,0.488584,0.169631,0.4639,0.56248,0.273878,0.00903802,0.500922,0.376098,0.500105,0.389123,0.0993883,0.1667,0.133211,0.116907,0.565967,0.451406,0.683557,0.361689,0.289284,0.241971,0.263726,0.151053,0.477267,0.368791,0.485034,0.43963,0.297904,0.551399,0.625257,0.412086,0.371597,0.547611,0.353179,0.479366,0.297272,0.41916,0.000258646,0.18144,0.000181333,0.554803,0.455388,0.473509,0.0251749,0.335015,0.435559,0.53418,0.28015,0.492484,0.529209,0.397471,0.449258,0.330704,0.443138,0.519779,0.364755,0.312488,0.547073,0.48939,0.395736,0.404755,0.238065,0.12262,0.62882,0.585012,0.481224,0.204547,0.452254,0.259924,0.136638,0.137048,0.353983,0.194753,0.104944,0.136955,0.642324,0.554772,0.469052,0.425619,0.50814,0.429061,0.202353,0.240717,0.162041,0.292976,0.161384,0.255196,0.167238,0.190639,0.307532,0.265287,0.113346,0.168727,0.221472,0.095012,0.320667,0.456504,0.607439,0.5938,0.679098,0.334729,0.557075,0.545435,0.448658,0.497569,0.611294,0.541437,0.406439,0.589165,0.559083,0.313926,0.373141,0.459861,0.447066,0.594101,0.512982,0.649607,0.279812,0.481032,0.0312514,0.278645,0.439191,0.431751,0.586217,0.588503,0.535591,0.381036,0.491941,0.230489,0.653021,0.494548,0.462673,0.23568,0.213047,0.638022,0.394858,0.369527,0.569966,0.178571,0.568909,0.247225,0.48895,0.403105,0.366377,0.476867,0.540268,0.459344,0.697624
}}
}}

Revision as of 10:48, 19 October 2012


Full id: C1085_liposarcoma_placenta_Olfactory_amniotic_Hair_mesothelioma_Smooth



Phase1 CAGE Peaks

Hg19::chr5:95066730..95066782,+p4@RHOBTB3
Hg19::chr5:95066823..95066879,+p2@RHOBTB3
Hg19::chr5:95067004..95067024,+p5@RHOBTB3
Hg19::chr5:95067025..95067058,+p1@RHOBTB3
Hg19::chr5:95067060..95067082,+p3@RHOBTB3
Hg19::chr5:95067089..95067108,+p6@RHOBTB3
Hg19::chr5:95067128..95067139,+p8@RHOBTB3
Hg19::chr5:95067165..95067168,+p12@RHOBTB3


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><br>

Uber Anatomy
Ontology termp-valuen
multi-tissue structure1.03e-21342
anatomical cluster7.23e-19373
cell layer9.17e-18309
epithelium1.85e-17306
skeletal muscle tissue8.77e-1662
striated muscle tissue8.77e-1662
myotome8.77e-1662
structure with developmental contribution from neural crest1.62e-15132
dense mesenchyme tissue2.20e-1573
muscle tissue2.45e-1564
musculature2.45e-1564
musculature of body2.45e-1564
paraxial mesoderm6.67e-1572
presumptive paraxial mesoderm6.67e-1572
somite1.39e-1471
presomitic mesoderm1.39e-1471
presumptive segmental plate1.39e-1471
dermomyotome1.39e-1471
trunk paraxial mesoderm1.39e-1471
anatomical conduit3.42e-14240
trunk mesenchyme1.53e-13122
epithelial vesicle3.28e-1378
tube4.27e-13192
multi-cellular organism1.22e-12656
mesenchyme1.37e-12160
entire embryonic mesenchyme1.37e-12160
central nervous system5.65e-1281
nervous system8.41e-1289
brain9.04e-1268
future brain9.04e-1268
neural plate5.93e-1182
presumptive neural plate5.93e-1182
ectoderm-derived structure1.00e-10171
ectoderm1.00e-10171
presumptive ectoderm1.00e-10171
organ system subdivision1.28e-10223
multilaminar epithelium1.35e-1083
anatomical system1.67e-10624
organism subdivision1.99e-10264
anatomical group2.36e-10625
neural tube3.47e-1056
neural rod3.47e-1056
future spinal cord3.47e-1056
neural keel3.47e-1056
unilaminar epithelium4.96e-10148
neurectoderm8.48e-1086
regional part of nervous system1.57e-0953
regional part of brain1.57e-0953
germ layer2.90e-09560
germ layer / neural crest2.90e-09560
embryonic tissue2.90e-09560
presumptive structure2.90e-09560
germ layer / neural crest derived structure2.90e-09560
epiblast (generic)2.90e-09560
embryonic structure9.79e-09564
pre-chordal neural plate1.25e-0861
trunk1.29e-08199
regional part of forebrain4.00e-0841
forebrain4.00e-0841
anterior neural tube4.00e-0841
future forebrain4.00e-0841
developing anatomical structure7.11e-08581
organ part1.78e-07218
telencephalon2.49e-0734
splanchnic layer of lateral plate mesoderm2.66e-0783
embryo4.82e-07592
brain grey matter5.04e-0734
gray matter5.04e-0734
ecto-epithelium8.37e-07104
epithelial tube8.75e-07117


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
BHLHE40#8553739.26283685360522.13093689260982e-112.55221236384492e-09
CCNT2#90586.336201576962633.84606837428661e-071.87613047614255e-05
CTBP2#1488862.71700033932814.13860279872435e-157.33839622573807e-13
CTCF#1066474.690224326440655.26249365325459e-050.000893819441620193
E2F1#186984.907389214879322.97124777369457e-060.0001015425871194
E2F6#187674.390011265235218.25033297218753e-050.00124032895535093
EBF1#187977.793158490747881.62130676909081e-066.14842620396063e-05
EGR1#195874.364656707958878.58120841941444e-050.00128636834522065
EP300#203386.77394172622322.25366016107097e-071.19114379333042e-05
ETS1#211378.512665806927048.8174082362229e-073.82425788531098e-05
GATA1#2623813.56030814380048.7300552826276e-108.1845443775794e-08
HEY1#2346284.040111043105711.4081650274634e-050.000339177461492736
HMGN3#932488.178547723350594.99020179935884e-083.19541192963359e-06
IRF1#365987.63716375356398.63190100943299e-085.13094541561851e-06
JUNB#3726830.61063265982111.29143502615752e-121.79595449662937e-10
MAX#414975.645986070381231.48396919857828e-050.000351917027997995
MYC#460985.22228187160941.80650725138099e-066.77206786887938e-05
POLR2A#543082.147453176558070.002210725788971910.0127244965926942
RAD21#588579.060654658524295.73112922357867e-072.63912436058789e-05
REST#597856.031267947580010.0005105473532543910.00442976281685929
SIN3A#2594285.408884726815141.36410592556506e-065.35585935188305e-05
SMC3#912659.403083028083036.12099279950925e-050.00100387934514439
SP1#666764.273786033605670.0005904726864288940.00494414951478772
STAT1#6772820.70658749719922.95008695392417e-113.42337923756541e-09
TAF1#687283.343046285745296.40776711117462e-050.00104386334319758
TBP#690883.706770687096392.80450451364125e-050.00059231475611765
TCF12#693879.305156789413124.76792693502233e-072.25014695511431e-05
TCF7L2#6934810.77017656313735.51536816569572e-094.40045481938193e-07
TFAP2A#7020816.5186343730451.79963993911652e-101.88140736337728e-08
TFAP2C#7022810.80922860986025.35792840387033e-094.28794394307903e-07
USF1#739186.361499277207963.72538670743375e-071.83266915844406e-05
ZBTB7A#5134187.35190930787591.17052559937328e-076.76527521156316e-06
ZNF263#1012788.221841637010684.78378813558924e-083.10512149840152e-06



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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