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Coexpression cluster:C3938: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!3.29e-20!365;UBERON:0001017!1.23e-18!82;UBERON:0005743!1.18e-17!86;UBERON:0000073!3.15e-17!94;UBERON:0001016!3.15e-17!94;UBERON:0002616!1.21e-15!59;UBERON:0001049!2.73e-15!57;UBERON:0005068!2.73e-15!57;UBERON:0006241!2.73e-15!57;UBERON:0007135!2.73e-15!57;UBERON:0000955!6.14e-15!69;UBERON:0006238!6.14e-15!69;UBERON:0000914!4.63e-14!83;UBERON:0002329!4.63e-14!83;UBERON:0003077!4.63e-14!83;UBERON:0003059!4.63e-14!83;UBERON:0007282!4.63e-14!83;UBERON:0009618!4.63e-14!83;UBERON:0007285!4.63e-14!83;UBERON:0004121!1.49e-13!169;UBERON:0001893!2.92e-13!34;UBERON:0001869!3.51e-13!32;UBERON:0002020!4.25e-13!34;UBERON:0003528!4.25e-13!34;UBERON:0002791!6.64e-13!33;UBERON:0000033!7.96e-13!123;UBERON:0004290!8.95e-13!70;UBERON:0000924!1.80e-12!173;UBERON:0006601!1.80e-12!173;UBERON:0000153!2.87e-12!129;UBERON:0007811!2.87e-12!129;UBERON:0003080!3.24e-12!42;UBERON:0002780!8.86e-12!41;UBERON:0001890!8.86e-12!41;UBERON:0006240!8.86e-12!41;UBERON:0003075!2.05e-11!86;UBERON:0007284!2.05e-11!86;UBERON:0000486!7.52e-11!82;UBERON:0000956!3.18e-10!25;UBERON:0000203!3.18e-10!25;UBERON:0002346!5.26e-10!90;UBERON:0003056!5.68e-10!61;UBERON:0001134!2.03e-09!61;UBERON:0002036!2.03e-09!61;UBERON:0003082!2.03e-09!61;UBERON:0002385!4.66e-09!63;UBERON:0001015!4.66e-09!63;UBERON:0000383!4.66e-09!63;UBERON:0002619!1.09e-08!22;UBERON:0002199!2.66e-08!45;UBERON:0002416!2.66e-08!45;UBERON:0001950!3.33e-08!20;UBERON:0000119!3.39e-08!312;UBERON:0000483!4.74e-08!309;UBERON:0002097!6.64e-08!40;UBERON:0000468!8.67e-08!659;UBERON:0000481!5.01e-07!347
|ontology_enrichment_uberon=UBERON:0000475!3.29e-20!365;UBERON:0001017!1.23e-18!82;UBERON:0005743!1.18e-17!86;UBERON:0000073!3.15e-17!94;UBERON:0001016!3.15e-17!94;UBERON:0002616!1.21e-15!59;UBERON:0001049!2.73e-15!57;UBERON:0005068!2.73e-15!57;UBERON:0006241!2.73e-15!57;UBERON:0007135!2.73e-15!57;UBERON:0000955!6.14e-15!69;UBERON:0006238!6.14e-15!69;UBERON:0000914!4.63e-14!83;UBERON:0002329!4.63e-14!83;UBERON:0003077!4.63e-14!83;UBERON:0003059!4.63e-14!83;UBERON:0007282!4.63e-14!83;UBERON:0009618!4.63e-14!83;UBERON:0007285!4.63e-14!83;UBERON:0004121!1.49e-13!169;UBERON:0001893!2.92e-13!34;UBERON:0001869!3.51e-13!32;UBERON:0002020!4.25e-13!34;UBERON:0003528!4.25e-13!34;UBERON:0002791!6.64e-13!33;UBERON:0000033!7.96e-13!123;UBERON:0004290!8.95e-13!70;UBERON:0000924!1.80e-12!173;UBERON:0006601!1.80e-12!173;UBERON:0000153!2.87e-12!129;UBERON:0007811!2.87e-12!129;UBERON:0003080!3.24e-12!42;UBERON:0002780!8.86e-12!41;UBERON:0001890!8.86e-12!41;UBERON:0006240!8.86e-12!41;UBERON:0003075!2.05e-11!86;UBERON:0007284!2.05e-11!86;UBERON:0000486!7.52e-11!82;UBERON:0000956!3.18e-10!25;UBERON:0000203!3.18e-10!25;UBERON:0002346!5.26e-10!90;UBERON:0003056!5.68e-10!61;UBERON:0001134!2.03e-09!61;UBERON:0002036!2.03e-09!61;UBERON:0003082!2.03e-09!61;UBERON:0002385!4.66e-09!63;UBERON:0001015!4.66e-09!63;UBERON:0000383!4.66e-09!63;UBERON:0002619!1.09e-08!22;UBERON:0002199!2.66e-08!45;UBERON:0002416!2.66e-08!45;UBERON:0001950!3.33e-08!20;UBERON:0000119!3.39e-08!312;UBERON:0000483!4.74e-08!309;UBERON:0002097!6.64e-08!40;UBERON:0000468!8.67e-08!659;UBERON:0000481!5.01e-07!347
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279640042003354!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109505973040083
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0906475,0.0558058,0.28262,0.517717,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.26144,0.0286025,0.549354,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.00836526,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.131452,0.00681584,0.448776,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.739716,0.00475792,0.21727,0.289306,0.119215,0.192475,0.177967,0.547859,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.0163112,0.0987169,0.519327,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.0298844,0.0759837,0.286863,0.152372,0.194941,0.218271,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.504592,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.220462,0.166967,0.0190329,0.0813902,0.184948,0.156261,0.311847,0.511859,0.0590944,0.247324,0.178389,0.218229,0.231073,0.407281,0.619906,0.0360851,0.0168763,0.131093,0.0434602,0.133616,0.418146,0.36927,0.449036,0.0973145,0.231447,0.544776,0.43956,0.37006,0.0189483,0.448797,0.197484,0.396996,0.36145,0.406019,0.381071,0.580441,0.643768,0.432035,0.000369536,0.000164197,0.48809,0.50058,0.443185,0.169835,0.616975,0.60734,0.227104,0.518585,0.000486104,0.38649,0.284625,0.00583062,0.55194,6.64072e-05,0.28907,0.164197,0.462688,0.287881,0.574635,0.478174,0.336276,0.468444,0.00355636,0.446557,0.243383,0.0186777,0.390974,0.000456298,0.683217,0.161598,0.00310283,0.644754,0.496032,0.0239796,0.37357,0.0203982,0.0282154,0.78384,0.0132585,0.43491,0.0222555,0.200493,0.20558,0.300504,0.25656,0.0189087,0.349197,0.383291,0.156104,0.141318,1.97791e-05,0.0961477,0.000626916,0.354789,0.163828,0.230581,0.120226,0.28424,0.562405,0.314429,0.181415,0.00475227,0.78,0.616388,0.408413,0.516511,0.322213,0.656109,0.00873429,0.61031,0.387276,0.522605,0.0816402,0.000151141,0.0267088,0.416621,0.416292,0.462712,0.148994,0.579431,0.204817,0.452428,0.138871,0.308032,0.166905,0.19783,0.0833851,0.316453,0.48065,0.175199,0.332919,0.373557,0.523625,0.408861,0.365487,0.534741,0.39088,0.363192,0.236011,0.0222706,0.273398,0.375787,0.4466,0.351067,0.275347,0.0830022,0.0524515,0.241132,0.371414,0.30666,0.303709,8.00304e-05,0.0867777,0.035296,0.250964,0.383276,0.457886,0.156714,0.220231,0.509064,0.196976,0.191517,0.463751,0.0145214,0.307334,0.459728,0.283463,0.563586,0.472935,0.399569,0.273281,0.368095,0.275089,0.384593,0.138622,0.359231,0.339729,0.197805,0.608187,0.387069,0.00817676,0.52832,0.0502872,0.000613177,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.0140817,0.219428,0.0233135,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.0370716,0.30793,0.180606,0.159884,0.257294,0.150733,0.0254879,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.0437875,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.00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}}
}}

Revision as of 14:24, 5 September 2012


Full id: C3938_Fibroblast_serous_Preadipocyte_tenocyte_Synoviocyte_Smooth_mesenchymal



Phase1 CAGE Peaks

Hg19::chr1:215256074..215256113,+p1@KCNK2
Hg19::chr1:215256114..215256128,+p7@KCNK2
Hg19::chr1:215256131..215256143,+p15@KCNK2


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
organism subdivision3.29e-20365
central nervous system1.23e-1882
regional part of nervous system3.15e-1794
nervous system3.15e-1794
regional part of brain1.21e-1559
neural tube2.73e-1557
neural rod2.73e-1557
future spinal cord2.73e-1557
neural keel2.73e-1557
brain6.14e-1569
future brain6.14e-1569
somite4.63e-1483
paraxial mesoderm4.63e-1483
presomitic mesoderm4.63e-1483
presumptive segmental plate4.63e-1483
trunk paraxial mesoderm4.63e-1483
presumptive paraxial mesoderm4.63e-1483
ectoderm-derived structure1.49e-13169
telencephalon2.92e-1334
cerebral hemisphere3.51e-1332
gray matter4.25e-1334
brain grey matter4.25e-1334
regional part of telencephalon6.64e-1333
head7.96e-13123
dermomyotome8.95e-1370
ectoderm1.80e-12173
presumptive ectoderm1.80e-12173
anterior region of body2.87e-12129
craniocervical region2.87e-12129
anterior neural tube3.24e-1242
regional part of forebrain8.86e-1241
forebrain8.86e-1241
future forebrain8.86e-1241
neural plate2.05e-1186
presumptive neural plate2.05e-1186
multilaminar epithelium7.52e-1182
cerebral cortex3.18e-1025
pallium3.18e-1025
neurectoderm5.26e-1090
pre-chordal neural plate5.68e-1061
skeletal muscle tissue2.03e-0961
striated muscle tissue2.03e-0961
myotome2.03e-0961
muscle tissue4.66e-0963
musculature4.66e-0963
musculature of body4.66e-0963
regional part of cerebral cortex1.09e-0822
integument2.66e-0845
integumental system2.66e-0845
neocortex3.33e-0820
cell layer3.39e-08312
epithelium4.74e-08309
skin of body6.64e-0840
multi-cellular organism8.67e-08659
multi-tissue structure5.01e-07347


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#1066435.360256373075030.0064925092527670.0279640042003354
ZNF263#1012738.221841637010680.001799043925565870.0109505973040083



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.