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Coexpression cluster:C3858: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!8.69e-24!57;UBERON:0005068!8.69e-24!57;UBERON:0006241!8.69e-24!57;UBERON:0007135!8.69e-24!57;UBERON:0000475!1.06e-23!365;UBERON:0002616!2.34e-23!59;UBERON:0000073!5.43e-23!94;UBERON:0001016!5.43e-23!94;UBERON:0000955!1.76e-22!69;UBERON:0006238!1.76e-22!69;UBERON:0002346!4.82e-22!90;UBERON:0003075!1.69e-21!86;UBERON:0007284!1.69e-21!86;UBERON:0001017!3.25e-21!82;UBERON:0005743!8.24e-21!86;UBERON:0000033!2.09e-20!123;UBERON:0000924!8.05e-19!173;UBERON:0006601!8.05e-19!173;UBERON:0003080!9.30e-19!42;UBERON:0000153!1.03e-18!129;UBERON:0007811!1.03e-18!129;UBERON:0002780!1.47e-18!41;UBERON:0001890!1.47e-18!41;UBERON:0006240!1.47e-18!41;UBERON:0004121!3.50e-18!169;UBERON:0001893!4.19e-17!34;UBERON:0002020!4.23e-17!34;UBERON:0003528!4.23e-17!34;UBERON:0001869!1.15e-16!32;UBERON:0002791!1.89e-16!33;UBERON:0003056!1.77e-15!61;UBERON:0000914!2.84e-15!83;UBERON:0002329!2.84e-15!83;UBERON:0003077!2.84e-15!83;UBERON:0003059!2.84e-15!83;UBERON:0007282!2.84e-15!83;UBERON:0009618!2.84e-15!83;UBERON:0007285!2.84e-15!83;UBERON:0002619!1.60e-14!22;UBERON:0000468!2.29e-14!659;UBERON:0000119!1.09e-13!312;UBERON:0000483!1.56e-13!309;UBERON:0000956!1.67e-13!25;UBERON:0000203!1.67e-13!25;UBERON:0001950!1.98e-13!20;UBERON:0004290!6.60e-13!70;UBERON:0000486!1.99e-12!82;UBERON:0000481!2.42e-12!347;UBERON:0001134!3.09e-11!61;UBERON:0002036!3.09e-11!61;UBERON:0003082!3.09e-11!61;UBERON:0007023!4.16e-11!115;UBERON:0002385!5.40e-11!63;UBERON:0001015!5.40e-11!63;UBERON:0000383!5.40e-11!63;UBERON:0000467!2.41e-10!625;UBERON:0000480!4.05e-10!626;UBERON:0002050!8.16e-10!605;UBERON:0005423!8.16e-10!605;UBERON:0000923!1.07e-09!604;UBERON:0005291!1.07e-09!604;UBERON:0006598!1.07e-09!604;UBERON:0002532!1.07e-09!604;UBERON:0000922!1.74e-09!612;UBERON:0000025!1.58e-08!194;UBERON:0004111!1.81e-07!241;UBERON:0000477!3.39e-07!286;UBERON:0005256!4.23e-07!143;UBERON:0000062!6.22e-07!511
|ontology_enrichment_uberon=UBERON:0001049!8.69e-24!57;UBERON:0005068!8.69e-24!57;UBERON:0006241!8.69e-24!57;UBERON:0007135!8.69e-24!57;UBERON:0000475!1.06e-23!365;UBERON:0002616!2.34e-23!59;UBERON:0000073!5.43e-23!94;UBERON:0001016!5.43e-23!94;UBERON:0000955!1.76e-22!69;UBERON:0006238!1.76e-22!69;UBERON:0002346!4.82e-22!90;UBERON:0003075!1.69e-21!86;UBERON:0007284!1.69e-21!86;UBERON:0001017!3.25e-21!82;UBERON:0005743!8.24e-21!86;UBERON:0000033!2.09e-20!123;UBERON:0000924!8.05e-19!173;UBERON:0006601!8.05e-19!173;UBERON:0003080!9.30e-19!42;UBERON:0000153!1.03e-18!129;UBERON:0007811!1.03e-18!129;UBERON:0002780!1.47e-18!41;UBERON:0001890!1.47e-18!41;UBERON:0006240!1.47e-18!41;UBERON:0004121!3.50e-18!169;UBERON:0001893!4.19e-17!34;UBERON:0002020!4.23e-17!34;UBERON:0003528!4.23e-17!34;UBERON:0001869!1.15e-16!32;UBERON:0002791!1.89e-16!33;UBERON:0003056!1.77e-15!61;UBERON:0000914!2.84e-15!83;UBERON:0002329!2.84e-15!83;UBERON:0003077!2.84e-15!83;UBERON:0003059!2.84e-15!83;UBERON:0007282!2.84e-15!83;UBERON:0009618!2.84e-15!83;UBERON:0007285!2.84e-15!83;UBERON:0002619!1.60e-14!22;UBERON:0000468!2.29e-14!659;UBERON:0000119!1.09e-13!312;UBERON:0000483!1.56e-13!309;UBERON:0000956!1.67e-13!25;UBERON:0000203!1.67e-13!25;UBERON:0001950!1.98e-13!20;UBERON:0004290!6.60e-13!70;UBERON:0000486!1.99e-12!82;UBERON:0000481!2.42e-12!347;UBERON:0001134!3.09e-11!61;UBERON:0002036!3.09e-11!61;UBERON:0003082!3.09e-11!61;UBERON:0007023!4.16e-11!115;UBERON:0002385!5.40e-11!63;UBERON:0001015!5.40e-11!63;UBERON:0000383!5.40e-11!63;UBERON:0000467!2.41e-10!625;UBERON:0000480!4.05e-10!626;UBERON:0002050!8.16e-10!605;UBERON:0005423!8.16e-10!605;UBERON:0000923!1.07e-09!604;UBERON:0005291!1.07e-09!604;UBERON:0006598!1.07e-09!604;UBERON:0002532!1.07e-09!604;UBERON:0000922!1.74e-09!612;UBERON:0000025!1.58e-08!194;UBERON:0004111!1.81e-07!241;UBERON:0000477!3.39e-07!286;UBERON:0005256!4.23e-07!143;UBERON:0000062!6.22e-07!511
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426,0.517717,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.013859,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.0694567,0.219556,0.0394698,0.0596469,0.00236266,0.122476,0.108872,0.11002,0.26144,0.0286025,0.190156,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.118532,0.132886,0.0774373,0.109194,0.128564,0.131452,0.323837,0.0226843,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.389379,0.00475792,0.21727,0.289306,0.119215,0.192475,0.177967,0.0465298,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.43617,0.0611073,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.0122477,0.194941,0.218271,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.504592,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.0149597,0.09066,0.0597157,0.166967,0.188651,0.0813902,0.184948,0.156261,0.0546539,0.511859,0.0590944,0.247324,0.178389,0.218229,0.231073,0.407281,0.619906,0.0360851,0.412187,0.131093,0.0434602,0.133616,0.103051,0.36927,0.449036,0.0973145,0.231447,0.0455669,0.43956,0.37006,0.42622,0.448797,0.197484,0.396996,0.36145,0.0160226,0.0841307,0.057779,0.643768,0.432035,0.366326,0.390366,0.0305485,0.50058,0.443185,0.00696618,0.875915,0.151996,0.227104,0.00667974,0.250246,0.38649,0.284625,0.504757,0.00143312,0.0108655,0.28907,0.164197,0.128922,0.287881,0.574635,0.478174,0.0642229,0.00403041,0.258219,0.446557,0.243383,0.777351,0.390974,0.73485,0.319063,0.161598,0.164332,0.644754,0.150692,0.21803,0.0805771,0.78509,0.0282154,0.199161,0.399222,0.771991,0.20342,0.200493,0.20558,0.300504,0.25656,0.425963,0.349197,0.383291,0.156104,0.141318,0.411941,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.562405,0.314429,0.181415,0.282286,0.0674279,0.24884,0.01635,0.165147,0.322213,0.656109,0.33942,0.243065,0.387276,0.169614,0.221908,0.537348,0.222037,0.0175112,0.416292,0.462712,0.734551,0.579431,0.0225745,0.452428,0.138871,0.308032,0.166905,0.19783,0.0833851,0.316453,0.140384,0.175199,0.332919,0.373557,0.170369,0.408861,0.365487,0.178743,0.0140668,0.363192,0.236011,0.203486,0.273398,0.375787,0.119167,0.351067,0.275347,0.0830022,0.00618487,0.241132,0.371414,0.00623664,0.0516603,0.0323359,0.386538,0.000833313,0.250964,0.383276,0.0243456,0.504711,0.220231,0.159791,0.00149391,0.191517,0.463751,0.601877,0.307334,0.0246928,0.283463,0.563586,0.472935,0.0151656,0.273281,0.368095,0.275089,0.384593,0.000564944,0.359231,0.339729,0.197805,0.0690807,0.387069,0.332774,0.173874,0.299887,0.266492,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.0224033,0.179412,0.193601,0.220904,0.222977,0.341681,0.0542164,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.0157468,0.176789,0.0969345,0.202137,0.0541163,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.0457735,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.0203812,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.0232618,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252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}}
}}

Revision as of 11:50, 5 September 2012


Full id: C3858_cerebellum_Skeletal_Fibroblast_myxofibrosarcoma_Preadipocyte_Adipocyte_mesenchymal



Phase1 CAGE Peaks

Hg19::chr1:145075847..145075982,-p4@PDE4DIP
Hg19::chr1:145075992..145076044,-p5@PDE4DIP
Hg19::chr1:145076048..145076059,-p19@PDE4DIP


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>


Cell Type
Ontology termp-valuen
non-terminally differentiated cell2.18e-28180
fibroblast3.02e-1875
muscle precursor cell1.82e-1157
myoblast1.82e-1157
multi-potent skeletal muscle stem cell1.82e-1157
muscle cell3.42e-1054
contractile cell1.75e-0959
electrically responsive cell1.02e-0860
electrically active cell1.02e-0860
skin fibroblast6.96e-0723
preadipocyte8.72e-0712
Uber Anatomy
Ontology termp-valuen
neural tube8.69e-2457
neural rod8.69e-2457
future spinal cord8.69e-2457
neural keel8.69e-2457
organism subdivision1.06e-23365
regional part of brain2.34e-2359
regional part of nervous system5.43e-2394
nervous system5.43e-2394
brain1.76e-2269
future brain1.76e-2269
neurectoderm4.82e-2290
neural plate1.69e-2186
presumptive neural plate1.69e-2186
central nervous system3.25e-2182
head2.09e-20123
ectoderm8.05e-19173
presumptive ectoderm8.05e-19173
anterior neural tube9.30e-1942
anterior region of body1.03e-18129
craniocervical region1.03e-18129
regional part of forebrain1.47e-1841
forebrain1.47e-1841
future forebrain1.47e-1841
ectoderm-derived structure3.50e-18169
telencephalon4.19e-1734
gray matter4.23e-1734
brain grey matter4.23e-1734
cerebral hemisphere1.15e-1632
regional part of telencephalon1.89e-1633
pre-chordal neural plate1.77e-1561
somite2.84e-1583
paraxial mesoderm2.84e-1583
presomitic mesoderm2.84e-1583
presumptive segmental plate2.84e-1583
trunk paraxial mesoderm2.84e-1583
presumptive paraxial mesoderm2.84e-1583
regional part of cerebral cortex1.60e-1422
multi-cellular organism2.29e-14659
cell layer1.09e-13312
epithelium1.56e-13309
cerebral cortex1.67e-1325
pallium1.67e-1325
neocortex1.98e-1320
dermomyotome6.60e-1370
multilaminar epithelium1.99e-1282
multi-tissue structure2.42e-12347
skeletal muscle tissue3.09e-1161
striated muscle tissue3.09e-1161
myotome3.09e-1161
adult organism4.16e-11115
muscle tissue5.40e-1163
musculature5.40e-1163
musculature of body5.40e-1163
anatomical system2.41e-10625
anatomical group4.05e-10626
embryonic structure8.16e-10605
developing anatomical structure8.16e-10605
germ layer1.07e-09604
embryonic tissue1.07e-09604
presumptive structure1.07e-09604
epiblast (generic)1.07e-09604
embryo1.74e-09612
tube1.58e-08194
anatomical conduit1.81e-07241
anatomical cluster3.39e-07286
trunk mesenchyme4.23e-07143
organ6.22e-07511


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
CTBP2#1488362.71700033932814.049570681927e-060.000129813723894958
RAD21#5885310.35503389545630.0009004912073565420.00664216407974503
REST#597839.650028716128020.001112636247114590.00767723421065015
SUZ12#23512350.11578091106297.93834897779404e-060.000222390887578281
ZNF263#1012738.221841637010680.001799043925565870.0109442188107045
ZNF274#107822947.830769230771.47205921117966e-065.6835634734341e-05



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.