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Coexpression cluster:C3250: Difference between revisions

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|ontology_enrichment_disease=DOID:162!2.66e-09!235;DOID:14566!6.23e-09!239;DOID:305!3.01e-08!106
|ontology_enrichment_disease=DOID:162!2.66e-09!235;DOID:14566!6.23e-09!239;DOID:305!3.01e-08!106
|ontology_enrichment_uberon=UBERON:0000119!3.64e-15!312;UBERON:0000483!2.33e-14!309;UBERON:0000481!5.36e-14!347;UBERON:0004921!3.48e-12!129;UBERON:0004185!3.48e-12!129;UBERON:0004119!6.14e-12!169;UBERON:0000925!6.14e-12!169;UBERON:0006595!6.14e-12!169;UBERON:0001007!1.48e-11!155;UBERON:0001555!1.48e-11!155;UBERON:0007026!1.48e-11!155;UBERON:0000477!1.60e-11!286;UBERON:0005177!1.80e-11!107;UBERON:0005172!4.92e-11!55;UBERON:0005173!4.92e-11!55;UBERON:0003104!9.05e-10!238;UBERON:0009142!9.05e-10!238;UBERON:0002417!9.29e-10!61;UBERON:0000916!9.29e-10!61;UBERON:0009569!1.52e-09!113;UBERON:0000077!1.96e-09!130;UBERON:0001048!8.07e-09!168;UBERON:0001041!1.03e-08!98;UBERON:0002107!1.05e-08!19;UBERON:0006925!1.05e-08!19;UBERON:0008836!1.05e-08!19;UBERON:0000063!1.57e-08!97;UBERON:0000475!2.79e-08!365;UBERON:0009497!3.22e-08!25;UBERON:0000015!3.22e-08!25;UBERON:0002423!3.22e-08!25;UBERON:0006235!3.22e-08!25;UBERON:0004161!3.22e-08!25;UBERON:0004111!3.31e-08!241;UBERON:0002365!4.21e-08!31;UBERON:0002330!4.21e-08!31;UBERON:0005911!4.62e-08!82;UBERON:0000490!8.65e-08!138;UBERON:0000466!9.13e-08!126;UBERON:0002100!9.56e-08!216;UBERON:0008835!1.10e-07!22;UBERON:0003894!1.10e-07!22;UBERON:0000064!1.43e-07!219;UBERON:0009854!2.11e-07!23;UBERON:0007499!4.54e-07!25;UBERON:0001737!6.00e-07!9;UBERON:0009856!7.65e-07!26;UBERON:0002104!7.68e-07!21;UBERON:0000970!9.09e-07!20;UBERON:0003929!9.32e-07!54
|ontology_enrichment_uberon=UBERON:0000119!3.64e-15!312;UBERON:0000483!2.33e-14!309;UBERON:0000481!5.36e-14!347;UBERON:0004921!3.48e-12!129;UBERON:0004185!3.48e-12!129;UBERON:0004119!6.14e-12!169;UBERON:0000925!6.14e-12!169;UBERON:0006595!6.14e-12!169;UBERON:0001007!1.48e-11!155;UBERON:0001555!1.48e-11!155;UBERON:0007026!1.48e-11!155;UBERON:0000477!1.60e-11!286;UBERON:0005177!1.80e-11!107;UBERON:0005172!4.92e-11!55;UBERON:0005173!4.92e-11!55;UBERON:0003104!9.05e-10!238;UBERON:0009142!9.05e-10!238;UBERON:0002417!9.29e-10!61;UBERON:0000916!9.29e-10!61;UBERON:0009569!1.52e-09!113;UBERON:0000077!1.96e-09!130;UBERON:0001048!8.07e-09!168;UBERON:0001041!1.03e-08!98;UBERON:0002107!1.05e-08!19;UBERON:0006925!1.05e-08!19;UBERON:0008836!1.05e-08!19;UBERON:0000063!1.57e-08!97;UBERON:0000475!2.79e-08!365;UBERON:0009497!3.22e-08!25;UBERON:0000015!3.22e-08!25;UBERON:0002423!3.22e-08!25;UBERON:0006235!3.22e-08!25;UBERON:0004161!3.22e-08!25;UBERON:0004111!3.31e-08!241;UBERON:0002365!4.21e-08!31;UBERON:0002330!4.21e-08!31;UBERON:0005911!4.62e-08!82;UBERON:0000490!8.65e-08!138;UBERON:0000466!9.13e-08!126;UBERON:0002100!9.56e-08!216;UBERON:0008835!1.10e-07!22;UBERON:0003894!1.10e-07!22;UBERON:0000064!1.43e-07!219;UBERON:0009854!2.11e-07!23;UBERON:0007499!4.54e-07!25;UBERON:0001737!6.00e-07!9;UBERON:0009856!7.65e-07!26;UBERON:0002104!7.68e-07!21;UBERON:0000970!9.09e-07!20;UBERON:0003929!9.32e-07!54
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0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,1.43241e-05,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,5.99252e-06,0.219556,0.0394698,0.0596469,0.103658,0.122476,0.108872,0.11002,0.26144,0.0286025,0.549354,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.00335855,0.217069,0.190048,0.131088,0.394069,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.131452,0.00681584,0.120459,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.153605,0.655293,0.21727,0.289306,0.119215,0.192475,0.177967,0.547859,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.0472142,0.0355833,0.125606,0.175094,9.8105e-10,6.6291e-06,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.152372,0.194941,0.218271,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.15663,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.0461822,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.585505,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.161789,0.0590944,0.247324,0.178389,0.218229,0.231073,0.407281,0.252227,0.0360851,0.0168763,0.131093,0.0434602,0.133616,0.418146,0.0785808,0.449036,0.0162067,0.231447,0.544776,0.43956,0.37006,0.42622,0.448797,0.197484,0.396996,0.36145,0.406019,0.381071,0.216033,0.643768,0.432035,0.366326,0.390366,0.48809,0.50058,0.443185,0.522904,3.32586e-07,5.34955e-09,0.227104,0.518585,0.617852,0.38649,0.284625,0.000799065,0.55194,0.375373,0.28907,0.164197,0.462688,0.287881,0.574635,0.478174,0.336276,0.468444,0.258219,0.446557,0.243383,0.000171205,0.390974,0.73485,0.683217,0.161598,0.751174,0.644754,0.496032,0.0239796,0.37357,5.07251e-06,0.477353,8.52247e-08,0.0508568,6.59077e-09,0.20342,0.200493,0.20558,0.300504,0.25656,0.425963,0.349197,0.383291,0.156104,0.141318,0.411941,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.562405,0.314429,0.0175523,0.282286,0.446891,0.24884,0.408413,0.165147,0.322213,0.656109,0.33942,0.61031,0.387276,0.522605,1.90459e-08,0.180745,0.222037,0.416621,0.416292,0.462712,0.382478,0.579431,0.204817,0.452428,0.138871,0.00583733,0.166905,0.19783,0.0833851,0.316453,0.48065,0.175199,0.332919,0.373557,0.523625,0.408861,0.365487,0.534741,0.39088,0.363192,0.236011,0.203486,0.273398,0.375787,0.4466,0.351067,0.275347,0.637444,0.305885,0.241132,0.371414,0.30666,0.303709,0.495883,0.386538,0.508064,0.250964,0.383276,0.457886,0.504711,0.220231,0.509064,0.196976,0.191517,0.463751,0.601877,0.307334,0.459728,0.283463,0.563586,0.472935,0.399569,0.273281,0.368095,0.275089,0.384593,0.47795,0.359231,0.339729,0.197805,0.608187,0.387069,0.332774,0.52832,0.299887,0.634365,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.119514,0.179412,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.0233967,0.247588,0.222339,0.00231953,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.0284767,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.0273485,0.246105,0.0159159,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.0157468,0.176789,0.00485777,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.0597546,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.0143647,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435
}}
}}

Revision as of 14:00, 5 September 2012


Full id: C3250_liver_Hepatocyte_Melanocyte_Monocytederived_placenta_Meningeal_Pericytes



Phase1 CAGE Peaks

Hg19::chr12:125348399..125348419,-p1@SCARB1
Hg19::chr12:125348434..125348445,-p4@SCARB1
Hg19::chr12:125348448..125348472,-p2@SCARB1


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 cell1.64e-27254
embryonic cell1.77e-12248
lining cell2.29e-0857
barrier cell2.29e-0857
meso-epithelial cell1.72e-0744
endothelial cell2.42e-0735
endodermal cell2.85e-0759
Uber Anatomy
Ontology termp-valuen
cell layer3.64e-15312
epithelium2.33e-14309
multi-tissue structure5.36e-14347
subdivision of digestive tract3.48e-12129
endodermal part of digestive tract3.48e-12129
endoderm-derived structure6.14e-12169
endoderm6.14e-12169
presumptive endoderm6.14e-12169
digestive system1.48e-11155
digestive tract1.48e-11155
primitive gut1.48e-11155
anatomical cluster1.60e-11286
trunk region element1.80e-11107
abdomen element4.92e-1155
abdominal segment element4.92e-1155
mesenchyme9.05e-10238
entire embryonic mesenchyme9.05e-10238
abdominal segment of trunk9.29e-1061
abdomen9.29e-1061
subdivision of trunk1.52e-09113
mixed endoderm/mesoderm-derived structure1.96e-09130
primordium8.07e-09168
foregut1.03e-0898
liver1.05e-0819
digestive gland1.05e-0819
liver bud1.05e-0819
organ segment1.57e-0897
organism subdivision2.79e-08365
epithelium of foregut-midgut junction3.22e-0825
anatomical boundary3.22e-0825
hepatobiliary system3.22e-0825
foregut-midgut junction3.22e-0825
septum transversum3.22e-0825
anatomical conduit3.31e-08241
exocrine gland4.21e-0831
exocrine system4.21e-0831
endo-epithelium4.62e-0882
unilaminar epithelium8.65e-08138
immaterial anatomical entity9.13e-08126
trunk9.56e-08216
hepatic diverticulum1.10e-0722
liver primordium1.10e-0722
organ part1.43e-07219
digestive tract diverticulum2.11e-0723
epithelial sac4.54e-0725
larynx6.00e-079
sac7.65e-0726
visual system7.68e-0721
eye9.09e-0720
gut epithelium9.32e-0754
Disease
Ontology termp-valuen
cancer2.66e-09235
disease of cellular proliferation6.23e-09239
carcinoma3.01e-08106


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#90536.336201576962630.003930750035764890.0189347171710368
CTCF#1066435.360256373075030.0064925092527670.0278571617373869
CTCFL#140690319.74647435897440.0001298372005551160.00171299486972913
E2F6#187635.017155731697390.00791769806886330.0320771352113741
EBF1#187938.9064668465690.00141523283560980.00912886802039728
EGR1#195834.988179094810140.008056488137383440.0319357636383721
ELF1#199734.258097958807540.01295179875054610.0460437371403187
GABPB1#255337.067683836182170.002832212825417420.0153698869978576
IRF1#365937.63716375356390.002244692747297240.0127728814337461
MAX#414936.452555509007120.003721913834265510.0185933683601289
MXI1#460139.96157162875930.001011470541259020.00718667745142874
MYC#460935.22228187160940.007020843755740150.0293429069192743
POU2F2#545239.106124057742520.001324165192682130.00880071837587686
RAD21#5885310.35503389545630.0009004912073565420.0066220533167941
SIN3A#2594235.408884726815140.006318961977991520.0275689727637838
SMC3#9126315.04493284493280.0002935825420371870.00308248387532138
SP1#666735.69838137814090.005403962701712170.0245651560654676
SPI1#668838.204323508522730.001810593189410520.0108851336696319
TCF12#6938310.63446490218640.0008313523990202070.00628033368544458
TFAP2A#7020316.5186343730450.0002218033880766340.00247567853450204
TFAP2C#7022310.80922860986020.0007916746575753130.00613593391929559
YY1#752834.911170749853860.008441455341808260.0328226788698106
ZBTB7A#5134137.35190930787590.002516255860282270.0139717819018565



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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