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Coexpression cluster:C1061: Difference between revisions

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|full_id=C1061_skeletal_Bronchial_pancreas_iPS_diffuse_Mesenchymal_Smooth
|full_id=C1061_skeletal_Bronchial_pancreas_iPS_diffuse_Mesenchymal_Smooth
|id=C1061
|id=C1061
|ontology_enrichment_celltype=CL:0002371!2.13e-12!591;CL:0000144!2.21e-11!625;CL:0000055!6.88e-10!180;CL:0000548!5.10e-09!679;CL:0000004!5.10e-09!679;CL:0000255!5.10e-09!679;CL:0000183!1.43e-08!59;CL:0000012!1.97e-08!682;CL:0000393!2.39e-08!60;CL:0000211!2.39e-08!60;CL:0002321!8.22e-08!248;CL:0000680!1.00e-07!57;CL:0000056!1.00e-07!57;CL:0000355!1.00e-07!57;CL:0000220!1.21e-07!246;CL:0000187!1.37e-07!54;CL:0000222!1.96e-07!119;CL:0000192!2.13e-07!42;CL:0000514!2.13e-07!42
|ontology_enrichment_celltype=CL:0002371!2.54e-11!588;CL:0000548!1.61e-08!679;CL:0000255!1.61e-08!679;CL:0000393!3.29e-08!61;CL:0000211!3.29e-08!61;CL:0000183!3.35e-08!59;CL:0000680!1.37e-07!58;CL:0000056!1.37e-07!58;CL:0000355!1.37e-07!58;CL:0002321!1.53e-07!250;CL:0000187!1.87e-07!55;CL:0000222!2.09e-07!121;CL:0000192!2.71e-07!43;CL:0000514!2.71e-07!43
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004290!3.91e-10!70;UBERON:0000914!3.35e-09!83;UBERON:0002329!3.35e-09!83;UBERON:0003077!3.35e-09!83;UBERON:0003059!3.35e-09!83;UBERON:0007282!3.35e-09!83;UBERON:0009618!3.35e-09!83;UBERON:0007285!3.35e-09!83;UBERON:0000486!3.84e-09!82;UBERON:0001134!2.99e-08!61;UBERON:0002036!2.99e-08!61;UBERON:0003082!2.99e-08!61;UBERON:0002385!4.55e-08!63;UBERON:0001015!4.55e-08!63;UBERON:0000383!4.55e-08!63;UBERON:0001637!1.68e-07!42;UBERON:0003509!1.68e-07!42;UBERON:0004572!1.68e-07!42;UBERON:0005256!3.15e-07!143;UBERON:0002049!9.42e-07!79;UBERON:0007798!9.42e-07!79
|ontology_enrichment_uberon=UBERON:0007503!7.29e-11!78;UBERON:0002329!1.17e-09!71;UBERON:0003059!1.17e-09!71;UBERON:0007282!1.17e-09!71;UBERON:0004290!1.17e-09!71;UBERON:0009618!1.17e-09!71;UBERON:0007524!1.43e-09!73;UBERON:0003077!3.38e-09!72;UBERON:0007285!3.38e-09!72;UBERON:0000486!1.18e-08!83;UBERON:0001134!6.07e-08!62;UBERON:0002036!6.07e-08!62;UBERON:0003082!6.07e-08!62;UBERON:0002385!8.83e-08!64;UBERON:0001015!8.83e-08!64;UBERON:0000383!8.83e-08!64;UBERON:0000926!3.53e-07!315;UBERON:0004120!3.53e-07!315;UBERON:0006603!3.53e-07!315;UBERON:0001637!4.97e-07!42;UBERON:0003509!4.97e-07!42;UBERON:0004572!4.97e-07!42;UBERON:0005256!8.28e-07!122
|tf_chipseq_enrich=CTCF#10664;5:3.35016023317189:0.00764385314602122:0.0314892860017873!POLR2A#5430;8:2.14745317655807:0.00221072578897191:0.0127223931383313
|tf_chipseq_enrich=CTCF#10664;5:3.35016023317189:0.00764385314602122:0.0314892860017873!POLR2A#5430;8:2.14745317655807:0.00221072578897191:0.0127223931383313
|tfbs_overrepresentation=0.0683183,0.148901,0.965456,0.00779524,0.0225521,0.0636992,0.110615,0.760146,0.0848916,0.0670884,0.00794804,0.493877,0.427578,0.301671,0.348998,0.0129692,0.000814364,0.031679,0.134803,0.038041,0.427322,0.315644,0.203945,0.233475,0.107054,0.476489,0.465564,0.224005,0.338892,0.230018,0.0242778,0.275959,0.0473641,0.000466088,0.167712,0.209702,0.60047,0.110518,0.289619,0.168138,0.237041,0.0642921,0.0621735,0.418594,0.290836,0.093749,0.0981932,0.413814,0.00410661,0.0473291,0.00115883,0.138034,0.176339,0.229169,0.00318358,0.0991916,0.0376375,0.471522,0.195469,1.51752e-05,0.0765682,0.350502,0.264034,0.189928,0.138981,0.129036,0.685923,0.152128,0.21338,0.0864158,0.362556,0.17045,0.0262409,0.287531,0.0198121,0.0449986,0.237072,0.112317,0.0962742,0.0192234,0.235123,0.0324959,0.109358,0.277702,0.065903,0.538689,0.162509,4.87396e-05,0.918195,0.158699,0.212656,0.12683,0.234568,0.121395,0.21181,0.278097,0.904111,4.63696e-07,0.0283856,0.210866,0.0112255,0.0567549,0.00836279,0.00474443,0.00467744,0.105454,0.0151262,0.0996563,0.339859,0.20448,0.415891,0.08811,0.0703263,0.0464689,0.247671,0.0874941,0.0533212,0.0109107,0.000770269,0.208244,0.385121,0.136772,0.331405,0.0244241,0.250229,0.096075,0.223928,0.0389643,0.0236487,0.000684068,0.15109,0.187322,0.145395,3.69625e-05,0.00588318,0.00377101,0.0142067,0.0104197,0.0856983,0.0105126,0.059589,0.305135,0.455648,0.363816,0.911133,0.0161652,0.242306,0.209139,0.100504,0.290656,0.449653,0.338748,0.412289,0.069324,0.109875,0.283569,0.187146,0.000743595,0.131992,0.087425,0.0328271,0.234343,0.0440056,0.347181,0.573425,0.276476,0.103223,0.304631,0.00560862,0.631236,0.410329,0.000742123,0.8104,0.137927,0.021309,0.222543,0.331842,0.414399,0.000213633,0.0922244,0.00130807,0.29418,0.0714241,0.00458918,0.18472,0.286375,0.416713,0.10358,0.00172262,0.398511,1.63469e-05,0.424801,0.00550021,0.0332789,0.272958,0.120656,0.0204509,0.152795,0.170383,0.26639,0.220771,0.153064,0.0801204,0.153558,0.323763,0.0475412,0.00025798,0.00109387,0.459969,0.407776,0.00721361,0.254651,0.291346,0.00428436,0.0802066,0.389728,0.0837009,0.247049,0.000764826,0.0347043,0.335144,0.711334,0.0110391,0.00138088,0.185037,0.30302,0.328766,0.213152,2.79e-05,0.151857,0.894484,0.371554,0.10772,0.191224,0.235781,0.229621,0.121035,2.32856e-06,0.378787,0.000545264,0.0022676,0.0291647,0.241356,0.206521,2.46747e-05,0.00752532,0.00164045,6.46345e-11,0.130189,0.0442822,9.09736e-06,1.78445e-06,0.105076,0.00282788,0.240662,0.0794631,0.0374947,0.122314,0.174963,0.675694,0.156722,0.401493,0.378539,0.306175,0.0894087,0.201841,0.202064,7.62498e-06,0.284712,0.188919,0.0579948,0.160003,0.543505,0.793729,0.000116962,0.0982663,0.05418,0.0324449,0.426446,0.580787,0.504904,0.64733,0.945023,0.813753,0.297165,0.274443,0.554495,0.793274,0.354548,0.627136,0.0104583,0.0048637,0.0475956,0.655692,0.0180628,0.921959,0.207972,0.0145428,0.000591936,0.390849,0.0312973,0.226444,0.106645,0.0339216,0.00223056,0.0620512,0.267081,1.67253e-05,0.0291039,0.773523,0.00192384,0.00714729,0.938031,0.0530057,0.0152136,0.00173407,0.419391,0.527275,0.541539,0.57865,0.0727316,0.00222164,0.00391478,0.00506122,0.556408,0.914984,0.589283,1.08405e-05,0.200357,0.601376,0.795055,0.00920119,0.00364216,0.603063,0.000429871,0.202294,0.00908113,0.00932622,0.0142871,0.0173425,0.231449,0.989856,0.5004,0.576349,1.05854e-05,0.421708,0.678158,0.0182562,0.000243122,0.268852,0.000142458,0.853878,0.585497,1.52886e-05,0.585986,0.508315,0.378278,0.16896,0.183237,0.420064,0.696144,0.895777,0.410586,0.758256,0.0806852,0.00601958,1.53215e-05,0.212706,0.141298,0.632259,0.390354,0.00028346,0.187131,0.500188,0.939244,0.685681,0.844309,0.238882,0.103941,0.0977304,0.597604,0.652313,0.953354,0.580536,0.81409,0.0647387,0.498619,0.000143335,0.444096,0.364444,0.0266041,0.181019,0.258036,0.766712,0.131808,0.994589,0.663224,0.00887755,0.342575,0.727086,0.00190028,0.469004,0.00154934,0.539342,0.00111785,0.11942,0.325113,0.191277,0.320286,0.241774,0.878405,0.237496,0.0617218,0.309445,0.00330823,0.0173907,0.702924,0.556188,0.586731,0.0131259,0.00150642,0.117884,0.150277,0.0524705,0.421612,3.81714e-05,0.234178,0.976132,0.127155,0.862948,0.533204,0.0201606,0.204349,0.302846,0.631352,0.220681,0.00834291,0.0248266,0.859142,0.00133352,0.0374931,0.352414,0.0347258,0.109018,0.220397,0.151053,0.0160339,0.00554698,0.0286159,0.0191137,0.0294548,0.512519,0.0135771,0.0592011,0.929578,0.0198264,0.175401,0.141685,0.112226,0.194711,0.146244,0.065791,5.82701e-07,3.56e-06,0.789854,0.788696,0.433218,0.00417731,4.67517e-05,0.111931,6.63742e-05,0.0513091,0.057911,0.0372604,0.573186,0.158807,0.722166,0.0470509,0.251803,0.583243,0.147483,9.77246e-06,0.390797,0.277129,0.255099,0.222257,0.0249284,0.37149,0.260746,0.112737,0.0103413,0.0491152,0.308422,0.467323,0.113432,0.678228,0.127781,0.206068,0.000905883,0.101411,0.0402326,0.0295078,0.0242295,0.115487,0.0557832,0.427434,0.123376,0.00325933,0.404386,0.305458,0.00195559,1.73767e-06,0.0885159,0.216979,0.234229,0.0297344,6.76729e-06,0.260596,0.0561916,0.012783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}}
}}

Revision as of 10:46, 19 October 2012


Full id: C1061_skeletal_Bronchial_pancreas_iPS_diffuse_Mesenchymal_Smooth



Phase1 CAGE Peaks

Hg19::chr19:3980551..3980576,-p@chr19:3980551..3980576
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Hg19::chr19:3980592..3980608,-p@chr19:3980592..3980608
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Hg19::chr19:3981964..3982023,-p@chr19:3981964..3982023
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Hg19::chr19:3982038..3982062,-p@chr19:3982038..3982062
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Hg19::chr19:3982295..3982322,-p@chr19:3982295..3982322
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Hg19::chr19:3982362..3982381,-p@chr19:3982362..3982381
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Hg19::chr19:3982382..3982401,-p@chr19:3982382..3982401
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Hg19::chr19:3984170..3984233,-p2@EEF2


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
somatic cell2.54e-11588
animal cell1.61e-08679
eukaryotic cell1.61e-08679
electrically responsive cell3.29e-0861
electrically active cell3.29e-0861
contractile cell3.35e-0859
muscle precursor cell1.37e-0758
myoblast1.37e-0758
multi-potent skeletal muscle stem cell1.37e-0758
embryonic cell1.53e-07250
muscle cell1.87e-0755
mesodermal cell2.09e-07121
smooth muscle cell2.71e-0743
smooth muscle myoblast2.71e-0743
Uber Anatomy
Ontology termp-valuen
epithelial vesicle7.29e-1178
somite1.17e-0971
presomitic mesoderm1.17e-0971
presumptive segmental plate1.17e-0971
dermomyotome1.17e-0971
trunk paraxial mesoderm1.17e-0971
dense mesenchyme tissue1.43e-0973
paraxial mesoderm3.38e-0972
presumptive paraxial mesoderm3.38e-0972
multilaminar epithelium1.18e-0883
skeletal muscle tissue6.07e-0862
striated muscle tissue6.07e-0862
myotome6.07e-0862
muscle tissue8.83e-0864
musculature8.83e-0864
musculature of body8.83e-0864
mesoderm3.53e-07315
mesoderm-derived structure3.53e-07315
presumptive mesoderm3.53e-07315
artery4.97e-0742
arterial blood vessel4.97e-0742
arterial system4.97e-0742
trunk mesenchyme8.28e-07122


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#1066453.350160233171890.007643853146021220.0314892860017873
POLR2A#543082.147453176558070.002210725788971910.0127223931383313



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.