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Coexpression cluster:C4633: Difference between revisions

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|ontology_enrichment_disease=DOID:2394!4.45e-08!14
|ontology_enrichment_disease=DOID:2394!4.45e-08!14
|ontology_enrichment_uberon=UBERON:0002049!2.12e-33!79;UBERON:0007798!2.12e-33!79;UBERON:0000055!1.14e-30!69;UBERON:0003914!7.69e-28!118;UBERON:0004872!4.23e-27!84;UBERON:0001981!5.32e-27!60;UBERON:0007500!5.32e-27!60;UBERON:0004537!5.32e-27!60;UBERON:0006965!5.32e-27!60;UBERON:0004535!1.05e-26!110;UBERON:0001009!3.10e-26!113;UBERON:0001637!4.37e-25!42;UBERON:0003509!4.37e-25!42;UBERON:0004572!4.37e-25!42;UBERON:0000486!4.36e-23!82;UBERON:0000490!6.10e-23!138;UBERON:0004290!8.31e-23!70;UBERON:0004573!3.16e-21!33;UBERON:0004571!3.16e-21!33;UBERON:0001134!3.92e-21!61;UBERON:0002036!3.92e-21!61;UBERON:0003082!3.92e-21!61;UBERON:0002385!1.18e-19!63;UBERON:0001015!1.18e-19!63;UBERON:0000383!1.18e-19!63;UBERON:0000914!1.58e-19!83;UBERON:0002329!1.58e-19!83;UBERON:0003077!1.58e-19!83;UBERON:0003059!1.58e-19!83;UBERON:0007282!1.58e-19!83;UBERON:0009618!1.58e-19!83;UBERON:0007285!1.58e-19!83;UBERON:0005256!3.18e-19!143;UBERON:0000947!2.18e-13!21;UBERON:0010191!2.18e-13!21;UBERON:0002100!3.34e-13!216;UBERON:0000119!1.24e-11!312;UBERON:0000483!3.23e-11!309;UBERON:0000926!4.95e-09!448;UBERON:0004120!4.95e-09!448;UBERON:0006603!4.95e-09!448;UBERON:0000487!1.02e-08!22;UBERON:0000468!2.16e-08!659;UBERON:0000467!2.89e-08!625;UBERON:0000480!4.00e-08!626;UBERON:0006914!4.60e-08!25;UBERON:0003104!5.26e-08!238;UBERON:0009142!5.26e-08!238;UBERON:0001986!5.88e-08!18;UBERON:0004638!5.88e-08!18;UBERON:0004852!5.88e-08!18;UBERON:0004237!6.31e-08!10;UBERON:0004695!6.31e-08!10;UBERON:0002111!6.31e-08!10;UBERON:0004178!6.31e-08!10;UBERON:0004111!8.43e-08!241;UBERON:0000475!2.68e-07!365;UBERON:0003081!3.42e-07!216;UBERON:0000025!4.02e-07!194;UBERON:0000477!4.63e-07!286;UBERON:0003915!6.75e-07!9;UBERON:0004700!6.75e-07!9;UBERON:0001917!6.75e-07!9
|ontology_enrichment_uberon=UBERON:0002049!2.12e-33!79;UBERON:0007798!2.12e-33!79;UBERON:0000055!1.14e-30!69;UBERON:0003914!7.69e-28!118;UBERON:0004872!4.23e-27!84;UBERON:0001981!5.32e-27!60;UBERON:0007500!5.32e-27!60;UBERON:0004537!5.32e-27!60;UBERON:0006965!5.32e-27!60;UBERON:0004535!1.05e-26!110;UBERON:0001009!3.10e-26!113;UBERON:0001637!4.37e-25!42;UBERON:0003509!4.37e-25!42;UBERON:0004572!4.37e-25!42;UBERON:0000486!4.36e-23!82;UBERON:0000490!6.10e-23!138;UBERON:0004290!8.31e-23!70;UBERON:0004573!3.16e-21!33;UBERON:0004571!3.16e-21!33;UBERON:0001134!3.92e-21!61;UBERON:0002036!3.92e-21!61;UBERON:0003082!3.92e-21!61;UBERON:0002385!1.18e-19!63;UBERON:0001015!1.18e-19!63;UBERON:0000383!1.18e-19!63;UBERON:0000914!1.58e-19!83;UBERON:0002329!1.58e-19!83;UBERON:0003077!1.58e-19!83;UBERON:0003059!1.58e-19!83;UBERON:0007282!1.58e-19!83;UBERON:0009618!1.58e-19!83;UBERON:0007285!1.58e-19!83;UBERON:0005256!3.18e-19!143;UBERON:0000947!2.18e-13!21;UBERON:0010191!2.18e-13!21;UBERON:0002100!3.34e-13!216;UBERON:0000119!1.24e-11!312;UBERON:0000483!3.23e-11!309;UBERON:0000926!4.95e-09!448;UBERON:0004120!4.95e-09!448;UBERON:0006603!4.95e-09!448;UBERON:0000487!1.02e-08!22;UBERON:0000468!2.16e-08!659;UBERON:0000467!2.89e-08!625;UBERON:0000480!4.00e-08!626;UBERON:0006914!4.60e-08!25;UBERON:0003104!5.26e-08!238;UBERON:0009142!5.26e-08!238;UBERON:0001986!5.88e-08!18;UBERON:0004638!5.88e-08!18;UBERON:0004852!5.88e-08!18;UBERON:0004237!6.31e-08!10;UBERON:0004695!6.31e-08!10;UBERON:0002111!6.31e-08!10;UBERON:0004178!6.31e-08!10;UBERON:0004111!8.43e-08!241;UBERON:0000475!2.68e-07!365;UBERON:0003081!3.42e-07!216;UBERON:0000025!4.02e-07!194;UBERON:0000477!4.63e-07!286;UBERON:0003915!6.75e-07!9;UBERON:0004700!6.75e-07!9;UBERON:0001917!6.75e-07!9
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0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.26144,0.0286025,0.549354,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.131452,0.687347,0.448776,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.739716,0.288159,0.21727,0.289306,0.119215,0.192475,0.177967,0.547859,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.911304,0.936279,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.152372,0.194941,0.218271,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.504592,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.220462,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.511859,0.0590944,0.247324,0.178389,0.218229,0.231073,0.407281,0.619906,0.0360851,0.412187,0.131093,0.0434602,0.133616,0.418146,0.36927,0.449036,0.0973145,0.231447,0.544776,0.43956,0.0789454,0.42622,0.448797,0.197484,0.396996,0.36145,0.406019,0.381071,0.580441,0.643768,0.432035,0.722159,0.390366,0.48809,0.50058,0.443185,0.169835,0.875915,0.871256,0.227104,0.518585,0.617852,0.38649,0.284625,0.504757,0.55194,0.729153,0.28907,0.164197,0.462688,0.287881,0.574635,0.478174,0.336276,0.468444,0.258219,0.446557,0.243383,0.442897,0.390974,0.73485,0.319063,0.161598,0.751174,0.644754,0.496032,0.799185,0.37357,0.454657,0.477353,0.78384,0.746954,0.771991,0.20342,0.200493,0.20558,0.300504,0.25656,0.425963,0.349197,0.383291,0.156104,0.141318,0.411941,0.0961477,0.055627,0.354789,0.163828,0.230581,0.120226,0.28424,0.562405,0.314429,0.181415,0.282286,0.446891,0.616388,0.408413,0.516511,0.322213,0.656109,0.33942,0.243065,0.387276,0.522605,0.802166,0.537348,0.222037,0.416621,0.10205,0.462712,0.734551,0.579431,0.204817,0.122646,0.138871,0.673493,0.166905,0.19783,0.0833851,0.316453,0.48065,0.175199,0.332919,0.373557,0.523625,0.408861,0.365487,0.534741,0.39088,0.363192,0.236011,0.203486,0.273398,0.375787,0.119167,0.351067,0.0419637,0.269604,0.305885,0.241132,0.371414,0.30666,0.303709,0.495883,0.386538,0.508064,0.250964,0.383276,0.457886,0.504711,0.220231,0.509064,0.196976,0.191517,0.463751,0.235208,0.307334,0.459728,0.283463,0.563586,0.472935,0.399569,0.273281,0.368095,0.275089,0.384593,0.47795,0.359231,0.339729,0.197805,0.608187,0.387069,0.332774,0.52832,0.299887,0.266492,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435
}}
}}

Revision as of 14:16, 5 September 2012


Full id: C4633_hepatic_spindle_chorionic_bone_Smooth_Fibroblast_basal



Phase1 CAGE Peaks

Hg19::chr7:100781146..100781169,+p@chr7:100781146..100781169
+
Hg19::chr7:100781561..100781583,+p@chr7:100781561..100781583
+
Hg19::chr7:100782236..100782279,+p@chr7:100782236..100782279
+


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
mesodermal cell2.34e-35119
non-terminally differentiated cell7.18e-29180
muscle precursor cell9.49e-2457
myoblast9.49e-2457
multi-potent skeletal muscle stem cell9.49e-2457
contractile cell3.48e-2359
muscle cell2.62e-2254
smooth muscle cell2.18e-2042
smooth muscle myoblast2.18e-2042
embryonic cell2.33e-19248
vascular associated smooth muscle cell3.27e-1932
somatic cell5.45e-18591
electrically responsive cell1.12e-1760
electrically active cell1.12e-1760
animal cell1.25e-15679
eukaryotic cell1.25e-15679
fibroblast5.45e-1375
lining cell1.11e-1257
barrier cell1.11e-1257
endothelial cell of vascular tree3.84e-1124
endothelial cell8.79e-1035
meso-epithelial cell9.93e-0944
multi fate stem cell2.06e-08430
native cell2.26e-08722
cardiocyte2.88e-0816
somatic stem cell3.49e-08436
blood vessel endothelial cell5.88e-0818
embryonic blood vessel endothelial progenitor cell5.88e-0818
aortic smooth muscle cell6.31e-0810
stem cell2.97e-07444
endothelial cell of artery6.75e-079
Uber Anatomy
Ontology termp-valuen
vasculature2.12e-3379
vascular system2.12e-3379
vessel1.14e-3069
epithelial tube7.69e-28118
splanchnic layer of lateral plate mesoderm4.23e-2784
blood vessel5.32e-2760
epithelial tube open at both ends5.32e-2760
blood vasculature5.32e-2760
vascular cord5.32e-2760
cardiovascular system1.05e-26110
circulatory system3.10e-26113
artery4.37e-2542
arterial blood vessel4.37e-2542
arterial system4.37e-2542
multilaminar epithelium4.36e-2382
unilaminar epithelium6.10e-23138
dermomyotome8.31e-2370
systemic artery3.16e-2133
systemic arterial system3.16e-2133
skeletal muscle tissue3.92e-2161
striated muscle tissue3.92e-2161
myotome3.92e-2161
muscle tissue1.18e-1963
musculature1.18e-1963
musculature of body1.18e-1963
somite1.58e-1983
paraxial mesoderm1.58e-1983
presomitic mesoderm1.58e-1983
presumptive segmental plate1.58e-1983
trunk paraxial mesoderm1.58e-1983
presumptive paraxial mesoderm1.58e-1983
trunk mesenchyme3.18e-19143
aorta2.18e-1321
aortic system2.18e-1321
trunk3.34e-13216
cell layer1.24e-11312
epithelium3.23e-11309
mesoderm4.95e-09448
mesoderm-derived structure4.95e-09448
presumptive mesoderm4.95e-09448
simple squamous epithelium1.02e-0822
multi-cellular organism2.16e-08659
anatomical system2.89e-08625
anatomical group4.00e-08626
squamous epithelium4.60e-0825
mesenchyme5.26e-08238
entire embryonic mesenchyme5.26e-08238
endothelium5.88e-0818
blood vessel endothelium5.88e-0818
cardiovascular system endothelium5.88e-0818
blood vessel smooth muscle6.31e-0810
arterial system smooth muscle6.31e-0810
artery smooth muscle tissue6.31e-0810
aorta smooth muscle tissue6.31e-0810
anatomical conduit8.43e-08241
organism subdivision2.68e-07365
lateral plate mesoderm3.42e-07216
tube4.02e-07194
anatomical cluster4.63e-07286
endothelial tube6.75e-079
arterial system endothelium6.75e-079
endothelium of artery6.75e-079
Disease
Ontology termp-valuen
ovarian cancer4.45e-0814


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
JUNB#3726220.40708843988080.003131462199438740.0164560119073756



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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