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Coexpression cluster:C4165: Difference between revisions

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|ontology_enrichment_disease=DOID:2394!9.19e-10!14
|ontology_enrichment_disease=DOID:2394!9.19e-10!14
|ontology_enrichment_uberon=UBERON:0000055!2.38e-25!69;UBERON:0001981!2.28e-24!60;UBERON:0007500!2.28e-24!60;UBERON:0004537!2.28e-24!60;UBERON:0006965!2.28e-24!60;UBERON:0001637!4.21e-24!42;UBERON:0003509!4.21e-24!42;UBERON:0004572!4.21e-24!42;UBERON:0004872!1.91e-22!84;UBERON:0002049!1.39e-20!79;UBERON:0007798!1.39e-20!79;UBERON:0004573!1.90e-20!33;UBERON:0004571!1.90e-20!33;UBERON:0001009!2.61e-15!113;UBERON:0004535!2.66e-15!110;UBERON:0003081!5.49e-14!216;UBERON:0000947!6.51e-14!21;UBERON:0010191!6.51e-14!21;UBERON:0002204!6.67e-14!167;UBERON:0003914!1.09e-13!118;UBERON:0000914!6.06e-12!83;UBERON:0002329!6.06e-12!83;UBERON:0003077!6.06e-12!83;UBERON:0003059!6.06e-12!83;UBERON:0007282!6.06e-12!83;UBERON:0009618!6.06e-12!83;UBERON:0007285!6.06e-12!83;UBERON:0001986!4.22e-10!18;UBERON:0004638!4.22e-10!18;UBERON:0004852!4.22e-10!18;UBERON:0004290!1.71e-09!70;UBERON:0006914!2.34e-09!25;UBERON:0000487!3.82e-09!22;UBERON:0000486!7.88e-09!82;UBERON:0001134!2.77e-08!61;UBERON:0002036!2.77e-08!61;UBERON:0003082!2.77e-08!61;UBERON:0004237!4.86e-08!10;UBERON:0004695!4.86e-08!10;UBERON:0002111!4.86e-08!10;UBERON:0004178!4.86e-08!10;UBERON:0000490!7.08e-08!138;UBERON:0002385!1.25e-07!63;UBERON:0001015!1.25e-07!63;UBERON:0000383!1.25e-07!63;UBERON:0003915!1.55e-07!9;UBERON:0004700!1.55e-07!9;UBERON:0001917!1.55e-07!9;UBERON:0000926!2.56e-07!448;UBERON:0004120!2.56e-07!448;UBERON:0006603!2.56e-07!448;UBERON:0000467!4.45e-07!625;UBERON:0000480!5.73e-07!626;UBERON:0000468!6.75e-07!659
|ontology_enrichment_uberon=UBERON:0000055!2.38e-25!69;UBERON:0001981!2.28e-24!60;UBERON:0007500!2.28e-24!60;UBERON:0004537!2.28e-24!60;UBERON:0006965!2.28e-24!60;UBERON:0001637!4.21e-24!42;UBERON:0003509!4.21e-24!42;UBERON:0004572!4.21e-24!42;UBERON:0004872!1.91e-22!84;UBERON:0002049!1.39e-20!79;UBERON:0007798!1.39e-20!79;UBERON:0004573!1.90e-20!33;UBERON:0004571!1.90e-20!33;UBERON:0001009!2.61e-15!113;UBERON:0004535!2.66e-15!110;UBERON:0003081!5.49e-14!216;UBERON:0000947!6.51e-14!21;UBERON:0010191!6.51e-14!21;UBERON:0002204!6.67e-14!167;UBERON:0003914!1.09e-13!118;UBERON:0000914!6.06e-12!83;UBERON:0002329!6.06e-12!83;UBERON:0003077!6.06e-12!83;UBERON:0003059!6.06e-12!83;UBERON:0007282!6.06e-12!83;UBERON:0009618!6.06e-12!83;UBERON:0007285!6.06e-12!83;UBERON:0001986!4.22e-10!18;UBERON:0004638!4.22e-10!18;UBERON:0004852!4.22e-10!18;UBERON:0004290!1.71e-09!70;UBERON:0006914!2.34e-09!25;UBERON:0000487!3.82e-09!22;UBERON:0000486!7.88e-09!82;UBERON:0001134!2.77e-08!61;UBERON:0002036!2.77e-08!61;UBERON:0003082!2.77e-08!61;UBERON:0004237!4.86e-08!10;UBERON:0004695!4.86e-08!10;UBERON:0002111!4.86e-08!10;UBERON:0004178!4.86e-08!10;UBERON:0000490!7.08e-08!138;UBERON:0002385!1.25e-07!63;UBERON:0001015!1.25e-07!63;UBERON:0000383!1.25e-07!63;UBERON:0003915!1.55e-07!9;UBERON:0004700!1.55e-07!9;UBERON:0001917!1.55e-07!9;UBERON:0000926!2.56e-07!448;UBERON:0004120!2.56e-07!448;UBERON:0006603!2.56e-07!448;UBERON:0000467!4.45e-07!625;UBERON:0000480!5.73e-07!626;UBERON:0000468!6.75e-07!659
|tf_chipseq_enrich=EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167782552212515!FOS#2353;3:8.9979553088944:0.00137249927241713:0.0089920614460807!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00437611525167183!JUN#3725;3:12.5128291923363:0.000510331399272625:0.004449699533197
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1,0.000222233,0.275244,0.00481323,0.0160457,0.141119,0.211595,0.0300692,0.131551,1.1923e-11,0.052362,0.208866,0.000676703,0.00327141,0.0974211,1.1672e-06,0.00796449,0.0906475,0.0558058,0.28262,0.000941007,0.137332,0.0145999,0.0656973,0.0241929,0.026334,9.12913e-05,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.00160873,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.0217163,0.0488949,0.174921,0.0791124,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.000251928,0.00782667,0.108872,0.11002,0.000276129,0.0286025,0.00896808,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.000173683,0.237101,0.286988,0.0761239,4.60407e-05,9.74644e-05,0.182701,0.335058,0.000603748,0.141463,0.167267,0.000517983,0.0889592,0.0538132,0.28711,0.0473033,0.094881,0.00315933,0.132886,0.0774373,0.00619136,0.128564,0.131452,0.687347,0.448776,0.051838,0.0993999,0.0500365,0.061829,0.00292564,0.0936516,0.0109165,0.0340203,0.0741807,0.277091,0.047822,0.655293,0.21727,0.00514993,0.119215,0.192475,0.177967,0.547859,0.057571,0.047591,0.000170831,0.0608699,1.88926e-06,0.300597,0.0713214,0.0271723,0.0472142,7.71484e-06,0.125606,0.00102956,0.911304,0.936279,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.000134535,0.057168,0.234298,0.0759837,0.286863,0.152372,0.194941,0.218271,0.101607,0.060512,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.504592,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.000166026,0.15503,0.0154015,0.193653,0.137219,0.0282663,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.00464715,0.264079,0.249049,0.140533,0.000178916,0.0364628,0.103667,0.113069,0.025556,0.16791,0.09066,0.585505,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.161789,0.0590944,0.0334734,0.0169521,0.218229,0.231073,0.0972686,0.619906,0.0360851,0.0998546,0.131093,0.0434602,0.133616,0.0177337,0.36927,0.449036,0.407369,0.0291288,0.544776,0.0210947,0.37006,0.42622,0.022688,0.00150618,0.396996,0.36145,0.406019,0.0841307,0.580441,0.643768,0.432035,0.366326,0.0140037,0.48809,0.0334527,0.443185,0.522904,0.875915,0.871256,0.227104,0.166658,0.617852,0.00161115,0.284625,0.156746,0.192225,0.729153,0.28907,0.0142854,0.128922,0.00506733,0.574635,0.138768,0.336276,0.468444,1.5463e-05,0.0222932,0.243383,0.777351,0.0889613,0.73485,0.683217,0.161598,0.751174,0.644754,0.496032,0.799185,0.37357,0.78509,0.477353,0.452741,0.746954,0.771991,0.20342,0.200493,0.00171127,0.00583368,0.25656,0.425963,0.349197,1.17258e-05,0.156104,0.141318,0.411941,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.0513026,0.314429,0.181415,0.282286,0.78,0.0727621,0.408413,0.516511,0.322213,0.656109,0.33942,0.61031,0.0871388,0.0391112,0.802166,0.537348,0.222037,0.416621,0.10205,0.462712,0.734551,0.215157,0.204817,3.3743e-06,0.00049814,0.308032,0.166905,0.19783,0.0833851,0.000645205,0.000585352,0.175199,0.0628556,0.373557,0.170369,0.408861,0.00124345,0.534741,0.000165487,0.363192,0.236011,0.203486,0.273398,0.0123025,0.4466,0.351067,0.275347,0.269604,0.305885,0.241132,0.371414,0.30666,0.303709,0.495883,0.386538,0.508064,0.250964,0.0131557,0.457886,0.504711,0.220231,0.509064,0.196976,0.00136659,0.0254647,0.601877,0.307334,0.459728,0.044623,0.00164832,0.135386,0.0151656,0.273281,0.368095,0.275089,0.0133102,0.47795,0.359231,0.00876091,0.197805,0.0690807,0.387069,0.000809836,0.52832,0.00579439,0.266492,0.205413,0.0165618,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.0189519,0.0719199,0.264884,0.162568,0.00135583,0.163057,0.0260582,0.0233135,0.0900729,0.0953646,0.000872573,0.252184,0.378361,0.255516,0.20753,0.0224033,0.179412,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.00803363,0.179889,0.0279371,0.27872,0.0855609,0.131118,0.20837,0.0335483,0.222339,0.0673329,0.20847,0.00394192,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.0251995,0.0132793,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.0377094,0.203781,0.21382,0.00176424,0.141867,0.193031,0.249101,0.115972,0.224568,0.0331281,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.0257454,9.87797e-05,0.202065,0.106739,0.0536053,0.0537737,0.0120432,0.078016,0.0407233,0.0537355,0.319922,0.00371523,0.211332,0.187731,0.233626,0.189559,0.0812887,0.000169901,4.62091e-05,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.00168003,0.295769,0.00499908,0.347036,0.141729,0.0037817,0.0359756,0.200105,0.0280973,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.0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}}
}}

Revision as of 12:52, 5 September 2012


Full id: C4165_schwannoma_CD14_Smooth_Fibroblast_mesenchymal_Mesenchymal_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr2:197143317..197143335,-p14@HECW2
Hg19::chr2:197143341..197143358,-p8@HECW2
Hg19::chr2:197143373..197143393,-p6@HECW2


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
non-terminally differentiated cell1.01e-19180
multi fate stem cell5.17e-16430
somatic cell1.49e-15591
somatic stem cell2.14e-15436
mesodermal cell1.78e-14119
stem cell1.80e-14444
vascular associated smooth muscle cell1.94e-1432
fibroblast4.58e-1475
endothelial cell of vascular tree3.03e-1324
animal cell1.46e-10679
eukaryotic cell1.46e-10679
smooth muscle cell3.96e-1042
smooth muscle myoblast3.96e-1042
blood vessel endothelial cell4.22e-1018
embryonic blood vessel endothelial progenitor cell4.22e-1018
CD14-positive, CD16-negative classical monocyte5.85e-1042
muscle precursor cell8.97e-1057
myoblast8.97e-1057
multi-potent skeletal muscle stem cell8.97e-1057
native cell7.02e-09722
classical monocyte1.46e-0845
muscle cell1.59e-0854
aortic smooth muscle cell4.86e-0810
contractile cell5.21e-0859
endothelial cell5.76e-0835
endothelial cell of artery1.55e-079
mesenchymal cell4.52e-07358
electrically responsive cell5.80e-0760
electrically active cell5.80e-0760
skin fibroblast6.32e-0723
Uber Anatomy
Ontology termp-valuen
vessel2.38e-2569
blood vessel2.28e-2460
epithelial tube open at both ends2.28e-2460
blood vasculature2.28e-2460
vascular cord2.28e-2460
artery4.21e-2442
arterial blood vessel4.21e-2442
arterial system4.21e-2442
splanchnic layer of lateral plate mesoderm1.91e-2284
vasculature1.39e-2079
vascular system1.39e-2079
systemic artery1.90e-2033
systemic arterial system1.90e-2033
circulatory system2.61e-15113
cardiovascular system2.66e-15110
lateral plate mesoderm5.49e-14216
aorta6.51e-1421
aortic system6.51e-1421
musculoskeletal system6.67e-14167
epithelial tube1.09e-13118
somite6.06e-1283
paraxial mesoderm6.06e-1283
presomitic mesoderm6.06e-1283
presumptive segmental plate6.06e-1283
trunk paraxial mesoderm6.06e-1283
presumptive paraxial mesoderm6.06e-1283
endothelium4.22e-1018
blood vessel endothelium4.22e-1018
cardiovascular system endothelium4.22e-1018
dermomyotome1.71e-0970
squamous epithelium2.34e-0925
simple squamous epithelium3.82e-0922
multilaminar epithelium7.88e-0982
skeletal muscle tissue2.77e-0861
striated muscle tissue2.77e-0861
myotome2.77e-0861
blood vessel smooth muscle4.86e-0810
arterial system smooth muscle4.86e-0810
artery smooth muscle tissue4.86e-0810
aorta smooth muscle tissue4.86e-0810
unilaminar epithelium7.08e-08138
muscle tissue1.25e-0763
musculature1.25e-0763
musculature of body1.25e-0763
endothelial tube1.55e-079
arterial system endothelium1.55e-079
endothelium of artery1.55e-079
mesoderm2.56e-07448
mesoderm-derived structure2.56e-07448
presumptive mesoderm2.56e-07448
anatomical system4.45e-07625
anatomical group5.73e-07626
multi-cellular organism6.75e-07659
Disease
Ontology termp-valuen
ovarian cancer9.19e-1014


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)

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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
EP300#203336.77394172622320.003216880500103790.0167782552212515
FOS#235338.99795530889440.001372499272417130.0089920614460807
GATA2#2624312.7449317335540.0004829527704283790.00437611525167183
JUN#3725312.51282919233630.0005103313992726250.004449699533197



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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