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Difference between revisions of "Coexpression cluster:C1063"

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|ontology_enrichment_disease=DOID:2394!6.93e-07!14
 
|ontology_enrichment_disease=DOID:2394!6.93e-07!14
 
|ontology_enrichment_uberon=UBERON:0000475!7.56e-11!365;UBERON:0007023!9.11e-10!115;UBERON:0001049!5.36e-07!57;UBERON:0005068!5.36e-07!57;UBERON:0006241!5.36e-07!57;UBERON:0007135!5.36e-07!57
 
|ontology_enrichment_uberon=UBERON:0000475!7.56e-11!365;UBERON:0007023!9.11e-10!115;UBERON:0001049!5.36e-07!57;UBERON:0005068!5.36e-07!57;UBERON:0006241!5.36e-07!57;UBERON:0007135!5.36e-07!57
 +
|tf_chipseq_enrich=HEY1#23462;6:3.03008328232928:0.00400172346648327:0.0191863378375819!HMGN3#9324;6:6.13391079251294:7.49603650739774e-05:0.00116102410914447!IRF3#3661;2:11.7454880528724:0.0116448804945314:0.0425312003486052!NR2C2#7182;8:32.6146109052409:7.77358645491975e-13:1.11214465173338e-10!RFX5#5993;4:6.02395541359755:0.0025264968061986:0.0139914523539199
 
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43343,0.392173,0.450361,0.125132,0.401145,0.349581,0.0857811,0.681349,0.48369,0.101821,0.151258,0.765247,0.294186,0.264629,0.267153,0.554314,0.0744668,0.88063,0.340579,0.10027,0.216542,0.140095,0.339551,0.541739,0.479289,0.429978,0.312506,0.737097,0.514064,0.594251,0.190339,0.39643,0.203718,0.416086,0.66316,0.346997,0.33418,0.386217,8.12538e-13,0.219989,0.627646,0.594435,0.121222,0.233436,0.792498,0.316293,0.193405,0.265337,0.307168,0.313275,0.201885,0.795728,0.132332,0.243599,0.127929,0.1565,0.188908,0.230656,0.339566,0.0881682,0.18579,0.579058,0.0303365,0.941584,0.479647,0.597758,0.28717,0.434522,0.407023,0.879571,0.146252,0.12193,0.150122,0.154198,0.401916,0.0719341,0.179067,0.491271,0.600481,0.0920973,0.300879,0.40148,0.998435,0.452104,0.460251,0.48128,0.0381891,0.169668,0.264355,0.126386,0.235621,0.45894,0.189069,0.117159,0.267581,0.1766,0.495277,0.358721,0.0973803,0.0561172,0.115553,0.13739,0.276387,0.229078,0.396303,0.255961,0.487366,0.145278,0.509288,0.190011,0.59406,0.356502,0.439115,0.481419,0.248532,0.652258,0.397384,0.671042,0.354931,0.158525,0.43239,0.348785,0.846337,0.36346,0.180408,0.226687,0.152678,0.340038,0.35297,0.239072,0.000105049,0.39215,0.436719,0.325366,0.498702,0.0435325,0.595929,0.28677,0.208355,0.658265,0.273994,0.272914,0.423557,0.400864,0.233355,0.558548,0.534095,0.332254,0.24444,0.548105,0.253118,0.273827,0.0667061,0.387479,0.223866,0.904489,0.385626,0.427353,0.202588,0.420356,0.364345,0.630887,0.29963,0.149927,0.531236,0.407834,0.481345,0.503758,0.752108,0.924193,0.0933565,0.757541,0.312516,0.111737,0.317827,0.423292,0.707417,0.0773817,0.752206,0.504402,0.877369,0.786493,0.708393,0.772671,0.795749,2.84675e-06,0.74047,0.697643,0.750697,0.721788,0.00969894,0.000580134,0.778763,0.663186,0.732791,0.106409,0.552306,0.790157,0.586755,0.652484,0.995774,0.496897,0.85764,0.923096,0.728237,0.590655,0.846474,0.882448,0.969291,0.597402,0.0127958,0.0016228,0.595604,0.897663,0.823504,0.0252308,0.00178608,0.00894772,0.793528,0.524662,0.908843,0.733501,0.970984,0.591309,0.375011,0.171247,0.299144,0.839155,0.425885,0.712705,0.915485,0.516094,0.774038,0.880509,0.980597,0.454729,0.000384777,0.458665,0.246976,0.00872336,0.772399,0.00118791,0.724441,0.364029,0.333879,0.757271,0.236293,0.63458,0.689159,0.0127125,0.502911,0.289349,0.590067,0.889628,0.634568,0.413633,0.00217632,0.114636,0.00032833,0.0537094,0.0472273,0.645528,0.541553,0.66902,0.459537,0.729164,0.860789,0.986712,0.87196,0.488054,0.762387,0.76203,0.809211,0.970896,0.900712,0.457276,0.799317,0.328805,0.949451,0.385504,0.444467,0.000100634,0.637438,0.825729,0.401684,0.660264,0.71269,0.861581,0.753866,0.702714,0.870027,0.733391,0.699838,0.512211,0.45485,0.20989,0.357763,0.21092,0.684354,0.576345,0.287129,0.622298,0.520881,0.0371672,0.0760525,6.69836e-05,0.839028,0.728293,0.00336624,0.537256,0.724424,0.804607,0.846436,0.484879,0.00341862,0.442887,0.432731,0.810194,0.444848,0.624396,0.806372,0.588879,0.890421,0.818739,0.743413,0.573115,0.705962,0.575942,0.72599,0.823302,0.694833,0.669433,0.44442,0.917799,0.72892,0.660067,0.865189,0.613531,0.931641,0.45836,0.403985,0.194485,0.578712,0.458152,0.0873966,0.109171,0.55014,0.426623,0.180477,0.559835,0.376936,0.431837,0.377907,0.483463,0.463074,0.222529,0.234528,0.383967,0.182225,0.13552,0.544718,0.462199,0.794152,0.409798,0.436622,0.486064,0.489702,0.672033,0.629206,6.3174e-05,0.445913,0.42387,0.296003,0.447485,0.0845698,0.229886,0.297555,0.410714,0.49649,0.581581,0.212206,0.31257,0.463718,0.531673,0.488584,0.169631,0.4639,0.56248,0.273878,0.342908,0.500922,0.376098,0.500105,0.389123,0.0993883,0.1667,0.133211,0.116907,0.565967,0.451406,0.683557,0.361689,0.289284,0.241971,0.263726,0.151053,0.477267,0.368791,0.485034,0.43963,0.297904,0.551399,0.625257,0.412086,0.371597,1.96607e-05,0.353179,0.479366,0.297272,0.41916,0.42109,0.18144,0.54956,0.554803,0.455388,0.473509,0.462252,0.335015,0.435559,0.53418,0.28015,0.492484,0.529209,0.397471,0.449258,0.330704,0.443138,0.519779,0.364755,0.312488,0.547073,0.48939,0.395736,0.0959524,0.238065,0.452384,0.62882,0.585012,0.481224,0.204547,0.452254,0.259924,0.136638,0.137048,0.353983,0.194753,0.104944,0.136955,0.642324,0.554772,0.469052,0.425619,0.50814,0.429061,0.202353,0.240717,3.5346e-05,0.292976,0.161384,0.255196,0.167238,0.190639,0.307532,0.265287,0.113346,0.168727,0.221472,0.095012,0.320667,0.456504,0.607439,0.0630067,0.679098,0.334729,0.000202631,0.545435,0.0226633,0.497569,0.070456,0.541437,0.406439,0.589165,0.559083,0.313926,0.373141,0.459861,0.447066,0.594101,0.512982,0.000758682,0.279812,0.481032,0.147402,0.278645,0.439191,0.431751,0.586217,0.588503,0.535591,0.381036,0.491941,0.230489,0.653021,0.494548,0.462673,0.23568,0.213047,0.638022,0.0145621,0.369527,0.569966,0.178571,0.568909,0.247225,0.48895,0.403105,0.366377,0.476867,0.540268,0.459344,0.697624
 
}}
 
}}

Revision as of 02:55, 5 September 2012


Full id: C1063_tenocyte_Mesenchymal_Fibroblast_Chondrocyte_mesenchymal_Olfactory_Smooth



Phase1 CAGE Peaks

Hg19::chr19:56028873..56028888,+p@chr19:56028873..56028888
+
Hg19::chr19:56028889..56028917,+p@chr19:56028889..56028917
+
Hg19::chr19:56028924..56028947,+p@chr19:56028924..56028947
+
Hg19::chr19:56028958..56028984,+p@chr19:56028958..56028984
+
Hg19::chr19:56028989..56029016,+p@chr19:56028989..56029016
+
Hg19::chr19:56029020..56029035,+p@chr19:56029020..56029035
+
Hg19::chr19:56029083..56029113,+p@chr19:56029083..56029113
+
Hg19::chr19:56029117..56029151,+p@chr19:56029117..56029151
+


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 cell1.32e-16180
fibroblast2.91e-1375
skin fibroblast3.89e-0723
Uber Anatomy
Ontology termp-valuen
organism subdivision7.56e-11365
adult organism9.11e-10115
neural tube5.36e-0757
neural rod5.36e-0757
future spinal cord5.36e-0757
neural keel5.36e-0757
Disease
Ontology termp-valuen
ovarian cancer6.93e-0714


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
HEY1#2346263.030083282329280.004001723466483270.0191863378375819
HMGN3#932466.133910792512947.49603650739774e-050.00116102410914447
IRF3#3661211.74548805287240.01164488049453140.0425312003486052
NR2C2#7182832.61461090524097.77358645491975e-131.11214465173338e-10
RFX5#599346.023955413597550.00252649680619860.0139914523539199



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.