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Coexpression cluster:C3342: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007023!5.77e-18!114;UBERON:0000481!7.54e-14!342;UBERON:0000479!2.25e-12!773;UBERON:0007100!7.60e-12!27;UBERON:0000468!1.81e-11!656;UBERON:0000948!2.02e-10!24;UBERON:0005498!2.02e-10!24;UBERON:0004140!2.02e-10!24;UBERON:0009881!2.02e-10!24;UBERON:0004141!2.02e-10!24;UBERON:0003084!2.02e-10!24;UBERON:0007005!2.02e-10!24;UBERON:0004139!2.02e-10!24;UBERON:0004291!2.02e-10!24;UBERON:0007524!1.66e-09!73;UBERON:0000062!2.28e-09!503;UBERON:0003077!4.85e-09!72;UBERON:0007285!4.85e-09!72;UBERON:0002385!5.46e-09!64;UBERON:0001015!5.46e-09!64;UBERON:0000383!5.46e-09!64;UBERON:0003104!6.28e-09!160;UBERON:0009142!6.28e-09!160;UBERON:0002329!6.84e-09!71;UBERON:0003059!6.84e-09!71;UBERON:0007282!6.84e-09!71;UBERON:0004290!6.84e-09!71;UBERON:0009618!6.84e-09!71;UBERON:0001134!2.57e-08!62;UBERON:0002036!2.57e-08!62;UBERON:0003082!2.57e-08!62;UBERON:0000467!3.98e-08!624;UBERON:0000480!5.53e-08!625;UBERON:0010314!7.70e-08!132;UBERON:0007503!1.08e-07!78;UBERON:0003103!1.27e-07!68;UBERON:0003102!1.40e-07!99;UBERON:0000477!1.95e-07!373;UBERON:0005256!3.10e-07!122;UBERON:0000486!6.28e-07!83
|ontology_enrichment_uberon=UBERON:0007023!5.77e-18!114;UBERON:0000481!7.54e-14!342;UBERON:0000479!2.25e-12!773;UBERON:0007100!7.60e-12!27;UBERON:0000468!1.81e-11!656;UBERON:0000948!2.02e-10!24;UBERON:0005498!2.02e-10!24;UBERON:0004140!2.02e-10!24;UBERON:0009881!2.02e-10!24;UBERON:0004141!2.02e-10!24;UBERON:0003084!2.02e-10!24;UBERON:0007005!2.02e-10!24;UBERON:0004139!2.02e-10!24;UBERON:0004291!2.02e-10!24;UBERON:0007524!1.66e-09!73;UBERON:0000062!2.28e-09!503;UBERON:0003077!4.85e-09!72;UBERON:0007285!4.85e-09!72;UBERON:0002385!5.46e-09!64;UBERON:0001015!5.46e-09!64;UBERON:0000383!5.46e-09!64;UBERON:0003104!6.28e-09!160;UBERON:0009142!6.28e-09!160;UBERON:0002329!6.84e-09!71;UBERON:0003059!6.84e-09!71;UBERON:0007282!6.84e-09!71;UBERON:0004290!6.84e-09!71;UBERON:0009618!6.84e-09!71;UBERON:0001134!2.57e-08!62;UBERON:0002036!2.57e-08!62;UBERON:0003082!2.57e-08!62;UBERON:0000467!3.98e-08!624;UBERON:0000480!5.53e-08!625;UBERON:0010314!7.70e-08!132;UBERON:0007503!1.08e-07!78;UBERON:0003103!1.27e-07!68;UBERON:0003102!1.40e-07!99;UBERON:0000477!1.95e-07!373;UBERON:0005256!3.10e-07!122;UBERON:0000486!6.28e-07!83
|tfbs_overrepresentation=0.0114172,0.0586687,0.134243,1.87775e-05,0.199763,0.287811,0.000938367,0.0172144,0.03272,0.000333258,0.139423,0.225367,0.188771,0.000367918,0.0116452,0.0619003,0.010441,0.0982016,0.00142191,0.108057,0.188635,0.132577,3.5527e-08,0.0948982,0.0415721,0.00198832,0.0236364,0.0907212,0.000554732,0.0933697,0.204953,0.114046,0.0180314,0.0233668,0.0665252,0.000107245,0.688181,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.00115331,0.111283,1.04722e-05,0.154071,0.0541794,6.0767e-05,0.0929951,0.00153794,0.0384161,0.00599201,0.212709,0.0783235,0.00577992,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.0709764,0.0600088,0.0860723,0.167053,1.07995e-05,9.50108e-07,0.089036,0.00742795,2.80156e-05,0.0171177,0.000161406,0.0436945,0.0372495,0.00725252,0.0956287,0.00234531,0.0425,0.114846,3.03235e-05,0.00327964,0.064341,0.209032,0.0028047,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.00375405,0.115028,0.0124566,0.153631,0.0927458,1.14229e-06,0.00168491,0.0422457,0.141874,0.0370665,0.0259741,0.00084924,0.00229559,0.00862108,0.144217,0.0400492,0.0177901,0.0339971,0.149552,0.0176855,0.000187023,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.000112432,0.102368,0.176912,0.000133364,0.0147934,0.0843604,0.134932,0.0595773,7.39968e-05,0.0572164,0.0227861,0.125792,0.108101,0.00215071,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.000716344,0.013844,0.0693171,0.00505227,0.00365114,0.0389418,0.120833,0.200647,6.57584e-07,2.22131e-06,0.0265818,0.0427088,0.117549,7.37694e-05,0.00239446,0.0516985,0.0337251,0.227719,0.00469088,0.000289805,0.000604898,0.0413643,0.114283,0.0400322,7.90463e-09,0.0403542,4.47691e-05,0.0172085,0.00995227,0.00384591,0.0541353,0.0799324,0.090079,5.80919e-07,2.29494e-06,0.178449,0.0356339,3.2496e-05,0.00782633,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.00100145,0.00595679,0.0187509,0.122935,7.95188e-06,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.00411171,0.060398,0.0308319,6.05487e-07,0.136451,0.037005,0.0042906,0.0121616,4.52842e-06,0.178359,1.82852e-09,0.104357,0.000325955,0.000261991,2.87248e-10,4.2282e-05,0.0142864,0.100942,4.37286e-05,0.10299,0.0105855,0.00135672,0.0128655,0.0137227,0.0738599,1.4687e-10,0.138852,0.085973,3.85687e-05,0.00183069,0.569726,0.0133328,0.0418404,0.00300396,0.0959204,0.0931946,0.00113319,0.00377835,0.163502,0.214803,0.182472,0.348993,0.00500828,0.0830921,0.116283,0.136838,3.44988e-08,0.111647,6.35068e-07,9.05256e-06,0.159052,0.185164,0.01843,0.0980288,0.0980899,0.159674,0.107242,0.201859,1.06426e-06,0.0585224,0.0619218,0.0163125,0.163376,0.128096,0.0345133,0.0810678,0.0811639,6.46253e-08,0.000300991,0.0755168,0.278352,0.063292,0.0356268,0.446759,0.00386209,0.000733101,0.000407334,0.00212189,0.0381789,0.0691572,0.000626254,0.00163772,0.00879988,0.228731,0.00083951,0.0185583,0.0376513,0.446302,0.00137759,0.053682,0.0313047,0.0619618,0.0018019,0.00791734,0.00116194,0.615744,0.0408801,0.00531795,0.0159894,0.39729,0.000290219,0.00244849,2.68728e-06,0.00120175,0.0176124,0.10624,0.109988,0.0620388,0.218329,8.6146e-09,0.0124294,0.000464237,0.000107655,0.00734087,0.168255,0.0117562,0.415647,0.0297533,6.76778e-07,0.000355279,0.301787,4.83115e-07,0.00695027,0.223503,0.503224,0.0669244,0.000396188,0.000629694,0.000273712,0.00529148,3.09818e-06,3.45546e-06,0.102333,1.78751e-06,0.0280875,0.000335927,0.373868,0.57762,0.0154652,0.18237,0.0359955,0.0964442,0.747852,0.275351,0.0304678,0.0012387,0.346319,0.00117453,0.00415948,0.258117,0.000781971,0.0367769,0.00691094,0.0338468,0.00471332,0.00419907,0.0141151,0.0670502,0.0730934,0.0012205,0.0641718,0.0582356,0.00029074,0.0002295,0.000159654,0.0462094,0.0477082,0.0225539,0.218623,0.000612438,0.117923,0.001033,1.42689e-06,0.00241532,0.0897888,0.0129683,0.50215,0.294698,0.34331,0.477304,0.289204,5.85515e-05,0.109738,0.000362229,0.000315884,0.0193295,0.228096,0.00847033,0.0209597,0.0129079,0.0530502,1.81028e-06,0.00466824,0.420626,0.165111,0.311758,0.335105,0.144809,7.03762e-07,0.385517,0.376191,0.0032214,0.00368553,0.00329638,0.152681,0.0465712,0.137098,0.259235,0.00952201,9.20626e-08,0.00870714,0.048108,0.284593,0.00911104,2.4453e-06,5.64763e-09,0.601433,8.82943e-06,0.0391885,2.91941e-09,1.69523e-05,0.0741332,0.226257,0.0965765,0.0175765,5.16074e-07,0.464871,0.166672,0.0228979,0.00713629,0.000779217,0.020698,0.269226,0.339277,0.0479524,1.36436e-06,6.12624e-07,0.0238793,0.168058,0.159617,0.238587,0.0799758,0.0293409,0.189515,0.0891382,0.0595618,0.00103044,0.0178839,0.347298,1.70045e-05,0.0699395,0.475069,0.404569,0.273024,0.630264,0.316179,0.0697683,0.0556835,0.0198561,0.00312417,0.0575676,0.144322,0.000139175,1.59413e-07,2.02556e-07,0.441735,0.191777,0.111931,0.0051519,0.0435386,0.00601662,0.000372475,0.000454603,0.10689,0.273326,0.0627924,0.0842821,0.0179103,3.8523e-05,0.279795,0.0140073,1.73429e-05,0.0152726,0.114583,0.00566743,0.0899537,0.0866966,0.0135136,0.107111,1.45442e-05,0.0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}}
}}

Revision as of 16:04, 26 November 2012


Full id: C3342_tenocyte_skin_umbilical_Fibroblast_trachea_heart_Synoviocyte



Phase1 CAGE Peaks

Hg19::chr12:91576471..91576491,-p5@DCN
Hg19::chr12:91576497..91576508,-p8@DCN
Hg19::chr12:91576561..91576613,-p1@DCN


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
fibroblast2.18e-1576
stromal cell1.57e-0728
skin fibroblast2.51e-0723
muscle precursor cell6.92e-0758
myoblast6.92e-0758
multi-potent skeletal muscle stem cell6.92e-0758
Uber Anatomy
Ontology termp-valuen
adult organism5.77e-18114
multi-tissue structure7.54e-14342
tissue2.25e-12773
primary circulatory organ7.60e-1227
multi-cellular organism1.81e-11656
heart2.02e-1024
primitive heart tube2.02e-1024
primary heart field2.02e-1024
anterior lateral plate mesoderm2.02e-1024
heart tube2.02e-1024
heart primordium2.02e-1024
cardiac mesoderm2.02e-1024
cardiogenic plate2.02e-1024
heart rudiment2.02e-1024
dense mesenchyme tissue1.66e-0973
organ2.28e-09503
paraxial mesoderm4.85e-0972
presumptive paraxial mesoderm4.85e-0972
muscle tissue5.46e-0964
musculature5.46e-0964
musculature of body5.46e-0964
mesenchyme6.28e-09160
entire embryonic mesenchyme6.28e-09160
somite6.84e-0971
presomitic mesoderm6.84e-0971
presumptive segmental plate6.84e-0971
dermomyotome6.84e-0971
trunk paraxial mesoderm6.84e-0971
skeletal muscle tissue2.57e-0862
striated muscle tissue2.57e-0862
myotome2.57e-0862
anatomical system3.98e-08624
anatomical group5.53e-08625
structure with developmental contribution from neural crest7.70e-08132
epithelial vesicle1.08e-0778
compound organ1.27e-0768
surface structure1.40e-0799
anatomical cluster1.95e-07373
trunk mesenchyme3.10e-07122
multilaminar epithelium6.28e-0783


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

No analysis results for this cluster

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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