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Coexpression cluster:C546: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!7.81e-20!115;UBERON:0000475!1.34e-13!365;UBERON:0000468!1.54e-12!659;UBERON:0000481!4.75e-12!347;UBERON:0000477!2.30e-09!286;UBERON:0000483!2.15e-08!309;UBERON:0000119!3.16e-08!312;UBERON:0004111!3.38e-08!241;UBERON:0000480!3.70e-08!626;UBERON:0000467!6.04e-08!625;UBERON:0007100!1.70e-07!27;UBERON:0000062!6.23e-07!511;UBERON:0002100!8.05e-07!216;UBERON:0005256!9.33e-07!143
|ontology_enrichment_uberon=UBERON:0007023!7.81e-20!115;UBERON:0000475!1.34e-13!365;UBERON:0000468!1.54e-12!659;UBERON:0000481!4.75e-12!347;UBERON:0000477!2.30e-09!286;UBERON:0000483!2.15e-08!309;UBERON:0000119!3.16e-08!312;UBERON:0004111!3.38e-08!241;UBERON:0000480!3.70e-08!626;UBERON:0000467!6.04e-08!625;UBERON:0007100!1.70e-07!27;UBERON:0000062!6.23e-07!511;UBERON:0002100!8.05e-07!216;UBERON:0005256!9.33e-07!143
|tfbs_overrepresentation=3.55939e-09,0.290083,0.000462679,0.241984,0.134409,0.853881,0.220501,0.190468,4.52773e-05,0.137198,0.572952,5.05041e-11,0.694405,0.000143166,0.014067,0.303784,0.213332,2.81714e-06,0.264861,0.47691,3.37901e-05,0.193353,0.0855959,0.0198,0.213853,2.83235e-09,1.82735e-10,0.416622,0.584971,0.107461,6.41625e-05,0.000719076,0.0979725,1.79827e-09,0.0589176,1.00382e-06,0.998644,0.220321,1.12762e-05,3.56352e-06,2.49605e-06,4.16038e-07,0.00188078,0.684122,0.166402,0.188753,0.197184,0.0284049,0.144943,0.519116,0.612542,0.270683,0.337835,0.424841,9.76024e-08,0.199071,5.73245e-05,1.26504e-05,0.370091,0.468598,0.155722,0.600306,0.478718,0.360835,0.272384,2.67324e-14,0.446144,0.295791,0.399517,0.0212613,1.70325e-12,1.87383e-11,0.410469,0.51345,0.041632,0.0932062,0.4373,0.223668,0.193549,0.0404083,0.434241,0.767388,0.218157,0.499075,0.00397676,0.806809,0.313986,0.735211,0.0204792,0.307337,0.398342,0.250391,0.0200762,0.240442,0.396968,3.72853e-09,5.1645e-06,0.0705029,0.423945,0.0375387,0.285013,2.24571e-05,0.579799,0.19268,0.75373,0.210857,0.324914,0.414082,3.84073e-05,0.0348464,0.680994,0.177989,0.600665,0.0961704,0.123463,0.176809,0.109917,0.0439496,0.00181813,0.00170397,0.00419881,0.159212,0.211273,0.398438,0.45772,0.0259828,0.416499,0.0809874,0.00174427,0.560171,3.92466e-09,0.356459,0.283854,0.122444,0.53318,0.477054,0.316158,0.275722,0.173362,0.0222073,0.122393,0.0436995,0.725372,0.249922,0.886949,0.334405,0.445471,0.392616,0.201549,1.03385e-20,0.718905,0.584778,0.0060575,0.141586,0.219122,0.507682,0.356162,4.51587e-07,0.259776,0.176676,4.62809e-13,0.433014,0.504808,0.59595,0.540259,0.497267,0.206669,0.53793,0.208176,7.47809e-05,2.03157e-11,0.568158,0.0280534,0.27049,0.0818583,0.000234389,0.575509,0.00622668,6.14987e-15,0.18585,0.624767,0.523049,0.145697,0.501404,0.352071,0.51177,3.35757e-06,0.20734,0.387496,0.000133339,0.473872,0.00711907,9.80162e-08,4.61001e-07,0.0314485,0.239082,0.078832,0.296967,0.327619,0.482258,0.411443,0.297442,0.162609,0.00569498,0.0103333,0.507298,1.17703e-13,5.43786e-05,0.729984,0.671502,0.233607,0.464493,2.51058e-11,7.62427e-05,1.80526e-12,0.28242,0.0200116,0.452821,0.308375,0.459846,0.579955,0.740299,0.617676,0.000578799,3.98926e-07,0.179441,0.571345,0.399148,0.00049048,0.295312,0.0546112,0.297574,0.2151,5.081e-07,0.112581,0.425557,0.239779,0.515999,0.63639,2.71444e-09,1.36217e-13,9.63866e-06,0.00310732,0.000159193,0.000788044,0.565633,0.382333,4.15451e-08,0.49243,0.000812092,0.00338564,0.000205369,0.687884,2.7834e-06,4.03036e-11,0.626861,5.74822e-12,0.721312,4.56555e-06,0.0647731,0.00605186,0.000141444,0.636081,0.540107,0.180475,0.380645,0.381012,0.421492,0.50935,0.00114713,4.00695e-06,0.309616,0.81107,0.431658,0.401444,0.197322,0.00133825,0.0312002,0.177486,0.861804,0.676413,1.29127e-07,0.521398,0.333817,3.72306e-09,3.61183e-10,0.820605,0.246527,0.0188639,6.83114e-05,0.000635297,0.00886318,1.07148e-08,0.000127712,4.9025e-05,0.180732,0.108481,0.135377,0.176319,2.0551e-06,1.47229e-08,6.75683e-09,0.691146,2.99178e-10,0.679034,0.0971285,0.483293,8.67924e-07,1.59153e-05,0.00159428,2.4716e-05,0.000307982,0.143598,0.000488675,0.241674,4.59854e-10,0.0357974,9.67533e-06,0.809337,0.00286786,0.0559263,1.72588e-08,1.67309e-05,0.761516,6.95931e-05,0.00298392,0.849069,1.85843e-11,1.00148e-06,2.85844e-09,1.22639e-05,0.716371,0.0131547,4.29329e-15,0.881044,1.37583e-08,0.00599103,0.00456009,0.613772,0.315936,0.263476,0.965771,0.259758,0.0382455,7.66879e-14,0.687707,1.84416e-19,0.0137992,0.534482,0.000230845,0.0202705,0.583348,1.01932e-07,2.33513e-10,0.846483,0.0752041,5.14282e-12,5.65877e-05,0.069804,0.685817,0.00675673,0.822555,1.25596e-10,0.356629,1.23464e-22,5.24296e-10,1.67726e-08,2.70196e-06,0.752898,8.59892e-09,0.000229512,0.0287873,0.356137,0.0173668,0.249424,9.51982e-10,0.000827094,0.317476,0.000190625,0.500885,0.305582,7.43638e-07,0.0343265,0.842157,0.0534009,2.8507e-05,0.182935,3.22267e-05,0.00905783,0.0736524,0.000131496,2.14888e-11,7.14404e-15,0.0384114,6.8971e-14,0.999816,0.672067,0.587879,4.08466e-05,0.00221067,1.13501e-11,5.07869e-05,2.16911e-17,1.35117e-06,0.241757,0.236808,0.204047,0.000388345,0.559756,0.0219603,0.00230986,0.000213092,0.565622,0.00019294,0.00549856,0.0191495,0.269526,8.76648e-09,8.70631e-06,0.000788351,0.0312789,0.0148705,5.3696e-11,4.28489e-10,1.67064e-11,4.20184e-11,4.92315e-06,0.0323606,0.729836,0.0115223,0.00134283,8.49387e-06,0.00239726,0.41675,0.832422,5.40034e-32,3.41968e-05,0.668565,9.52384e-08,0.258877,0.202433,9.85493e-05,4.0425e-06,0.334006,0.0991423,0.0481753,0.608006,0.323844,2.20311e-13,0.000648386,0.0381364,0.000419847,0.000945117,0.0709659,1.3994e-07,0.000403782,0.0642048,0.277231,0.702373,0.0783777,0.285365,0.00031117,0.0574746,6.10958e-05,0.0202456,0.963235,6.04741e-07,0.489655,0.0470221,0.22295,0.0051425,0.535251,0.559938,0.027315,0.836222,0.307527,0.934228,0.0973421,0.871668,0.0408974,0.531662,0.236407,0.651165,0.498231,0.130475,0.413826,7.65004e-08,0.018193,0.00425925,1.08924e-08,0.0218474,0.0401833,0.543267,0.737737,3.65352e-1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}}
}}

Revision as of 20:30, 8 August 2012


Full id: C546_Chondrocyte_heart_mature_Adipocyte_teratocarcinoma_aorta_dura



Phase1 CAGE Peaks

Hg19::chr1:203316711..203316750,-p14@FMOD
Hg19::chr1:203317084..203317101,-p10@FMOD
Hg19::chr1:203317142..203317164,-p9@FMOD
Hg19::chr1:203317172..203317190,-p12@FMOD
Hg19::chr1:203317193..203317209,-p11@FMOD
Hg19::chr1:203317210..203317231,-p4@FMOD
Hg19::chr1:203317215..203317230,+p@chr1:203317215..203317230
+
Hg19::chr1:203317232..203317258,+p@chr1:203317232..203317258
+
Hg19::chr1:203317238..203317258,-p7@FMOD
Hg19::chr1:203317259..203317301,-p6@FMOD
Hg19::chr1:203317308..203317324,-p5@FMOD
Hg19::chr1:203317353..203317375,-p3@FMOD
Hg19::chr1:203317378..203317395,-p8@FMOD
Hg19::chr1:203317396..203317407,-p15@FMOD
Hg19::chr1:203320210..203320240,-p1@FMOD
Hg19::chr1:203320243..203320268,-p2@FMOD
Hg19::chr1:203444976..203444984,+p7@PRELP


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


GO IDGO nameFDR corrected p-value
GO:0005578proteinaceous extracellular matrix0.00341442593854242
GO:0007181transforming growth factor beta receptor complex assembly0.00341442593854242
GO:0044421extracellular region part0.00692871299278988
GO:0007179transforming growth factor beta receptor signaling pathway0.0213257131623092
GO:0043623cellular protein complex assembly0.0216017803139587
GO:0007178transmembrane receptor protein serine/threonine kinase signaling pathway0.0216017803139587
GO:0005201extracellular matrix structural constituent0.0299456268119611
GO:0001501skeletal development0.0444663593839121



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
non-terminally differentiated cell4.36e-10180
fat cell1.43e-0915
fibroblast2.66e-0875
Uber Anatomy
Ontology termp-valuen
adult organism7.81e-20115
organism subdivision1.34e-13365
multi-cellular organism1.54e-12659
multi-tissue structure4.75e-12347
anatomical cluster2.30e-09286
epithelium2.15e-08309
cell layer3.16e-08312
anatomical conduit3.38e-08241
anatomical group3.70e-08626
anatomical system6.04e-08625
primary circulatory organ1.70e-0727
organ6.23e-07511
trunk8.05e-07216
trunk mesenchyme9.33e-07143


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.