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Coexpression cluster:C1009: Difference between revisions

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{{Coexpression_clusters
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to hexose stimulus!0.0225129102418388!9971$GO:0009749!response to glucose stimulus!0.0225129102418388!9971$GO:0008206!bile acid metabolic process!0.0225129102418388!9971$GO:0009743!response to carbohydrate stimulus!0.0225129102418388!9971$GO:0015020!glucuronosyltransferase activity!0.0325085945148712!133688$GO:0047485!protein N-terminus binding!0.0325085945148712!9971$GO:0010033!response to organic 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753,0.104944,0.136955,0.642324,0.554772,0.469052,0.425619,0.50814,0.429061,0.202353,0.240717,0.162041,0.292976,0.161384,0.255196,0.167238,0.190639,0.307532,0.265287,0.113346,0.168727,0.221472,0.095012,0.320667,0.456504,0.607439,0.5938,0.679098,0.334729,0.557075,0.545435,0.448658,0.497569,0.611294,0.541437,0.0968284,0.589165,0.559083,0.313926,9.67481e-06,0.459861,0.447066,0.594101,0.512982,0.649607,0.279812,0.481032,0.491197,0.278645,0.439191,0.431751,0.586217,0.588503,0.535591,0.381036,0.491941,0.230489,0.653021,0.494548,0.462673,0.23568,0.213047,0.27019,0.394858,0.369527,0.207064,0.178571,0.568909,0.0334453,0.48895,0.403105,0.366377,0.476867,0.540268,0.459344,0.335957|tfbs_overrepresentation_for_novel_motifs=0.348717,0.0151272,0.341646,0.481684,0.301904,0.480078,2.34058,2.3861,0.190005,0.0394821,0.450635,2.4794,0.152895,0.543352,0.300614,0.322799,0.774423,0.250594,0.491486,1.42096,0.341703,0.047825,0.472508,0.29709,1.77507,0.619829,0.135503,0.470396,1.49106,0.388322,0.429397,0.810962,0.220667,0.469827,0.742281,1.59108,2.07998,0.481208,0.685417,0.174436,0.268162,0.413601,0.775279,0.299183,0.0169887,0.371118,0.555735,0.440085,2.10498,0.304949,0.63387,0.567337,0.309329,0.887323,1.03948,0.546236,0.308962,0.514077,1.26716,1.27736,0.85167,0.558065,0.190442,0.746929,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,0.400869,0.573519,0.0911419,1.03748,0.149081,0.138565,2.54475,0.730167,0.797419,0.379656,0.96869,0.745864,0.575394,0.19474,0.986227,2.4135,0.9432,0.118789,0.659621,1.59442,1.22073,0.959334,0.827657,0.227232,0.302606,1.24975,0.162291,0.87,0.664183,0.106284,0.688301,0.822041,0.864454,0.778061,1.67288,0.446229,0.762347,0.539961,2.66369,1.42617,0.352381,0.861701,0.336372,1.1633,1.17281,0.265019,0.0278613,0.428232,0.710479,3.49131,1.02923,0.657218,0.477387,0.586509,1.28328,0.730921,0.548418,0.83262,1.07171,0.674618,0.960022,0.432175,1.08604,0.583225,1.23359,0.364369,1.90503,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,2.01337,0.703126,0.505785,0.686615,1.88987,0.410382,0.637373,0.0833399,0.0510299,0.960402,0.183004,0.557588,1.36372,0.643609,0.288769,0.385642,0.357927,1.15277,0.941964,0.796636,0.36101,0.71907,0.574616,0.213234,0.553354,0.00340764|tfbs_overrepresentation_jaspar=MA0003.1;0.140538,MA0004.1;0.455723,MA0006.1;0.300178,MA0007.1;0.437331,MA0009.1;0.918715,MA0014.1;0.727045,MA0017.1;0.337901,MA0019.1;0.602411,MA0024.1;3.16573,MA0025.1;1.05265,MA0027.1;2.5321,MA0028.1;0.315574,MA0029.1;0.832916,MA0030.1;0.821423,MA0031.1;0.756713,MA0038.1;0.557409,MA0040.1;0.838784,MA0041.1;0.474018,MA0042.1;0.442535,MA0043.1;0.919032,MA0046.1;0.90778,MA0048.1;0.0955945,MA0050.1;0.443405,MA0051.1;0.553205,MA0052.1;0.842664,MA0055.1;0.283474,MA0056.1;0,MA0057.1;1.05663,MA0058.1;0.362328,MA0059.1;0.361075,MA0060.1;0.190336,MA0061.1;0.165998,MA0063.1;0,MA0066.1;0.557833,MA0067.1;1.23721,MA0068.1;0.823119,MA0069.1;0.903908,MA0070.1;0.892666,MA0071.1;0.518907,MA0072.1;0.888148,MA0073.1;9.20286e-05,MA0074.1;0.552456,MA0076.1;0.377799,MA0077.1;0.880402,MA0078.1;0.652193,MA0081.1;0.361233,MA0083.1;0.926258,MA0084.1;1.42483,MA0087.1;0.885691,MA0088.1;0.054222,MA0089.1;0,MA0090.1;0.391903,MA0091.1;0.458301,MA0092.1;0.421159,MA0093.1;0.303084,MA0095.1;0,MA0098.1;0,MA0100.1;0.571227,MA0101.1;0.30624,MA0103.1;0.792149,MA0105.1;0.0818021,MA0106.1;0.59853,MA0107.1;0.236528,MA0108.2;0.753643,MA0109.1;0,MA0111.1;0.405141,MA0113.1;0.614917,MA0114.1;0.231781,MA0115.1;1.1606,MA0116.1;0.239768,MA0117.1;0.956472,MA0119.1;0.345493,MA0122.1;0.982472,MA0124.1;1.11898,MA0125.1;1.0347,MA0130.1;0,MA0131.1;0.670358,MA0132.1;0,MA0133.1;0,MA0135.1;0.949204,MA0136.1;0.564434,MA0139.1;0.155155,MA0140.1;0.516266,MA0141.1;0.359385,MA0142.1;0.724856,MA0143.1;0.615094,MA0144.1;0.218541,MA0145.1;0.0613434,MA0146.1;0.00761723,MA0147.1;0.243042,MA0148.1;0.480298,MA0149.1;0.506665,MA0062.2;0.161302,MA0035.2;0.515566,MA0039.2;0.00133745,MA0138.2;0.653421,MA0002.2;0.531206,MA0137.2;0.321796,MA0104.2;0.189646,MA0047.2;0.586412,MA0112.2;1.21228,MA0065.2;0.0631316,MA0150.1;0.386144,MA0151.1;0,MA0152.1;3.2939,MA0153.1;2.32222,MA0154.1;0.274121,MA0155.1;0.197713,MA0156.1;0.323987,MA0157.1;0.697424,MA0158.1;0,MA0159.1;0.243637,MA0160.1;0.495355,MA0161.1;0,MA0162.1;0.0163939,MA0163.1;0.0104024,MA0164.1;0.627336,MA0080.2;0.303167,MA0018.2;0.599912,MA0099.2;0.523145,MA0079.2;0.13841,MA0102.2;1.46209,MA0258.1;0.209744,MA0259.1;0.25092,MA0442.1;0}}
|full_id=C1009_kidney_liver_renal_Hepatocyte_small_temporal_pineal
|id=C1009
}}

Latest revision as of 11:35, 17 September 2013


Full id: C1009_kidney_liver_renal_Hepatocyte_small_temporal_pineal



Phase1 CAGE Peaks

Hg19::chr12:100897130..100897149,+p3@NR1H4
Hg19::chr5:35991404..35991414,-p4@UGT3A1
Hg19::chr5:35991417..35991426,-p5@UGT3A1
Hg19::chr5:35991427..35991444,-p3@UGT3A1
Hg19::chr5:35991458..35991478,-p1@UGT3A1
Hg19::chr5:35991486..35991509,-p2@UGT3A1
Hg19::chr5:35991543..35991554,-p6@UGT3A1
Hg19::chr7:47539812..47539818,-p@chr7:47539812..47539818
-


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:0009746response to hexose stimulus0.0225129102418388
GO:0009749response to glucose stimulus0.0225129102418388
GO:0008206bile acid metabolic process0.0225129102418388
GO:0009743response to carbohydrate stimulus0.0225129102418388
GO:0015020glucuronosyltransferase activity0.0325085945148712
GO:0047485protein N-terminus binding0.0325085945148712
GO:0010033response to organic substance0.0442824213577431



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
embryonic stem cell2.52e-105


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)
MA0003.10.140538
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.727045
MA0017.10.337901
MA0019.10.602411
MA0024.13.16573
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.0955945
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.283474
MA0056.10
MA0057.11.05663
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.165998
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.823119
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.19.20286e-05
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.054222
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.792149
MA0105.10.0818021
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.155155
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.10.0613434
MA0146.10.00761723
MA0147.10.243042
MA0148.10.480298
MA0149.10.506665
MA0062.20.161302
MA0035.20.515566
MA0039.20.00133745
MA0138.20.653421
MA0002.20.531206
MA0137.20.321796
MA0104.20.189646
MA0047.20.586412
MA0112.21.21228
MA0065.20.0631316
MA0150.10.386144
MA0151.10
MA0152.13.2939
MA0153.12.32222
MA0154.10.274121
MA0155.10.197713
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.10.0163939
MA0163.10.0104024
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.20.13841
MA0102.21.46209
MA0258.10.209744
MA0259.10.25092
MA0442.10



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
SIX5#147912612.81503651659421.01387748137864e-064.27658926808173e-05
SP1#666774.986083705873283.46905874958224e-050.000680257278910288
TAF1#687262.507284714308970.01111734475613860.0408803735295529
TBP#690862.780078015322290.006390181121263010.0278007217413808



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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