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Coexpression cluster:C535: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0540496261796572,0.0547554531121981,0.0428357178336246,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.099145253918139,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.279649371901492,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0647398703344467,0.055966461856338,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0456863240084368,0,0.941885120679188,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.18630690345421,0.125898678133584,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.234204722446876,0.873817870884167,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.834220194413992,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0450355340939671,0.178053883355609,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0|full_id=C535_medulloblastoma_small_pineal_retinoblastoma_eye_Retinal_retina|gostat_on_coexpression_clusters=GO:0042706!eye photoreceptor cell fate commitment!0.0171023195572825!5015$GO:0046552!photoreceptor cell fate commitment!0.0171023195572825!5015$GO:0040036!regulation of fibroblast growth factor receptor signaling pathway!0.0265895153713653!5015$GO:0003723!RNA binding!0.0265895153713653!23369;57060;10073$GO:0008190!eukaryotic initiation factor 4E binding!0.0265895153713653!5015$GO:0031369!translation initiation factor binding!0.0265895153713653!5015$GO:0000339!RNA cap binding!0.0265895153713653!10073$GO:0008589!regulation of smoothened signaling pathway!0.0265895153713653!5015$GO:0001754!eye photoreceptor cell differentiation!0.0265895153713653!5015$GO:0030901!midbrain development!0.0273468007267111!5015$GO:0046530!photoreceptor cell differentiation!0.0310704218977338!5015$GO:0007224!smoothened signaling pathway!0.0360475526660574!5015$GO:0048663!neuron fate commitment!0.0360475526660574!5015$GO:0001708!cell fate specification!0.0360475526660574!5015$GO:0008543!fibroblast growth factor receptor signaling pathway!0.0360475526660574!5015$GO:0003676!nucleic acid binding!0.0360475526660574!23369;57060;5015;23648;10073$GO:0030426!growth cone!0.0360475526660574!5015$GO:0030427!site of polarized growth!0.0360475526660574!5015$GO:0048592!eye morphogenesis!0.0454975813188519!5015$GO:0042472!inner ear morphogenesis!0.0454975813188519!5015$GO:0009953!dorsal/ventral pattern formation!0.0454975813188519!5015$GO:0042471!ear 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39,0.0575305,0.703387,0.0820727,0.00571136,0.422316,0.475343,0.659236,0.718477,0.0553813,0.353235,0.206028,0.618715,0.548955,0.23831,0.417903,0.29014,0.667931,0.438854,0.138224,0.351993,0.287905,0.406303,0.385098,0.138108,0.472513,0.0396878,0.268908,0.604845,0.368899,0.2099,0.268741,0.887496,0.247928,0.739543,0.692178,0.778608,0.696084,0.381488,0.117047,0.313171,0.521318,0.312026,0.465326,0.322192,0.362027,0.184368,0.0289059,0.225577,0.324764,0.0169301,0.191154,0.560281,0.371647,0.590466,0.127776,0.0977995,0.215128,0.0978054,0.236292,0.0095755,0.42959,0.325483,0.231412,0.101288,0.0432995,0.0992882,0.550957,0.0185285,0.729869,0.133575,0.300604,0.45178,0.186278,0.154942,0.406031,0.762087,0.500463,0.707429,0.699119,0.559141,0.562518,0.804042,0.639181,0.762826,0.426931,0.0779349,0.425267,0.147504,0.435115,0.398978,0.635414,0.00480079,0.256969,0.267577,0.341643,0.533598,0.453093,0.417276,0.2997,0.000506609,0.747622,0.0266239,0.37559,0.466832|tfbs_overrepresentation_for_novel_motifs=1.40379,0.239995,0.851188,0.241986,0.364884,0.240734,0.300393,0.428015,0.189397,0.574634,0.622824,0.335828,0.321549,0.291158,0.362746,0.127101,0.489874,0.590721,0.151825,0.267126,0.139663,0.944153,0.234854,1.18916,0.507569,0.354732,0.275679,0.233219,0.369737,0.741448,0.202067,0.522822,0.0662338,0.326663,0.0937035,0.0661915,0.0919402,0.677998,0.574398,0.04349,0.309718,0.556817,0.178207,0.360378,0.582213,0.15988,0.814646,1.13784,0.070646,0.115573,0.366671,0.310813,0.167715,0.592653,0.734926,0.293507,0.118135,0.737918,0.0979814,0.266768,0.559896,0.818961,0.0509632,0.465305,0.317765,0.4351,0.818746,1.17567,1.27821,1.01727,0.181085,0.200127,0.163729,0.73304,0.311418,0.118275,0.25554,0.450429,0.510572,0.165891,0.361134,0.464358,0.851126,0.43491,0.684728,0.117061,0.045598,0.232513,0.38876,1.27332,0.90828,0.659533,0.537982,0.245209,0.114084,0.263897,0.624534,0.576706,0.392699,0.642817,1.45531,0.532876,0.571612,0.493139,0.425079,0.214722,0.479058,0.288402,0.507144,0.104263,0.450084,0.569087,0.422755,0.639318,0.862131,0.631548,0.0757057,0.582778,0.433061,0.908139,0.725237,0.386689,0.23864,0.326716,0.968805,1.14454,0.80111,0.542501,0.765493,1.42219,0.660176,1.11467,0.779127,0.323981,0.920697,0.419578,0.19775,0.233646,0.879842,1.7239,1.32497,0.844052,0.296675,0.573485,0.426604,0.260955,0.412168,1.56567,0.188015,0.0681329,0.766653,0.0731131,0.660531,1.09632,2.26362,1.04704,0.374997,0.343221,0.507668,0.459614,0.842888,0.643319,0.509866,0.152845,0.440625,0.849678,0.223866,0.299321,1.46335|tfbs_overrepresentation_jaspar=MA0003.1;1.18389,MA0004.1;0.631966,MA0006.1;0.112549,MA0007.1;0.208008,MA0009.1;0.621697,MA0014.1;0.707627,MA0017.1;0.137108,MA0019.1;0.340029,MA0024.1;0.525161,MA0025.1;0.747404,MA0027.1;2.20546,MA0028.1;0.387666,MA0029.1;0.542771,MA0030.1;0.532314,MA0031.1;0.474026,MA0038.1;0.817744,MA0040.1;0.548121,MA0041.1;0.236024,MA0042.1;0.211928,MA0043.1;0.621991,MA0046.1;0.611559,MA0048.1;0.345177,MA0050.1;0.212584,MA0051.1;0.299199,MA0052.1;0.551663,MA0055.1;0.429976,MA0056.1;0,MA0057.1;0.832754,MA0058.1;0.91108,MA0059.1;0.15289,MA0060.1;0.742387,MA0061.1;0.155208,MA0063.1;0,MA0066.1;0.302992,MA0067.1;0.924196,MA0068.1;2.06391,MA0069.1;0.607975,MA0070.1;0.597583,MA0071.1;0.746772,MA0072.1;0.593415,MA0073.1;1.35603,MA0074.1;0.298586,MA0076.1;0.164578,MA0077.1;0.586275,MA0078.1;0.382364,MA0081.1;0.465308,MA0083.1;0.628701,MA0084.1;1.10674,MA0087.1;0.591148,MA0088.1;1.04103,MA0089.1;0,MA0090.1;0.174619,MA0091.1;0.636604,MA0092.1;1.08245,MA0093.1;0.366841,MA0095.1;0,MA0098.1;0,MA0100.1;0.314026,MA0101.1;0.116395,MA0103.1;0.34743,MA0105.1;0.14145,MA0106.1;0.33677,MA0107.1;0.551112,MA0108.2;0.471286,MA0109.1;0,MA0111.1;0.541878,MA0113.1;0.350573,MA0114.1;0.25223,MA0115.1;0.850405,MA0116.1;0.949722,MA0117.1;0.656858,MA0119.1;0.438293,MA0122.1;0.681203,MA0124.1;0.810546,MA0125.1;0.730403,MA0130.1;0,MA0131.1;0.398042,MA0132.1;0,MA0133.1;0,MA0135.1;0.650071,MA0136.1;0.30842,MA0139.1;0.0351037,MA0140.1;0.269307,MA0141.1;0.151722,MA0142.1;0.445733,MA0143.1;0.350722,MA0144.1;0.231909,MA0145.1;0.0322091,MA0146.1;1.52035,MA0147.1;0.269778,MA0148.1;0.240905,MA0149.1;0.261654,MA0062.2;0.62038,MA0035.2;0.268747,MA0039.2;0.593425,MA0138.2;0.38342,MA0002.2;0.0459391,MA0137.2;0.126444,MA0104.2;0.188874,MA0047.2;0.326636,MA0112.2;0.188138,MA0065.2;1.17085,MA0150.1;0.170499,MA0151.1;0,MA0152.1;0.274535,MA0153.1;0.714423,MA0154.1;1.4034,MA0155.1;0.173363,MA0156.1;0.4018,MA0157.1;0.421609,MA0158.1;0,MA0159.1;0.270712,MA0160.1;0.252705,MA0161.1;0,MA0162.1;0.566507,MA0163.1;0.745463,MA0164.1;0.361105,MA0080.2;0.366978,MA0018.2;0.337929,MA0099.2;0.27482,MA0079.2;2.57314,MA0102.2;1.14323,MA0258.1;0.0605489,MA0259.1;0.0828875,MA0442.1;0}}
|full_id=C535_medulloblastoma_small_pineal_retinoblastoma_eye_Retinal_retina
|id=C535
}}

Latest revision as of 11:25, 17 September 2013


Full id: C535_medulloblastoma_small_pineal_retinoblastoma_eye_Retinal_retina



Phase1 CAGE Peaks

Hg19::chr11:67290913..67290920,-p1@CABP2
Hg19::chr14:57268994..57269015,+p@chr14:57268994..57269015
+
Hg19::chr14:57271021..57271034,-p@chr14:57271021..57271034
-
Hg19::chr14:57271062..57271079,-p@chr14:57271062..57271079
-
Hg19::chr14:57277178..57277203,-p1@OTX2
Hg19::chr14:57278918..57278927,-p@chr14:57278918..57278927
-
Hg19::chr15:75918721..75918732,-p7@SNUPN
Hg19::chr17:55952035..55952049,-p@chr17:55952035..55952049
-
Hg19::chr17:67712324..67712342,+p@chr17:67712324..67712342
+
Hg19::chr1:205426201..205426247,-p@chr1:205426201..205426247
-
Hg19::chr1:54791102..54791151,-p6@SSBP3
Hg19::chr22:29025920..29025935,-p@chr22:29025920..29025935
-
Hg19::chr2:20552002..20552029,-p7@PUM2
Hg19::chr3:52001448..52001478,-p2@PCBP4
Hg19::chr6:35480705..35480718,-p4@TULP1
Hg19::chr7:105241331..105241343,-p2@EFCAB10
Hg19::chrX:118425471..118425477,+p1@ENST00000428222


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:0042706eye photoreceptor cell fate commitment0.0171023195572825
GO:0046552photoreceptor cell fate commitment0.0171023195572825
GO:0040036regulation of fibroblast growth factor receptor signaling pathway0.0265895153713653
GO:0003723RNA binding0.0265895153713653
GO:0008190eukaryotic initiation factor 4E binding0.0265895153713653
GO:0031369translation initiation factor binding0.0265895153713653
GO:0000339RNA cap binding0.0265895153713653
GO:0008589regulation of smoothened signaling pathway0.0265895153713653
GO:0001754eye photoreceptor cell differentiation0.0265895153713653
GO:0030901midbrain development0.0273468007267111
GO:0046530photoreceptor cell differentiation0.0310704218977338
GO:0007224smoothened signaling pathway0.0360475526660574
GO:0048663neuron fate commitment0.0360475526660574
GO:0001708cell fate specification0.0360475526660574
GO:0008543fibroblast growth factor receptor signaling pathway0.0360475526660574
GO:0003676nucleic acid binding0.0360475526660574
GO:0030426growth cone0.0360475526660574
GO:0030427site of polarized growth0.0360475526660574
GO:0048592eye morphogenesis0.0454975813188519
GO:0042472inner ear morphogenesis0.0454975813188519
GO:0009953dorsal/ventral pattern formation0.0454975813188519
GO:0042471ear morphogenesis0.0480699371691776



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 cell1.67e-225
neuron3.42e-096
neuroblast3.42e-096
electrically signaling cell3.42e-096
pigment cell1.79e-0814
neural cell1.03e-0725
neuronal stem cell4.15e-078
neurectodermal cell5.15e-0759


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)
MA0003.11.18389
MA0004.10.631966
MA0006.10.112549
MA0007.10.208008
MA0009.10.621697
MA0014.10.707627
MA0017.10.137108
MA0019.10.340029
MA0024.10.525161
MA0025.10.747404
MA0027.12.20546
MA0028.10.387666
MA0029.10.542771
MA0030.10.532314
MA0031.10.474026
MA0038.10.817744
MA0040.10.548121
MA0041.10.236024
MA0042.10.211928
MA0043.10.621991
MA0046.10.611559
MA0048.10.345177
MA0050.10.212584
MA0051.10.299199
MA0052.10.551663
MA0055.10.429976
MA0056.10
MA0057.10.832754
MA0058.10.91108
MA0059.10.15289
MA0060.10.742387
MA0061.10.155208
MA0063.10
MA0066.10.302992
MA0067.10.924196
MA0068.12.06391
MA0069.10.607975
MA0070.10.597583
MA0071.10.746772
MA0072.10.593415
MA0073.11.35603
MA0074.10.298586
MA0076.10.164578
MA0077.10.586275
MA0078.10.382364
MA0081.10.465308
MA0083.10.628701
MA0084.11.10674
MA0087.10.591148
MA0088.11.04103
MA0089.10
MA0090.10.174619
MA0091.10.636604
MA0092.11.08245
MA0093.10.366841
MA0095.10
MA0098.10
MA0100.10.314026
MA0101.10.116395
MA0103.10.34743
MA0105.10.14145
MA0106.10.33677
MA0107.10.551112
MA0108.20.471286
MA0109.10
MA0111.10.541878
MA0113.10.350573
MA0114.10.25223
MA0115.10.850405
MA0116.10.949722
MA0117.10.656858
MA0119.10.438293
MA0122.10.681203
MA0124.10.810546
MA0125.10.730403
MA0130.10
MA0131.10.398042
MA0132.10
MA0133.10
MA0135.10.650071
MA0136.10.30842
MA0139.10.0351037
MA0140.10.269307
MA0141.10.151722
MA0142.10.445733
MA0143.10.350722
MA0144.10.231909
MA0145.10.0322091
MA0146.11.52035
MA0147.10.269778
MA0148.10.240905
MA0149.10.261654
MA0062.20.62038
MA0035.20.268747
MA0039.20.593425
MA0138.20.38342
MA0002.20.0459391
MA0137.20.126444
MA0104.20.188874
MA0047.20.326636
MA0112.20.188138
MA0065.21.17085
MA0150.10.170499
MA0151.10
MA0152.10.274535
MA0153.10.714423
MA0154.11.4034
MA0155.10.173363
MA0156.10.4018
MA0157.10.421609
MA0158.10
MA0159.10.270712
MA0160.10.252705
MA0161.10
MA0162.10.566507
MA0163.10.745463
MA0164.10.361105
MA0080.20.366978
MA0018.20.337929
MA0099.20.27482
MA0079.22.57314
MA0102.21.14323
MA0258.10.0605489
MA0259.10.0828875
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

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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