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MCL coexpression mm9:473: Difference between revisions

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{{MCL_coexpression_mm9
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nucleoside, nucleotide and nucleic acid metabolic process;0.0474044833244923;22688,71389,232339,70208,209584,432508,109151!GO:0016070;RNA metabolic process;0.0474044833244923;22688,232339,70208,209584,432508,109151!GO:0003682;chromatin binding;0.0474044833244923;71389,109151!GO:0004386;helicase activity;0.0474044833244923;71389,109151!GO:0006333;chromatin assembly or disassembly;0.0474044833244923;71389,109151!GO:0010467;gene expression;0.0474044833244923;22688,232339,70208,209584,432508,109151!GO:0006355;regulation of transcription, DNA-dependent;0.0474044833244923;22688,232339,70208,432508,109151!GO:0006351;transcription, DNA-dependent;0.0474044833244923;22688,232339,70208,432508,109151!GO:0032774;RNA biosynthetic process;0.0474044833244923;22688,232339,70208,432508,109151!GO:0003677;DNA binding;0.0474044833244923;22688,71389,232339,432508,109151!GO:0045449;regulation of transcription;0.0474044833244923;22688,232339,70208,432508,109151!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic 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|gostat_on_MCL_coexpression=GO:0005634;nucleus;0.0474044833244923;72154,224694,243308,432508,109151,22688,71389,70208!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0474044833244923;22688,71389,232339,70208,209584,432508,109151!GO:0016070;RNA metabolic process;0.0474044833244923;22688,232339,70208,209584,432508,109151!GO:0003682;chromatin binding;0.0474044833244923;71389,109151!GO:0004386;helicase activity;0.0474044833244923;71389,109151!GO:0006333;chromatin assembly or disassembly;0.0474044833244923;71389,109151!GO:0010467;gene expression;0.0474044833244923;22688,232339,70208,209584,432508,109151!GO:0006355;regulation of transcription, DNA-dependent;0.0474044833244923;22688,232339,70208,432508,109151!GO:0006351;transcription, DNA-dependent;0.0474044833244923;22688,232339,70208,432508,109151!GO:0032774;RNA biosynthetic process;0.0474044833244923;22688,232339,70208,432508,109151!GO:0003677;DNA binding;0.0474044833244923;22688,71389,232339,432508,109151!GO:0045449;regulation of transcription;0.0474044833244923;22688,232339,70208,432508,109151!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0474044833244923;22688,232339,70208,432508,109151!GO:0006350;transcription;0.0474044833244923;22688,232339,70208,432508,109151!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0010371!4.60e-10!73;UBERON:0002346!6.60e-10!64;UBERON:0003075!6.60e-10!64;UBERON:0007284!6.60e-10!64;UBERON:0003056!1.23e-09!49;UBERON:0000468!3.74e-08!333;UBERON:0004121!3.17e-07!95;UBERON:0000924!3.17e-07!95;UBERON:0006601!3.17e-07!95;UBERON:0000153!9.30e-07!43
|tfbs_overrepresentation_for_novel_motifs=0.206403,0.393113,0.186933,0.238864,0.356286,0.250289,0.324772,0.460624,0.223561,0.563871,0.785008,0.314655,0.461246,0.335151,0.120865,0,1.26156,0.105493,0.1896,0.993192,0.483972,0.138504,0.888941,0.109412,0.561942,0.35869,0.401215,0.267095,1.37478,0.867592,0.255771,0.598971,0.339783,0.634402,0.384512,0.0584849,0.0985485,0.311629,0.290566,0.902111,0.349739,0.259911,0.252106,0.122151,0.147772,0.230148,0.433813,0.766153,0.198601,0.141659,0.48979,0.381972,0.11734,0.732469,0.749094,0.341233,0.147717,0.820802,0.0433654,0.900327,0.580338,0.390204,0.240695,0.479581,0.350748,1.28444,0.880067,1.22155,0.576002,1.07689,0.991414,0.823515,0.516236,0.781142,0.158223,1.36095,0.153229,0.423705,0.564426,0.491308,0.220193,0.521544,0.388944,0.443997,0.671442,0.348211,0.016756,0.125355,1.11664,1.38183,0.947651,0.676142,0.610915,0.114049,1.00206,0.547552,0.45422,0.613539,0.43404,0.469526,1.10792,0.59871,0.715894,0.490329,0.489372,0.719532,0.543989,0.276621,2.19788,0.487082,0.582521,0.717588,0.164285,0.292444,0.954503,0.106786,0.288832,0.241826,0.506861,0.31898,0.786314,0.46068,0.360259,0.422901,1.00724,0.567849,0.331666,0.60459,0.8786,0.747079,0.699779,0.233152,0.850049,0.352905,0.975524,0.135562,0.212784,0.722951,0.927716,1.74768,1.35029,0.884624,0.370659,0.608735,0.483498,0.260275,0.436593,1.7082,0.214583,0.111457,0.556427,0.434542,0.733963,0.954816,0.352111,0.81211,0.382849,0.128633,0.204546,1.79503,0.93695,0.670634,0.568261,1.09606,0.480505,0.345769,0.323091,0.313326,1.43556
|tfbs_overrepresentation_jaspar=MA0003.1;0.317607,MA0004.1;0.239244,MA0006.1;0.118059,MA0007.1;0.227553,MA0009.1;0.623671,MA0014.1;0.304428,MA0017.1;0.832511,MA0019.1;0.456268,MA0024.1;0.582844,MA0025.1;0.845702,MA0027.1;2.24512,MA0028.1;0.393672,MA0029.1;0.562703,MA0030.1;0.568779,MA0031.1;0.535959,MA0038.1;1.68155,MA0040.1;0.635404,MA0041.1;3.06992,MA0042.1;2.23894,MA0043.1;0.71494,MA0046.1;0.657417,MA0048.1;0.763962,MA0050.1;0.270164,MA0051.1;0.366328,MA0052.1;0.642973,MA0055.1;0.578069,MA0056.1;0,MA0057.1;0.431584,MA0058.1;0.167504,MA0059.1;0.176308,MA0060.1;4.54253,MA0061.1;0.615538,MA0063.1;0,MA0066.1;0.349199,MA0067.1;0.953264,MA0068.1;0.0216542,MA0069.1;0.643292,MA0070.1;0.634186,MA0071.1;0.269487,MA0072.1;0.626238,MA0073.1;0.000127125,MA0074.1;0.318792,MA0076.1;0.453214,MA0077.1;0.605975,MA0078.1;0.395048,MA0081.1;0.56362,MA0083.1;0.714187,MA0084.1;1.27474,MA0087.1;0.673355,MA0088.1;0.0106511,MA0089.1;0,MA0090.1;1.14829,MA0091.1;0.696557,MA0092.1;0.610874,MA0093.1;0.130107,MA0095.1;0,MA0098.1;0,MA0100.1;0.832335,MA0101.1;0.538493,MA0103.1;0.14251,MA0105.1;0.147614,MA0106.1;1.03774,MA0107.1;0.428571,MA0108.2;0.476838,MA0109.1;0,MA0111.1;0.635898,MA0113.1;0.377232,MA0114.1;0.291992,MA0115.1;0.717599,MA0116.1;0.756087,MA0117.1;0.686999,MA0119.1;0.183219,MA0122.1;0.705806,MA0124.1;0.901619,MA0125.1;0.830088,MA0130.1;0,MA0131.1;2.97464,MA0132.1;0,MA0133.1;0,MA0135.1;0.749615,MA0136.1;0.891604,MA0139.1;1.67613,MA0140.1;0.30902,MA0141.1;0.155997,MA0142.1;0.522654,MA0143.1;0.391481,MA0144.1;0.0881858,MA0145.1;1.15108,MA0146.1;1.31962,MA0147.1;0.0952713,MA0148.1;0.252062,MA0149.1;0.18682,MA0062.2;1.41609,MA0035.2;0.312946,MA0039.2;0.101713,MA0138.2;0.445088,MA0002.2;0.208749,MA0137.2;0.153989,MA0104.2;0.0641853,MA0047.2;0.357963,MA0112.2;0.54155,MA0065.2;0.160972,MA0150.1;0.227466,MA0151.1;0,MA0152.1;0.358055,MA0153.1;0.765498,MA0154.1;0.247047,MA0155.1;0.369691,MA0156.1;0.45173,MA0157.1;0.493416,MA0158.1;0,MA0159.1;0.101261,MA0160.1;0.254455,MA0161.1;0,MA0162.1;1.18203,MA0163.1;0.0289848,MA0164.1;0.892289,MA0080.2;0.430071,MA0018.2;0.344133,MA0099.2;0.439458,MA0079.2;0.140632,MA0102.2;1.32652,MA0258.1;0.271229,MA0259.1;0.299239,MA0442.1;0
}}

Latest revision as of 15:22, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:116814011..116814034,-p1@Cpsf6
Mm9::chr10:24589804..24589856,+p1@Med23
Mm9::chr17:33170312..33170356,-p1@Zfp763
Mm9::chr17:33495777..33495831,-p1@Zfp81
Mm9::chr18:25327494..25327530,+p1@AW554918
Mm9::chr2:160934772..160934827,-p1@Chd6
Mm9::chr2:37298793..37298859,+p1@Rabgap1
Mm9::chr3:154260009..154260052,-p1@Tyw3
Mm9::chr5:138882699..138882758,+p1@Zfp157
Mm9::chr5:139064066..139064121,+p1@A430033K04Rik
Mm9::chr6:118512244..118512298,-p1@Ankrd26
Mm9::chr7:46807844..46807882,+p@chr7:46807844..46807882
+
Mm9::chr8:93478822..93478958,+p1@Chd9
Mm9::chr9:20264394..20264448,-p1@Zfp26
Mm9::chr9:82869014..82869073,-p1@Phip


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

GO IDGO nameFDR corrected p-value
GO:0005634nucleus0.0474044833244923
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0474044833244923
GO:0016070RNA metabolic process0.0474044833244923
GO:0003682chromatin binding0.0474044833244923
GO:0004386helicase activity0.0474044833244923
GO:0006333chromatin assembly or disassembly0.0474044833244923
GO:0010467gene expression0.0474044833244923
GO:0006355regulation of transcription, DNA-dependent0.0474044833244923
GO:0006351transcription, DNA-dependent0.0474044833244923
GO:0032774RNA biosynthetic process0.0474044833244923
GO:0003677DNA binding0.0474044833244923
GO:0045449regulation of transcription0.0474044833244923
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0474044833244923
GO:0006350transcription0.0474044833244923



Relative expression of the co-expression cluster over median <br>Analyst:




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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
ecto-epithelium4.60e-1073
neurectoderm6.60e-1064
neural plate6.60e-1064
presumptive neural plate6.60e-1064
pre-chordal neural plate1.23e-0949
multi-cellular organism3.74e-08333
ectoderm-derived structure3.17e-0795
ectoderm3.17e-0795
presumptive ectoderm3.17e-0795
anterior region of body9.30e-0743


TFBS overrepresentation<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)
MA0003.10.317607
MA0004.10.239244
MA0006.10.118059
MA0007.10.227553
MA0009.10.623671
MA0014.10.304428
MA0017.10.832511
MA0019.10.456268
MA0024.10.582844
MA0025.10.845702
MA0027.12.24512
MA0028.10.393672
MA0029.10.562703
MA0030.10.568779
MA0031.10.535959
MA0038.11.68155
MA0040.10.635404
MA0041.13.06992
MA0042.12.23894
MA0043.10.71494
MA0046.10.657417
MA0048.10.763962
MA0050.10.270164
MA0051.10.366328
MA0052.10.642973
MA0055.10.578069
MA0056.10
MA0057.10.431584
MA0058.10.167504
MA0059.10.176308
MA0060.14.54253
MA0061.10.615538
MA0063.10
MA0066.10.349199
MA0067.10.953264
MA0068.10.0216542
MA0069.10.643292
MA0070.10.634186
MA0071.10.269487
MA0072.10.626238
MA0073.10.000127125
MA0074.10.318792
MA0076.10.453214
MA0077.10.605975
MA0078.10.395048
MA0081.10.56362
MA0083.10.714187
MA0084.11.27474
MA0087.10.673355
MA0088.10.0106511
MA0089.10
MA0090.11.14829
MA0091.10.696557
MA0092.10.610874
MA0093.10.130107
MA0095.10
MA0098.10
MA0100.10.832335
MA0101.10.538493
MA0103.10.14251
MA0105.10.147614
MA0106.11.03774
MA0107.10.428571
MA0108.20.476838
MA0109.10
MA0111.10.635898
MA0113.10.377232
MA0114.10.291992
MA0115.10.717599
MA0116.10.756087
MA0117.10.686999
MA0119.10.183219
MA0122.10.705806
MA0124.10.901619
MA0125.10.830088
MA0130.10
MA0131.12.97464
MA0132.10
MA0133.10
MA0135.10.749615
MA0136.10.891604
MA0139.11.67613
MA0140.10.30902
MA0141.10.155997
MA0142.10.522654
MA0143.10.391481
MA0144.10.0881858
MA0145.11.15108
MA0146.11.31962
MA0147.10.0952713
MA0148.10.252062
MA0149.10.18682
MA0062.21.41609
MA0035.20.312946
MA0039.20.101713
MA0138.20.445088
MA0002.20.208749
MA0137.20.153989
MA0104.20.0641853
MA0047.20.357963
MA0112.20.54155
MA0065.20.160972
MA0150.10.227466
MA0151.10
MA0152.10.358055
MA0153.10.765498
MA0154.10.247047
MA0155.10.369691
MA0156.10.45173
MA0157.10.493416
MA0158.10
MA0159.10.101261
MA0160.10.254455
MA0161.10
MA0162.11.18203
MA0163.10.0289848
MA0164.10.892289
MA0080.20.430071
MA0018.20.344133
MA0099.20.439458
MA0079.20.140632
MA0102.21.32652
MA0258.10.271229
MA0259.10.299239
MA0442.10
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