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MCL coexpression mm9:1678: Difference between revisions

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{{MCL_coexpression_mm9
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receptor activity;0.00887476712104064;11835!GO:0019102;male somatic sex determination;0.00887476712104064;11835!GO:0018993;somatic sex determination;0.00887476712104064;11835!GO:0030521;androgen receptor signaling pathway;0.00887476712104064;11835!GO:0004551;nucleotide diphosphatase activity;0.0248425410174104;83965!GO:0030238;male sex determination;0.0295695922158481;11835!GO:0030518;steroid hormone receptor signaling pathway;0.0329435578149615;11835!GO:0008584;male gonad development;0.0339808122707526;11835!GO:0030522;intracellular receptor-mediated signaling pathway;0.0339808122707526;11835!GO:0009166;nucleotide catabolic process;0.0339808122707526;83965!GO:0046546;development of primary male sexual characteristics;0.0339808122707526;11835!GO:0007530;sex determination;0.0339808122707526;11835!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0341843773290768;83965,107771,11835!GO:0046661;male sex differentiation;0.0341843773290768;11835!GO:0003700;transcription factor activity;0.0406319634478141;107771,11835!GO:0005819;spindle;0.0420720492191018;107771!GO:0005496;steroid binding;0.0446713847241321;11835!GO:0003707;steroid hormone receptor activity;0.0446713847241321;11835!GO:0004879;ligand-dependent nuclear receptor activity;0.0446713847241321;11835!GO:0008406;gonad development;0.0446713847241321;11835!GO:0048608;reproductive structure development;0.0446713847241321;11835!GO:0045137;development of primary sexual 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|gostat_on_MCL_coexpression=GO:0004882;androgen receptor activity;0.00887476712104064;11835!GO:0019102;male somatic sex determination;0.00887476712104064;11835!GO:0018993;somatic sex determination;0.00887476712104064;11835!GO:0030521;androgen receptor signaling pathway;0.00887476712104064;11835!GO:0004551;nucleotide diphosphatase activity;0.0248425410174104;83965!GO:0030238;male sex determination;0.0295695922158481;11835!GO:0030518;steroid hormone receptor signaling pathway;0.0329435578149615;11835!GO:0008584;male gonad development;0.0339808122707526;11835!GO:0030522;intracellular receptor-mediated signaling pathway;0.0339808122707526;11835!GO:0009166;nucleotide catabolic process;0.0339808122707526;83965!GO:0046546;development of primary male sexual characteristics;0.0339808122707526;11835!GO:0007530;sex determination;0.0339808122707526;11835!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0341843773290768;83965,107771,11835!GO:0046661;male sex differentiation;0.0341843773290768;11835!GO:0003700;transcription factor activity;0.0406319634478141;107771,11835!GO:0005819;spindle;0.0420720492191018;107771!GO:0005496;steroid binding;0.0446713847241321;11835!GO:0003707;steroid hormone receptor activity;0.0446713847241321;11835!GO:0004879;ligand-dependent nuclear receptor activity;0.0446713847241321;11835!GO:0008406;gonad development;0.0446713847241321;11835!GO:0048608;reproductive structure development;0.0446713847241321;11835!GO:0045137;development of primary sexual characteristics;0.0466507962139251;11835!
|ontology_enrichment_celltype=CL:0000221!2.85e-07!44;CL:0000133!2.85e-07!44;CL:0002319!5.85e-07!43;CL:0000117!7.44e-07!23;CL:0000337!7.44e-07!23;CL:0000055!7.67e-07!49
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!1.63e-24!73;UBERON:0001016!1.13e-23!75;UBERON:0000073!3.18e-23!54;UBERON:0001049!8.24e-22!52;UBERON:0005068!8.24e-22!52;UBERON:0006241!8.24e-22!52;UBERON:0007135!8.24e-22!52;UBERON:0002346!1.27e-21!64;UBERON:0003075!1.27e-21!64;UBERON:0007284!1.27e-21!64;UBERON:0004121!7.29e-21!95;UBERON:0000924!7.29e-21!95;UBERON:0006601!7.29e-21!95;UBERON:0000955!5.82e-19!47;UBERON:0006238!5.82e-19!47;UBERON:0010371!2.72e-18!73;UBERON:0002616!2.85e-18!46;UBERON:0003080!4.62e-16!40;UBERON:0010314!6.20e-16!92;UBERON:0003056!1.38e-15!49;UBERON:0002780!2.05e-15!39;UBERON:0001890!2.05e-15!39;UBERON:0006240!2.05e-15!39;UBERON:0002020!3.46e-14!34;UBERON:0003528!1.41e-11!29;UBERON:0002791!1.41e-11!29;UBERON:0001893!1.41e-11!29;UBERON:0004111!1.48e-09!122;UBERON:0002619!1.19e-08!17;UBERON:0002021!5.97e-08!10;UBERON:0000411!5.97e-08!10;UBERON:0001950!5.97e-08!10;UBERON:0000956!9.32e-08!21;UBERON:0001869!9.32e-08!21;UBERON:0000203!9.32e-08!21;UBERON:0000025!1.87e-07!114
|tfbs_overrepresentation_for_novel_motifs=0.557864,0.293744,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.310789,0.370407,0.668936,0.702872,1.47559,0.728641,0.424775,0,0.930881,0.397593,0.283802,1.64643,0.489529,0.44579,0.727684,1.04384,0.537749,0.757752,0.754069,0.641282,0.456327,0.227599,0.626183,1.03545,0.395107,0.704734,1.08876,0.454919,0.384813,0.699032,0.360612,0.876199,0.401916,0.631725,0.830062,0.426986,0.84962,0.591277,0.847828,0.658142,0.115788,0.459555,0.912738,0.786094,0.220111,1.18062,1.19842,0.73621,0.469329,0.689304,0.731291,0.734051,1.01481,0.796017,0.865544,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,1.26875,0.30684,0.152094,1.23259,0.257421,0.686172,0.253065,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.293164,1.1148,0.272382,0.0882907,0.227755,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.89388,0.806207,1.05152,0.848095,2.47367,0.384901,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,0.491483,0.550229,1.16464,0.495367,0.674448,1.41481,0.399936,1.64321,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,1.87987,1.14546,1.45154,1.3055,0.750642,1.43666,0.143464,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,0.651755,0.133815,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,0.191104
|tfbs_overrepresentation_jaspar=MA0003.1;0.406907,MA0004.1;0.603793,MA0006.1;1.07705,MA0007.1;0.587678,MA0009.1;1.06266,MA0014.1;0.736185,MA0017.1;0.449113,MA0019.1;0.874061,MA0024.1;1.01759,MA0025.1;1.30092,MA0027.1;2.72141,MA0028.1;0.43138,MA0029.1;0.995171,MA0030.1;1.00195,MA0031.1;0.965177,MA0038.1;0.757669,MA0040.1;1.07552,MA0041.1;0.522007,MA0042.1;0.507715,MA0043.1;1.1618,MA0046.1;1.09955,MA0048.1;0.593503,MA0050.1;0.645342,MA0051.1;0.767098,MA0052.1;1.08379,MA0055.1;0.0851423,MA0056.1;0,MA0057.1;0.562607,MA0058.1;0.50032,MA0059.1;0.513699,MA0060.1;0.330907,MA0061.1;0.955135,MA0063.1;0,MA0066.1;0.746072,MA0067.1;1.41352,MA0068.1;0.573319,MA0069.1;1.08414,MA0070.1;1.07418,MA0071.1;0.644448,MA0072.1;1.06547,MA0073.1;3.29146,MA0074.1;0.708108,MA0076.1;0.470037,MA0077.1;1.04318,MA0078.1;0.801834,MA0081.1;0.53877,MA0083.1;1.16099,MA0084.1;1.74401,MA0087.1;1.11687,MA0088.1;0.148348,MA0089.1;0,MA0090.1;0.566938,MA0091.1;0.617887,MA0092.1;0.567278,MA0093.1;0.440484,MA0095.1;0,MA0098.1;0,MA0100.1;0.695835,MA0101.1;0.523409,MA0103.1;1.16573,MA0105.1;1.28296,MA0106.1;0.809991,MA0107.1;0.454197,MA0108.2;0.897859,MA0109.1;0,MA0111.1;0.582193,MA0113.1;0.780358,MA0114.1;0.361633,MA0115.1;1.16466,MA0116.1;0.419688,MA0117.1;1.13165,MA0119.1;0.524046,MA0122.1;1.15196,MA0124.1;1.35963,MA0125.1;1.28445,MA0130.1;0,MA0131.1;0.869325,MA0132.1;0,MA0133.1;0,MA0135.1;1.19898,MA0136.1;0.729175,MA0139.1;1.45902,MA0140.1;2.79433,MA0141.1;0.482463,MA0142.1;0.950155,MA0143.1;0.797553,MA0144.1;0.365053,MA0145.1;0.927481,MA0146.1;0.475727,MA0147.1;0.378658,MA0148.1;0.621195,MA0149.1;0.529387,MA0062.2;0.706751,MA0035.2;0.700704,MA0039.2;0.285933,MA0138.2;0.861035,MA0002.2;0.299191,MA0137.2;0.479301,MA0104.2;0.315156,MA0047.2;0.75686,MA0112.2;0.157681,MA0065.2;0.929207,MA0150.1;0.587557,MA0151.1;0,MA0152.1;0.756973,MA0153.1;1.21594,MA0154.1;1.11105,MA0155.1;0.515751,MA0156.1;0.469089,MA0157.1;0.91689,MA0158.1;0,MA0159.1;0.389847,MA0160.1;0.624415,MA0161.1;0,MA0162.1;0.245828,MA0163.1;0.497328,MA0164.1;0.729558,MA0080.2;0.455167,MA0018.2;0.739807,MA0099.2;0.854449,MA0079.2;0.765158,MA0102.2;1.79669,MA0258.1;0.346619,MA0259.1;0.366802,MA0442.1;0
}}

Latest revision as of 17:19, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr15:64754697..64754724,-p@chr15:64754697..64754724
-
Mm9::chr17:44215774..44215859,+p1@Enpp5
Mm9::chr2:25562241..25562250,+p4@Bmyc
Mm9::chrX:100129517..100129546,-p1@Gm5126
Mm9::chrX:95345005..95345053,+p1@Ar


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:0004882androgen receptor activity0.00887476712104064
GO:0019102male somatic sex determination0.00887476712104064
GO:0018993somatic sex determination0.00887476712104064
GO:0030521androgen receptor signaling pathway0.00887476712104064
GO:0004551nucleotide diphosphatase activity0.0248425410174104
GO:0030238male sex determination0.0295695922158481
GO:0030518steroid hormone receptor signaling pathway0.0329435578149615
GO:0008584male gonad development0.0339808122707526
GO:0030522intracellular receptor-mediated signaling pathway0.0339808122707526
GO:0009166nucleotide catabolic process0.0339808122707526
GO:0046546development of primary male sexual characteristics0.0339808122707526
GO:0007530sex determination0.0339808122707526
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0341843773290768
GO:0046661male sex differentiation0.0341843773290768
GO:0003700transcription factor activity0.0406319634478141
GO:0005819spindle0.0420720492191018
GO:0005496steroid binding0.0446713847241321
GO:0003707steroid hormone receptor activity0.0446713847241321
GO:0004879ligand-dependent nuclear receptor activity0.0446713847241321
GO:0008406gonad development0.0446713847241321
GO:0048608reproductive structure development0.0446713847241321
GO:0045137development of primary sexual characteristics0.0466507962139251



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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
ectodermal cell2.85e-0744
neurectodermal cell2.85e-0744
neural cell5.85e-0743
CNS neuron (sensu Vertebrata)7.44e-0723
neuroblast (sensu Vertebrata)7.44e-0723
non-terminally differentiated cell7.67e-0749

Uber Anatomy
Ontology termp-valuen
central nervous system1.63e-2473
nervous system1.13e-2375
regional part of nervous system3.18e-2354
neural tube8.24e-2252
neural rod8.24e-2252
future spinal cord8.24e-2252
neural keel8.24e-2252
neurectoderm1.27e-2164
neural plate1.27e-2164
presumptive neural plate1.27e-2164
ectoderm-derived structure7.29e-2195
ectoderm7.29e-2195
presumptive ectoderm7.29e-2195
brain5.82e-1947
future brain5.82e-1947
ecto-epithelium2.72e-1873
regional part of brain2.85e-1846
anterior neural tube4.62e-1640
structure with developmental contribution from neural crest6.20e-1692
pre-chordal neural plate1.38e-1549
regional part of forebrain2.05e-1539
forebrain2.05e-1539
future forebrain2.05e-1539
gray matter3.46e-1434
brain grey matter1.41e-1129
regional part of telencephalon1.41e-1129
telencephalon1.41e-1129
anatomical conduit1.48e-09122
regional part of cerebral cortex1.19e-0817
occipital lobe5.97e-0810
visual cortex5.97e-0810
neocortex5.97e-0810
cerebral cortex9.32e-0821
cerebral hemisphere9.32e-0821
pallium9.32e-0821
tube1.87e-07114


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)
MA0003.10.406907
MA0004.10.603793
MA0006.11.07705
MA0007.10.587678
MA0009.11.06266
MA0014.10.736185
MA0017.10.449113
MA0019.10.874061
MA0024.11.01759
MA0025.11.30092
MA0027.12.72141
MA0028.10.43138
MA0029.10.995171
MA0030.11.00195
MA0031.10.965177
MA0038.10.757669
MA0040.11.07552
MA0041.10.522007
MA0042.10.507715
MA0043.11.1618
MA0046.11.09955
MA0048.10.593503
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.10.0851423
MA0056.10
MA0057.10.562607
MA0058.10.50032
MA0059.10.513699
MA0060.10.330907
MA0061.10.955135
MA0063.10
MA0066.10.746072
MA0067.11.41352
MA0068.10.573319
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.13.29146
MA0074.10.708108
MA0076.10.470037
MA0077.11.04318
MA0078.10.801834
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.10.148348
MA0089.10
MA0090.10.566938
MA0091.10.617887
MA0092.10.567278
MA0093.10.440484
MA0095.10
MA0098.10
MA0100.10.695835
MA0101.10.523409
MA0103.11.16573
MA0105.11.28296
MA0106.10.809991
MA0107.10.454197
MA0108.20.897859
MA0109.10
MA0111.10.582193
MA0113.10.780358
MA0114.10.361633
MA0115.11.16466
MA0116.10.419688
MA0117.11.13165
MA0119.10.524046
MA0122.11.15196
MA0124.11.35963
MA0125.11.28445
MA0130.10
MA0131.10.869325
MA0132.10
MA0133.10
MA0135.11.19898
MA0136.10.729175
MA0139.11.45902
MA0140.12.79433
MA0141.10.482463
MA0142.10.950155
MA0143.10.797553
MA0144.10.365053
MA0145.10.927481
MA0146.10.475727
MA0147.10.378658
MA0148.10.621195
MA0149.10.529387
MA0062.20.706751
MA0035.20.700704
MA0039.20.285933
MA0138.20.861035
MA0002.20.299191
MA0137.20.479301
MA0104.20.315156
MA0047.20.75686
MA0112.20.157681
MA0065.20.929207
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.11.11105
MA0155.10.515751
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.10.245828
MA0163.10.497328
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.20.765158
MA0102.21.79669
MA0258.10.346619
MA0259.10.366802
MA0442.10
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