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MCL coexpression mm9:1233: Difference between revisions

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{{MCL_coexpression_mm9
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development;0.0179696488248507;14561!GO:0048593;camera-type eye morphogenesis;0.0179696488248507;14561!GO:0001657;ureteric bud development;0.0179696488248507;14561!GO:0048592;eye morphogenesis;0.0179696488248507;14561!GO:0001656;metanephros development;0.0179696488248507;14561!GO:0001822;kidney development;0.0179696488248507;14561!GO:0048469;cell maturation;0.0179696488248507;14561!GO:0043010;camera-type eye development;0.0179696488248507;14561!GO:0001655;urogenital system development;0.0179696488248507;14561!GO:0045596;negative regulation of cell differentiation;0.0179696488248507;14561!GO:0021700;developmental maturation;0.0179696488248507;14561!GO:0001654;eye development;0.0179696488248507;14561!GO:0051093;negative regulation of developmental process;0.0179696488248507;14561!GO:0008285;negative regulation of cell proliferation;0.0189323085833249;14561!GO:0008083;growth factor activity;0.0214793458609544;14561!GO:0045595;regulation of cell differentiation;0.0214793458609544;14561!GO:0007423;sensory organ development;0.0245761373633988;14561!GO:0005125;cytokine activity;0.0267048947813754;14561!GO:0050793;regulation of developmental process;0.0302646717050117;14561!GO:0042127;regulation of cell proliferation;0.0356023667342355;14561!GO:0008283;cell 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|ontology_enrichment_celltype=CL:0000221!1.98e-18!44;CL:0000133!1.98e-18!44;CL:0002319!2.34e-18!43;CL:0000540!3.12e-15!33;CL:0000047!3.12e-15!33;CL:0000031!3.12e-15!33;CL:0000404!3.12e-15!33;CL:0000055!4.62e-15!49;CL:0000117!2.45e-12!23;CL:0000337!2.45e-12!23;CL:0000393!7.19e-12!39;CL:0000211!7.19e-12!39
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!2.73e-33!73;UBERON:0001016!7.25e-32!75;UBERON:0004121!5.60e-28!95;UBERON:0000924!5.60e-28!95;UBERON:0006601!5.60e-28!95;UBERON:0000073!1.39e-23!54;UBERON:0002346!3.31e-23!64;UBERON:0003075!3.31e-23!64;UBERON:0007284!3.31e-23!64;UBERON:0001049!2.31e-22!52;UBERON:0005068!2.31e-22!52;UBERON:0006241!2.31e-22!52;UBERON:0007135!2.31e-22!52;UBERON:0010371!8.19e-21!73;UBERON:0000955!2.64e-19!47;UBERON:0006238!2.64e-19!47;UBERON:0002616!1.21e-18!46;UBERON:0010314!2.41e-17!92;UBERON:0002020!2.61e-17!34;UBERON:0003080!2.15e-15!40;UBERON:0003056!4.33e-15!49;UBERON:0002780!8.04e-15!39;UBERON:0001890!8.04e-15!39;UBERON:0006240!8.04e-15!39;UBERON:0003528!2.31e-14!29;UBERON:0002791!2.31e-14!29;UBERON:0001893!2.31e-14!29;UBERON:0000025!7.97e-11!114;UBERON:0004111!2.14e-10!122;UBERON:0000956!5.33e-10!21;UBERON:0001869!5.33e-10!21;UBERON:0000203!5.33e-10!21;UBERON:0002619!1.04e-08!17;UBERON:0000468!8.12e-08!333;UBERON:0003076!8.87e-08!12;UBERON:0003057!8.87e-08!12;UBERON:0000922!5.84e-07!320
|tfbs_overrepresentation_for_novel_motifs=0.491922,1.24447,0.464605,0.535892,0.346849,0.550971,0.645383,0.691572,0.7141,0.594834,0.599767,0.632897,1.28144,0.6581,0.364314,0,0.856992,0.338549,0.656199,0.442204,0.426133,0.108444,0.657163,0.345236,0.472505,0.686615,0.223823,0.572827,1.02135,0.181062,0.558142,0.960397,0.336199,0.204204,0.956447,0.144368,0.326478,0.629145,0.303703,0.27383,0.342638,0.56353,0.0995018,1.7087,1.02402,0.524258,0.77511,0.589246,0.0835644,0.397446,0.839084,0.714419,0.517905,1.10437,1.12205,0.66551,0.406788,0.619643,0.614918,0.663395,0.939962,0.724164,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,1.1311,0.70565,0.366795,1.156,0.599223,0.57254,0.589776,0.763395,0.922432,0.430551,0.254777,0.874787,0.722675,0.676326,1.03903,8.00775,0.0610418,1.02367,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.2995,0.281222,0.244935,0.976308,0.775372,0.160254,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,0.428007,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,1.35637,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,2.99743,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,3.42279,0.540361,1.63283,1.10596,0.287383,0.678689,1.18867,0.71546,0.376898,0.48935,1.25034,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.325308,0.63125,7.66449
|tfbs_overrepresentation_jaspar=MA0003.1;8.33713,MA0004.1;2.28084,MA0006.1;0.359699,MA0007.1;0.52077,MA0009.1;0.987341,MA0014.1;6.82496,MA0017.1;0.387481,MA0019.1;1.87871,MA0024.1;0.942716,MA0025.1;1.22395,MA0027.1;2.64231,MA0028.1;0.370592,MA0029.1;0.920529,MA0030.1;0.927235,MA0031.1;0.890871,MA0038.1;0.686534,MA0040.1;1.00009,MA0041.1;0.457338,MA0042.1;0.443591,MA0043.1;1.08567,MA0046.1;1.02391,MA0048.1;0.486223,MA0050.1;0.57678,MA0051.1;0.695779,MA0052.1;1.00829,MA0055.1;0.0585191,MA0056.1;0,MA0057.1;0.895081,MA0058.1;2.90242,MA0059.1;0.449345,MA0060.1;0.757042,MA0061.1;0.307097,MA0063.1;0,MA0066.1;0.675169,MA0067.1;1.33603,MA0068.1;0.153907,MA0069.1;1.00864,MA0070.1;0.998765,MA0071.1;0.575909,MA0072.1;0.990133,MA0073.1;0.401473,MA0074.1;0.638014,MA0076.1;0.407465,MA0077.1;0.968053,MA0078.1;0.729877,MA0081.1;0.473489,MA0083.1;1.08487,MA0084.1;1.66561,MA0087.1;1.04109,MA0088.1;1.74419,MA0089.1;0,MA0090.1;0.500693,MA0091.1;0.55008,MA0092.1;1.25163,MA0093.1;3.60927,MA0095.1;0,MA0098.1;0,MA0100.1;0.626021,MA0101.1;1.16089,MA0103.1;0.398766,MA0105.1;1.09694,MA0106.1;1.74856,MA0107.1;0.392331,MA0108.2;0.824407,MA0109.1;0,MA0111.1;0.515457,MA0113.1;0.708789,MA0114.1;0.304661,MA0115.1;1.08851,MA0116.1;0.359483,MA0117.1;1.05576,MA0119.1;0.459301,MA0122.1;1.07591,MA0124.1;1.28237,MA0125.1;1.20757,MA0130.1;0,MA0131.1;0.796279,MA0132.1;0,MA0133.1;0,MA0135.1;1.1226,MA0136.1;0.658622,MA0139.1;0.243463,MA0140.1;0.625902,MA0141.1;0.419361,MA0142.1;0.876028,MA0143.1;0.725672,MA0144.1;0.307873,MA0145.1;1.24552,MA0146.1;3.00399,MA0147.1;0.320675,MA0148.1;0.553294,MA0149.1;0.464445,MA0062.2;0.204999,MA0035.2;0.630778,MA0039.2;3.59125,MA0138.2;0.788113,MA0002.2;0.246463,MA0137.2;0.416331,MA0104.2;2.05302,MA0047.2;0.685741,MA0112.2;0.76177,MA0065.2;1.24784,MA0150.1;0.520653,MA0151.1;0,MA0152.1;0.685852,MA0153.1;1.13945,MA0154.1;0.159217,MA0155.1;2.59807,MA0156.1;0.406559,MA0157.1;0.843181,MA0158.1;0,MA0159.1;1.58527,MA0160.1;0.556423,MA0161.1;0,MA0162.1;5.28077,MA0163.1;4.40286,MA0164.1;0.658997,MA0080.2;0.393257,MA0018.2;0.669032,MA0099.2;0.781628,MA0079.2;9.24173,MA0102.2;1.7182,MA0258.1;0.290587,MA0259.1;0.309517,MA0442.1;0
}}

Latest revision as of 16:36, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:128328919..128328934,-p2@Gdf11
Mm9::chr8:113245322..113245344,+p2@Mtss1l
Mm9::chr8:113245351..113245356,+p5@Mtss1l
Mm9::chr8:113245362..113245386,+p1@Mtss1l
Mm9::chr8:113245555..113245624,+p3@Mtss1l
Mm9::chr8:113265086..113265105,+p@chr8:113265086..113265105
+


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:0031016pancreas development0.0179696488248507
GO:0048593camera-type eye morphogenesis0.0179696488248507
GO:0001657ureteric bud development0.0179696488248507
GO:0048592eye morphogenesis0.0179696488248507
GO:0001656metanephros development0.0179696488248507
GO:0001822kidney development0.0179696488248507
GO:0048469cell maturation0.0179696488248507
GO:0043010camera-type eye development0.0179696488248507
GO:0001655urogenital system development0.0179696488248507
GO:0045596negative regulation of cell differentiation0.0179696488248507
GO:0021700developmental maturation0.0179696488248507
GO:0001654eye development0.0179696488248507
GO:0051093negative regulation of developmental process0.0179696488248507
GO:0008285negative regulation of cell proliferation0.0189323085833249
GO:0008083growth factor activity0.0214793458609544
GO:0045595regulation of cell differentiation0.0214793458609544
GO:0007423sensory organ development0.0245761373633988
GO:0005125cytokine activity0.0267048947813754
GO:0050793regulation of developmental process0.0302646717050117
GO:0042127regulation of cell proliferation0.0356023667342355
GO:0008283cell proliferation0.0494165342683395



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>

Uber Anatomy
Ontology termp-valuen
central nervous system2.73e-3373
nervous system7.25e-3275
ectoderm-derived structure5.60e-2895
ectoderm5.60e-2895
presumptive ectoderm5.60e-2895
regional part of nervous system1.39e-2354
neurectoderm3.31e-2364
neural plate3.31e-2364
presumptive neural plate3.31e-2364
neural tube2.31e-2252
neural rod2.31e-2252
future spinal cord2.31e-2252
neural keel2.31e-2252
ecto-epithelium8.19e-2173
brain2.64e-1947
future brain2.64e-1947
regional part of brain1.21e-1846
structure with developmental contribution from neural crest2.41e-1792
gray matter2.61e-1734
anterior neural tube2.15e-1540
pre-chordal neural plate4.33e-1549
regional part of forebrain8.04e-1539
forebrain8.04e-1539
future forebrain8.04e-1539
brain grey matter2.31e-1429
regional part of telencephalon2.31e-1429
telencephalon2.31e-1429
tube7.97e-11114
anatomical conduit2.14e-10122
cerebral cortex5.33e-1021
cerebral hemisphere5.33e-1021
pallium5.33e-1021
regional part of cerebral cortex1.04e-0817
multi-cellular organism8.12e-08333
posterior neural tube8.87e-0812
chordal neural plate8.87e-0812
embryo5.84e-07320


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)
MA0003.18.33713
MA0004.12.28084
MA0006.10.359699
MA0007.10.52077
MA0009.10.987341
MA0014.16.82496
MA0017.10.387481
MA0019.11.87871
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.370592
MA0029.10.920529
MA0030.10.927235
MA0031.10.890871
MA0038.10.686534
MA0040.11.00009
MA0041.10.457338
MA0042.10.443591
MA0043.11.08567
MA0046.11.02391
MA0048.10.486223
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.0585191
MA0056.10
MA0057.10.895081
MA0058.12.90242
MA0059.10.449345
MA0060.10.757042
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.153907
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.10.401473
MA0074.10.638014
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.11.74419
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.11.25163
MA0093.13.60927
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.11.16089
MA0103.10.398766
MA0105.11.09694
MA0106.11.74856
MA0107.10.392331
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.304661
MA0115.11.08851
MA0116.10.359483
MA0117.11.05576
MA0119.10.459301
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.10.796279
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.10.658622
MA0139.10.243463
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.11.24552
MA0146.13.00399
MA0147.10.320675
MA0148.10.553294
MA0149.10.464445
MA0062.20.204999
MA0035.20.630778
MA0039.23.59125
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.22.05302
MA0047.20.685741
MA0112.20.76177
MA0065.21.24784
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.159217
MA0155.12.59807
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.11.58527
MA0160.10.556423
MA0161.10
MA0162.15.28077
MA0163.14.40286
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.29.24173
MA0102.21.7182
MA0258.10.290587
MA0259.10.309517
MA0442.10
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