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MCL coexpression mm9:1500: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000160!2.45e-16!31;UBERON:0005409!1.54e-13!47;UBERON:0001007!1.78e-10!116;UBERON:0001555!1.78e-10!116;UBERON:0007026!1.78e-10!116;UBERON:0004119!2.03e-10!118;UBERON:0000925!2.03e-10!118;UBERON:0006595!2.03e-10!118;UBERON:0000344!7.18e-10!15;UBERON:0004921!1.32e-09!114;UBERON:0001242!1.11e-08!13;UBERON:0000060!1.11e-08!13;UBERON:0001262!1.11e-08!13;UBERON:0004786!1.11e-08!13;UBERON:0000010!2.86e-07!11;UBERON:0000485!7.15e-07!11
|ontology_enrichment_uberon=UBERON:0000160!2.45e-16!31;UBERON:0005409!1.54e-13!47;UBERON:0001007!1.78e-10!116;UBERON:0001555!1.78e-10!116;UBERON:0007026!1.78e-10!116;UBERON:0004119!2.03e-10!118;UBERON:0000925!2.03e-10!118;UBERON:0006595!2.03e-10!118;UBERON:0000344!7.18e-10!15;UBERON:0004921!1.32e-09!114;UBERON:0001242!1.11e-08!13;UBERON:0000060!1.11e-08!13;UBERON:0001262!1.11e-08!13;UBERON:0004786!1.11e-08!13;UBERON:0000010!2.86e-07!11;UBERON:0000485!7.15e-07!11
|tfbs_overrepresentation_for_novel_motifs=0.557864,1.02681,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.836099,3.8643,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,1.02841,0.775038,0.545768,1.22707,0.145201,0.727684,0.404661,0.537749,0.757752,0.754069,1.54767,1.15581,0.227599,1.51608,1.03545,0.395107,1.3018,1.08876,0.20704,0.384813,0.699032,0.360612,0.328675,0.401916,0.631725,0.134724,0.426986,1.78875,0.591277,1.97509,1.58288,0.370501,0.459555,0.912738,0.786094,0.627649,1.18062,1.19842,0.73621,0.469329,0.689304,0.26467,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,2.19087,0.30684,0.46305,1.23259,0.714607,0.245132,0.253065,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.293164,1.1148,0.0793594,0.0882907,3.47363,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.89388,0.297538,1.05152,0.848095,0.590368,0.384901,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,0.491483,0.550229,2.62018,1.23956,1.61686,1.41481,1.03353,0.328405,0.607321,0.932233,0.380707,1.23809,0.879184,2.99663,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,1.87987,1.14546,0.595426,1.3055,0.750642,1.43666,1.398,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,0.651755,0.133815,1.18223,0.908552,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,0.191104
|tfbs_overrepresentation_for_novel_motifs=0.557864,1.02681,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.836099,3.8643,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,1.02841,0.775038,0.545768,1.22707,0.145201,0.727684,0.404661,0.537749,0.757752,0.754069,1.54767,1.15581,0.227599,1.51608,1.03545,0.395107,1.3018,1.08876,0.20704,0.384813,0.699032,0.360612,0.328675,0.401916,0.631725,0.134724,0.426986,1.78875,0.591277,1.97509,1.58288,0.370501,0.459555,0.912738,0.786094,0.627649,1.18062,1.19842,0.73621,0.469329,0.689304,0.26467,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,2.19087,0.30684,0.46305,1.23259,0.714607,0.245132,0.253065,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.293164,1.1148,0.0793594,0.0882907,3.47363,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.89388,0.297538,1.05152,0.848095,0.590368,0.384901,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,0.491483,0.550229,2.62018,1.23956,1.61686,1.41481,1.03353,0.328405,0.607321,0.932233,0.380707,1.23809,0.879184,2.99663,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,1.87987,1.14546,0.595426,1.3055,0.750642,1.43666,1.398,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,0.651755,0.133815,1.18223,0.908552,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,0.191104
|tfbs_overrepresentation_jaspar=MA0003.1;1.36559,MA0004.1;0.603793,MA0006.1;0.419915,MA0007.1;0.587678,MA0009.1;1.06266,MA0014.1;1.13011,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;0.205696,MA0050.1;0.645342,MA0051.1;0.767098,MA0052.1;1.08379,MA0055.1;0.0851423,MA0056.1;0,MA0057.1;1.06992,MA0058.1;0.50032,MA0059.1;0.513699,MA0060.1;0.330907,MA0061.1;0.364227,MA0063.1;0,MA0066.1;0.746072,MA0067.1;1.41352,MA0068.1;1.08757,MA0069.1;1.08414,MA0070.1;1.07418,MA0071.1;1.55428,MA0072.1;1.06547,MA0073.1;0.00450236,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;4.3331,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;0.460936,MA0105.1;0.248108,MA0106.1;1.89733,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;1.30068,MA0122.1;1.15196,MA0124.1;1.35963,MA0125.1;1.28445,MA0130.1;0,MA0131.1;2.01917,MA0132.1;0,MA0133.1;0,MA0135.1;1.19898,MA0136.1;0.729175,MA0139.1;0.8026,MA0140.1;0.695713,MA0141.1;0.482463,MA0142.1;0.950155,MA0143.1;0.797553,MA0144.1;0.365053,MA0145.1;0.476962,MA0146.1;0.21827,MA0147.1;0.378658,MA0148.1;0.621195,MA0149.1;15.8574,MA0062.2;0.254018,MA0035.2;0.700704,MA0039.2;1.06086,MA0138.2;0.861035,MA0002.2;0.299191,MA0137.2;0.479301,MA0104.2;0.315156,MA0047.2;0.75686,MA0112.2;2.12679,MA0065.2;3.62841,MA0150.1;0.587557,MA0151.1;0,MA0152.1;0.756973,MA0153.1;1.21594,MA0154.1;0.587595,MA0155.1;0.99229,MA0156.1;0.469089,MA0157.1;0.91689,MA0158.1;0,MA0159.1;1.78974,MA0160.1;0.624415,MA0161.1;0,MA0162.1;0.898893,MA0163.1;2.36557,MA0164.1;0.729558,MA0080.2;0.455167,MA0018.2;0.739807,MA0099.2;1.98867,MA0079.2;3.38617,MA0102.2;1.79669,MA0258.1;0.91616,MA0259.1;0.366802,MA0442.1;0
}}
}}

Revision as of 13:26, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:128026678..128026698,-p1@Erbb3
Mm9::chr10:128026706..128026729,-p3@Erbb3
Mm9::chr10:128026735..128026750,-p2@Erbb3
Mm9::chr3:60806700..60806705,+p2@P2ry1
Mm9::chr3:60806708..60806733,+p1@P2ry1


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:0021545cranial nerve development0.0191702026015879
GO:0016328lateral plasma membrane0.0191702026015879
GO:0014037Schwann cell differentiation0.0191702026015879
GO:0016494C-X-C chemokine receptor activity0.0191702026015879
GO:0019958C-X-C chemokine binding0.0191702026015879
GO:0021675nerve development0.0191702026015879
GO:0043524negative regulation of neuron apoptosis0.0242636265920812
GO:0007422peripheral nervous system development0.0242636265920812
GO:0001637G-protein chemoattractant receptor activity0.0242636265920812
GO:0004950chemokine receptor activity0.0242636265920812
GO:0019956chemokine binding0.0242636265920812
GO:0043523regulation of neuron apoptosis0.0242636265920812
GO:0001608nucleotide receptor activity, G-protein coupled0.0242636265920812
GO:0045028purinergic nucleotide receptor activity, G-protein coupled0.0242636265920812
GO:0016502nucleotide receptor activity0.0242636265920812
GO:0001614purinergic nucleotide receptor activity0.0242636265920812
GO:0051402neuron apoptosis0.0242636265920812
GO:0010001glial cell differentiation0.0242636265920812
GO:0042063gliogenesis0.0247992843785981
GO:0016324apical plasma membrane0.0281500833507036
GO:0044459plasma membrane part0.0320131465064437
GO:0004714transmembrane receptor protein tyrosine kinase activity0.0323688831531588
GO:0019955cytokine binding0.0334538483107821
GO:0019199transmembrane receptor protein kinase activity0.0349252253364959
GO:0045177apical part of cell0.0353614959694466
GO:0005886plasma membrane0.0417949587817344
GO:0001653peptide receptor activity0.0417949587817344
GO:0008528peptide receptor activity, G-protein coupled0.0417949587817344
GO:0004888transmembrane receptor activity0.0442357757106788
GO:0042277peptide binding0.0496786384722613



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
epithelial cell4.90e-0725

Uber Anatomy
Ontology termp-valuen
intestine2.45e-1631
gastrointestinal system1.54e-1347
digestive system1.78e-10116
digestive tract1.78e-10116
primitive gut1.78e-10116
endoderm-derived structure2.03e-10118
endoderm2.03e-10118
presumptive endoderm2.03e-10118
mucosa7.18e-1015
subdivision of digestive tract1.32e-09114
intestinal mucosa1.11e-0813
anatomical wall1.11e-0813
wall of intestine1.11e-0813
gastrointestinal system mucosa1.11e-0813
peripheral nervous system2.86e-0711
simple columnar epithelium7.15e-0711


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)
MA0003.11.36559
MA0004.10.603793
MA0006.10.419915
MA0007.10.587678
MA0009.11.06266
MA0014.11.13011
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
MA0048.10.205696
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.10.0851423
MA0056.10
MA0057.11.06992
MA0058.10.50032
MA0059.10.513699
MA0060.10.330907
MA0061.10.364227
MA0063.10
MA0066.10.746072
MA0067.11.41352
MA0068.11.08757
MA0069.11.08414
MA0070.11.07418
MA0071.11.55428
MA0072.11.06547
MA0073.10.00450236
MA0074.10.708108
MA0076.10.470037
MA0077.11.04318
MA0078.10.801834
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.14.3331
MA0089.10
MA0090.10.566938
MA0091.10.617887
MA0092.10.567278
MA0093.10.440484
MA0095.10
MA0098.10
MA0100.10.695835
MA0101.10.523409
MA0103.10.460936
MA0105.10.248108
MA0106.11.89733
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
MA0119.11.30068
MA0122.11.15196
MA0124.11.35963
MA0125.11.28445
MA0130.10
MA0131.12.01917
MA0132.10
MA0133.10
MA0135.11.19898
MA0136.10.729175
MA0139.10.8026
MA0140.10.695713
MA0141.10.482463
MA0142.10.950155
MA0143.10.797553
MA0144.10.365053
MA0145.10.476962
MA0146.10.21827
MA0147.10.378658
MA0148.10.621195
MA0149.115.8574
MA0062.20.254018
MA0035.20.700704
MA0039.21.06086
MA0138.20.861035
MA0002.20.299191
MA0137.20.479301
MA0104.20.315156
MA0047.20.75686
MA0112.22.12679
MA0065.23.62841
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.10.587595
MA0155.10.99229
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.11.78974
MA0160.10.624415
MA0161.10
MA0162.10.898893
MA0163.12.36557
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.21.98867
MA0079.23.38617
MA0102.21.79669
MA0258.10.91616
MA0259.10.366802
MA0442.10
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