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MCL coexpression mm9:1643: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002371!2.96e-11!16;UBERON:0001474!3.55e-11!22;UBERON:0004765!3.55e-11!22;UBERON:0001434!3.55e-11!22;UBERON:0002193!1.09e-09!48;UBERON:0002405!1.09e-09!48;UBERON:0007023!3.05e-08!51;UBERON:0002390!3.53e-08!45;UBERON:0003061!3.53e-08!45;UBERON:0002204!3.40e-07!32
|ontology_enrichment_uberon=UBERON:0002371!2.96e-11!16;UBERON:0001474!3.55e-11!22;UBERON:0004765!3.55e-11!22;UBERON:0001434!3.55e-11!22;UBERON:0002193!1.09e-09!48;UBERON:0002405!1.09e-09!48;UBERON:0007023!3.05e-08!51;UBERON:0002390!3.53e-08!45;UBERON:0003061!3.53e-08!45;UBERON:0002204!3.40e-07!32
|tfbs_overrepresentation_for_novel_motifs=2.35102,0.612204,0.529553,0.603273,1.04755,0.618805,0.715644,0.812379,0.310789,0.370407,0.668936,0.702872,0.812978,0.728641,1.0876,0,0.930881,0.397593,0.283802,0.185796,0.489529,0.44579,0.727684,0.404661,0.537749,0.757752,1.38127,0.641282,0.456327,1.20535,0.626183,1.03545,0.395107,0.253145,0.425309,0.791367,1.00043,0.699032,0.360612,0.328675,0.401916,0.631725,0.134724,0.426986,0.0637209,0.591277,0.847828,1.58288,0.115788,0.459555,0.912738,0.786094,0.220111,1.18062,1.19842,0.73621,0.469329,0.689304,0.731291,1.74061,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,1.49829,2.78941,1.23259,0.257421,1.27178,0.253065,0.835925,0.997094,0.494135,1.50308,0.948899,0.794502,0.293164,1.1148,0.0793594,1.03552,0.645625,0.852952,1.85284,1.40768,1.11989,1.04863,1.06179,0.356133,0.3366,0.297538,1.05152,0.848095,0.20438,0.384901,1.03517,1.16282,0.913356,0.91226,1.52669,0.97421,0.653843,0.499439,1.23125,1.35621,1.16464,0.495367,0.674448,1.41481,0.399936,0.0998646,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.867604,1.39156,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,0.230371,3.34092,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,0.0513167
|tfbs_overrepresentation_for_novel_motifs=2.35102,0.612204,0.529553,0.603273,1.04755,0.618805,0.715644,0.812379,0.310789,0.370407,0.668936,0.702872,0.812978,0.728641,1.0876,0,0.930881,0.397593,0.283802,0.185796,0.489529,0.44579,0.727684,0.404661,0.537749,0.757752,1.38127,0.641282,0.456327,1.20535,0.626183,1.03545,0.395107,0.253145,0.425309,0.791367,1.00043,0.699032,0.360612,0.328675,0.401916,0.631725,0.134724,0.426986,0.0637209,0.591277,0.847828,1.58288,0.115788,0.459555,0.912738,0.786094,0.220111,1.18062,1.19842,0.73621,0.469329,0.689304,0.731291,1.74061,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,1.49829,2.78941,1.23259,0.257421,1.27178,0.253065,0.835925,0.997094,0.494135,1.50308,0.948899,0.794502,0.293164,1.1148,0.0793594,1.03552,0.645625,0.852952,1.85284,1.40768,1.11989,1.04863,1.06179,0.356133,0.3366,0.297538,1.05152,0.848095,0.20438,0.384901,1.03517,1.16282,0.913356,0.91226,1.52669,0.97421,0.653843,0.499439,1.23125,1.35621,1.16464,0.495367,0.674448,1.41481,0.399936,0.0998646,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.867604,1.39156,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,0.230371,3.34092,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,0.0513167
|tfbs_overrepresentation_jaspar=MA0003.1;0.211284,MA0004.1;0.603793,MA0006.1;0.419915,MA0007.1;0.587678,MA0009.1;1.06266,MA0014.1;0.0502051,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;1.7574,MA0050.1;1.55615,MA0051.1;1.80893,MA0052.1;1.08379,MA0055.1;0.0851423,MA0056.1;0,MA0057.1;0.192781,MA0058.1;0.50032,MA0059.1;0.513699,MA0060.1;0.881183,MA0061.1;0.364227,MA0063.1;0,MA0066.1;0.746072,MA0067.1;1.41352,MA0068.1;0.197245,MA0069.1;1.08414,MA0070.1;1.07418,MA0071.1;0.644448,MA0072.1;1.06547,MA0073.1;0.000589538,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;0.460936,MA0105.1;0.248108,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;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;0.529387,MA0062.2;0.254018,MA0035.2;0.700704,MA0039.2;0.140205,MA0138.2;0.861035,MA0002.2;0.809945,MA0137.2;0.479301,MA0104.2;0.315156,MA0047.2;0.75686,MA0112.2;0.47695,MA0065.2;0.158101,MA0150.1;0.587557,MA0151.1;0,MA0152.1;0.756973,MA0153.1;1.21594,MA0154.1;0.203217,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;0.0699535,MA0163.1;0.497328,MA0164.1;0.729558,MA0080.2;0.455167,MA0018.2;0.739807,MA0099.2;0.854449,MA0079.2;0.0381166,MA0102.2;1.79669,MA0258.1;0.346619,MA0259.1;0.366802,MA0442.1;0
}}
}}

Revision as of 13:39, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:37437253..37437276,+p2@Ly86
Mm9::chr13:37437284..37437301,+p1@Ly86
Mm9::chr17:34272526..34272616,+p1@H2-DMa
Mm9::chr19:44463324..44463335,+p@chr19:44463324..44463335
+
Mm9::chr7:100027264..100027271,-p@chr7:100027264..100027271
-


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:0010008endosome membrane0.0111713463617682
GO:0044440endosomal part0.0111713463617682
GO:0006955immune response0.0111713463617682
GO:0005765lysosomal membrane0.0111713463617682
GO:0045059positive thymic T cell selection0.0111713463617682
GO:0043368positive T cell selection0.0111713463617682
GO:0005771multivesicular body0.0111713463617682
GO:0042613MHC class II protein complex0.0111713463617682
GO:0045582positive regulation of T cell differentiation0.0111713463617682
GO:0051085chaperone cofactor-dependent protein folding0.0111713463617682
GO:0045061thymic T cell selection0.0111713463617682
GO:0006458'de novo' protein folding0.0111713463617682
GO:0051084'de novo' posttranslational protein folding0.0111713463617682
GO:0002376immune system process0.0111713463617682
GO:0045621positive regulation of lymphocyte differentiation0.0111713463617682
GO:0002495antigen processing and presentation of peptide antigen via MHC class II0.0111713463617682
GO:0005774vacuolar membrane0.0111713463617682
GO:0019886antigen processing and presentation of exogenous peptide antigen via MHC class II0.0111713463617682
GO:0045580regulation of T cell differentiation0.0111713463617682
GO:0045058T cell selection0.0111713463617682
GO:0002478antigen processing and presentation of exogenous peptide antigen0.0112649144841956
GO:0002504antigen processing and presentation of peptide or polysaccharide antigen via MHC class II0.0113499436687616
GO:0044437vacuolar part0.0114275476899699
GO:0045619regulation of lymphocyte differentiation0.0120893513204155
GO:0019884antigen processing and presentation of exogenous antigen0.0120893513204155
GO:0033077T cell differentiation in the thymus0.0126344989165626
GO:0005770late endosome0.0126699028249458
GO:0042611MHC protein complex0.0126699028249458
GO:0048002antigen processing and presentation of peptide antigen0.0154015745624465
GO:0050870positive regulation of T cell activation0.018824533378516
GO:0019882antigen processing and presentation0.0241392290912958
GO:0051251positive regulation of lymphocyte activation0.0242648977314301
GO:0030217T cell differentiation0.0242648977314301
GO:0050863regulation of T cell activation0.0243220607194743
GO:0016064immunoglobulin mediated immune response0.0258820835066117
GO:0019724B cell mediated immunity0.0258820835066117
GO:0051249regulation of lymphocyte activation0.0282219397142
GO:0050865regulation of cell activation0.0282219397142
GO:0002460adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.0282219397142
GO:0002250adaptive immune response0.0282219397142
GO:0030098lymphocyte differentiation0.0282219397142
GO:0002449lymphocyte mediated immunity0.0282219397142
GO:0050778positive regulation of immune response0.0282219397142
GO:0002684positive regulation of immune system process0.0282219397142
GO:0005886plasma membrane0.0282219397142
GO:0002443leukocyte mediated immunity0.0282219397142
GO:0050776regulation of immune response0.0308588446470944
GO:0002682regulation of immune system process0.0308588446470944
GO:0051240positive regulation of multicellular organismal process0.0309310587511431
GO:0042110T cell activation0.0309310587511431
GO:0006461protein complex assembly0.0320018973692504
GO:0002521leukocyte differentiation0.0320018973692504
GO:0006457protein folding0.0321371246181744
GO:0002252immune effector process0.0327506438198464
GO:0005768endosome0.0390333443011157
GO:0005764lysosome0.0390333443011157
GO:0000323lytic vacuole0.0390333443011157
GO:0046649lymphocyte activation0.0423440093609866
GO:0005773vacuole0.0423440093609866
GO:0045321leukocyte activation0.0438610383771851
GO:0030097hemopoiesis0.0438610383771851
GO:0006954inflammatory response0.0438610383771851
GO:0001775cell activation0.0458462073904284
GO:0048534hemopoietic or lymphoid organ development0.0473617803066281



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
common myeloid progenitor1.32e-0719

Uber Anatomy
Ontology termp-valuen
bone marrow2.96e-1116
bone element3.55e-1122
skeletal element3.55e-1122
skeletal system3.55e-1122
hemolymphoid system1.09e-0948
immune system1.09e-0948
adult organism3.05e-0851
hematopoietic system3.53e-0845
blood island3.53e-0845
musculoskeletal system3.40e-0732


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)
MA0003.10.211284
MA0004.10.603793
MA0006.10.419915
MA0007.10.587678
MA0009.11.06266
MA0014.10.0502051
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
MA0048.11.7574
MA0050.11.55615
MA0051.11.80893
MA0052.11.08379
MA0055.10.0851423
MA0056.10
MA0057.10.192781
MA0058.10.50032
MA0059.10.513699
MA0060.10.881183
MA0061.10.364227
MA0063.10
MA0066.10.746072
MA0067.11.41352
MA0068.10.197245
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.10.000589538
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
MA0103.10.460936
MA0105.10.248108
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
MA0140.10.695713
MA0141.10.482463
MA0142.10.950155
MA0143.10.797553
MA0144.10.365053
MA0145.10.476962
MA0146.10.21827
MA0147.10.378658
MA0148.10.621195
MA0149.10.529387
MA0062.20.254018
MA0035.20.700704
MA0039.20.140205
MA0138.20.861035
MA0002.20.809945
MA0137.20.479301
MA0104.20.315156
MA0047.20.75686
MA0112.20.47695
MA0065.20.158101
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.10.203217
MA0155.10.515751
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.10.0699535
MA0163.10.497328
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.20.0381166
MA0102.21.79669
MA0258.10.346619
MA0259.10.366802
MA0442.10
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