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MCL coexpression mm9:1608: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=UBERON:0004177!2.16e-21!29;UBERON:0005057!2.16e-21!29;UBERON:0002193!6.19e-20!48;UBERON:0002405!6.19e-20!48;UBERON:0002390!4.81e-19!45;UBERON:0003061!4.81e-19!45;UBERON:0003408!2.91e-18!24;UBERON:0002370!2.68e-17!23;UBERON:0000974!2.68e-17!23;UBERON:0004807!2.68e-17!23;UBERON:0005058!2.68e-17!23;UBERON:0003351!2.68e-17!23;UBERON:0009113!2.68e-17!23;UBERON:0003295!2.68e-17!23;UBERON:0009722!2.68e-17!23;UBERON:0005562!2.68e-17!23;UBERON:0007690!2.68e-17!23;UBERON:0001004!1.08e-16!42;UBERON:0006562!2.68e-16!24;UBERON:0001557!2.68e-16!24;UBERON:0001042!2.68e-16!24;UBERON:0008814!2.68e-16!24;UBERON:0009145!2.68e-16!24;UBERON:0000077!2.86e-16!35;UBERON:0000065!7.99e-16!41;UBERON:0000072!9.30e-14!27;UBERON:0001041!2.38e-12!80;UBERON:0007811!7.01e-11!36;UBERON:0003081!8.55e-11!87;UBERON:0000063!2.88e-10!35;UBERON:0005911!8.81e-10!69;UBERON:0001007!1.91e-08!116;UBERON:0001555!1.91e-08!116;UBERON:0007026!1.91e-08!116;UBERON:0004921!2.77e-08!114;UBERON:0004119!4.23e-08!118;UBERON:0000925!4.23e-08!118;UBERON:0006595!4.23e-08!118;UBERON:0000153!4.71e-08!43;UBERON:0001048!6.34e-08!134;UBERON:0000475!1.82e-07!150;UBERON:0000926!3.43e-07!120;UBERON:0004120!3.43e-07!120;UBERON:0006603!3.43e-07!120;UBERON:0003929!3.86e-07!55;UBERON:0002530!6.47e-07!65
|tfbs_overrepresentation_for_novel_motifs=0.557864,0.293744,0.529553,2.49835,0.406364,0.618805,0.715644,0.812379,0.310789,0.115752,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,0.397593,0.283802,0.545768,2.12626,0.145201,0.727684,1.84054,0.537749,0.757752,0.754069,0.641282,1.15581,0.227599,0.626183,1.03545,0.395107,0.253145,0.425309,4.15666,0.384813,0.699032,0.360612,2.39139,1.03785,0.631725,0.419293,0.426986,0.4934,0.591277,0.847828,0.658142,0.370501,0.459555,0.912738,0.786094,0.220111,1.18062,1.19842,0.73621,0.469329,0.689304,0.26467,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.827208,0.152094,1.23259,0.257421,0.245132,0.253065,0.835925,0.997094,0.494135,0.830212,0.948899,0.794502,0.796301,1.1148,0.0793594,0.0882907,0.645625,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.89388,0.297538,1.05152,0.848095,0.20438,0.384901,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,0.491483,0.550229,1.16464,0.495367,0.674448,1.41481,0.399936,0.0998646,1.47653,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.143464,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,0.230371,0.133815,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.997706,0.701187,0.191104
|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;0.205696,MA0050.1;0.645342,MA0051.1;0.767098,MA0052.1;1.08379,MA0055.1;0.28842,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;0.573319,MA0069.1;1.08414,MA0070.1;1.07418,MA0071.1;1.55428,MA0072.1;2.41915,MA0073.1;0.00450236,MA0074.1;0.708108,MA0076.1;0.470037,MA0077.1;1.04318,MA0078.1;0.801834,MA0081.1;1.33193,MA0083.1;1.16099,MA0084.1;1.74401,MA0087.1;1.11687,MA0088.1;0.453686,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;0.295945,MA0140.1;0.695713,MA0141.1;0.482463,MA0142.1;0.950155,MA0143.1;0.797553,MA0144.1;0.956957,MA0145.1;0.157686,MA0146.1;0.0604336,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;0.299191,MA0137.2;1.20517,MA0104.2;0.315156,MA0047.2;0.75686,MA0112.2;0.927461,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;0.173445,MA0156.1;0.469089,MA0157.1;0.91689,MA0158.1;0,MA0159.1;1.01146,MA0160.1;0.624415,MA0161.1;0,MA0162.1;0.0699535,MA0163.1;0.0644585,MA0164.1;0.729558,MA0080.2;0.455167,MA0018.2;0.739807,MA0099.2;0.854449,MA0079.2;0.30932,MA0102.2;1.79669,MA0258.1;1.63953,MA0259.1;0.366802,MA0442.1;0
}}

Latest revision as of 17:12, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:98340765..98340774,-p@chr11:98340765..98340774
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Mm9::chr11:98340830..98340833,-p@chr11:98340830..98340833
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Mm9::chr11:98370126..98370147,-p@chr11:98370126..98370147
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Mm9::chr1:89761676..89761681,+p@chr1:89761676..89761681
+
Mm9::chr1:89792712..89792716,+p@chr1:89792712..89792716
+


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

no results for this coexpression

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
CD4-positive, alpha-beta T cell5.34e-098
mature alpha-beta T cell8.79e-089
alpha-beta T cell8.79e-089
immature T cell8.79e-089
mature T cell8.79e-089
immature alpha-beta T cell8.79e-089
hematopoietic lineage restricted progenitor cell9.19e-0825
thymocyte1.75e-076
double negative thymocyte1.75e-076
naive T cell1.75e-076
double-positive, alpha-beta thymocyte1.75e-076
CD4-positive, alpha-beta thymocyte1.75e-076
naive thymus-derived CD4-positive, alpha-beta T cell1.75e-076
DN4 thymocyte1.75e-076
DN1 thymic pro-T cell1.75e-076
DN2 thymocyte1.75e-076
DN3 thymocyte1.75e-076
immature single positive thymocyte1.75e-076
early T lineage precursor1.75e-076
mature CD4 single-positive thymocyte1.75e-076
resting double-positive thymocyte1.75e-076
double-positive blast1.75e-076
CD69-positive double-positive thymocyte1.75e-076
CD69-positive, CD4-positive single-positive thymocyte1.75e-076
CD4-positive, CD8-intermediate double-positive thymocyte1.75e-076
CD24-positive, CD4 single-positive thymocyte1.75e-076
megakaryocyte progenitor cell2.82e-076
megakaryocyte2.82e-076
lymphoid lineage restricted progenitor cell4.74e-0712

Uber Anatomy
Ontology termp-valuen
hemopoietic organ2.16e-2129
immune organ2.16e-2129
hemolymphoid system6.19e-2048
immune system6.19e-2048
hematopoietic system4.81e-1945
blood island4.81e-1945
gland of gut2.91e-1824
thymus2.68e-1723
neck2.68e-1723
respiratory system epithelium2.68e-1723
hemolymphoid system gland2.68e-1723
pharyngeal epithelium2.68e-1723
thymic region2.68e-1723
pharyngeal gland2.68e-1723
entire pharyngeal arch endoderm2.68e-1723
thymus primordium2.68e-1723
early pharyngeal endoderm2.68e-1723
respiratory system1.08e-1642
pharynx2.68e-1624
upper respiratory tract2.68e-1624
chordate pharynx2.68e-1624
pharyngeal arch system2.68e-1624
pharyngeal region of foregut2.68e-1624
mixed endoderm/mesoderm-derived structure2.86e-1635
respiratory tract7.99e-1641
segment of respiratory tract9.30e-1427
foregut2.38e-1280
craniocervical region7.01e-1136
lateral plate mesoderm8.55e-1187
organ segment2.88e-1035
endo-epithelium8.81e-1069
digestive system1.91e-08116
digestive tract1.91e-08116
primitive gut1.91e-08116
subdivision of digestive tract2.77e-08114
endoderm-derived structure4.23e-08118
endoderm4.23e-08118
presumptive endoderm4.23e-08118
anterior region of body4.71e-0843
primordium6.34e-08134
organism subdivision1.82e-07150
mesoderm3.43e-07120
mesoderm-derived structure3.43e-07120
presumptive mesoderm3.43e-07120
gut epithelium3.86e-0755
gland6.47e-0765


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
MA0048.10.205696
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.10.28842
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
MA0068.10.573319
MA0069.11.08414
MA0070.11.07418
MA0071.11.55428
MA0072.12.41915
MA0073.10.00450236
MA0074.10.708108
MA0076.10.470037
MA0077.11.04318
MA0078.10.801834
MA0081.11.33193
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.10.453686
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
MA0139.10.295945
MA0140.10.695713
MA0141.10.482463
MA0142.10.950155
MA0143.10.797553
MA0144.10.956957
MA0145.10.157686
MA0146.10.0604336
MA0147.10.378658
MA0148.10.621195
MA0149.10.529387
MA0062.20.254018
MA0035.20.700704
MA0039.20.140205
MA0138.20.861035
MA0002.20.299191
MA0137.21.20517
MA0104.20.315156
MA0047.20.75686
MA0112.20.927461
MA0065.20.158101
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.10.203217
MA0155.10.173445
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.11.01146
MA0160.10.624415
MA0161.10
MA0162.10.0699535
MA0163.10.0644585
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.20.30932
MA0102.21.79669
MA0258.11.63953
MA0259.10.366802
MA0442.10
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