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MCL coexpression mm9:383: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=UBERON:0004177!6.45e-27!29;UBERON:0005057!6.45e-27!29;UBERON:0002390!1.11e-23!45;UBERON:0003061!1.11e-23!45;UBERON:0002193!1.97e-23!48;UBERON:0002405!1.97e-23!48;UBERON:0002370!1.33e-21!23;UBERON:0000974!1.33e-21!23;UBERON:0004807!1.33e-21!23;UBERON:0005058!1.33e-21!23;UBERON:0003351!1.33e-21!23;UBERON:0009113!1.33e-21!23;UBERON:0003295!1.33e-21!23;UBERON:0009722!1.33e-21!23;UBERON:0005562!1.33e-21!23;UBERON:0007690!1.33e-21!23;UBERON:0000065!3.15e-21!41;UBERON:0000077!5.80e-21!35;UBERON:0001004!1.60e-20!42;UBERON:0006562!1.91e-20!24;UBERON:0003408!1.91e-20!24;UBERON:0001557!1.91e-20!24;UBERON:0001042!1.91e-20!24;UBERON:0008814!1.91e-20!24;UBERON:0009145!1.91e-20!24;UBERON:0000072!1.70e-17!27;UBERON:0001041!6.86e-17!80;UBERON:0003081!4.76e-14!87;UBERON:0000063!1.43e-13!35;UBERON:0005911!1.61e-12!69;UBERON:0007811!1.18e-11!36;UBERON:0004921!5.86e-11!114;UBERON:0001007!1.40e-10!116;UBERON:0001555!1.40e-10!116;UBERON:0007026!1.40e-10!116;UBERON:0004119!3.22e-10!118;UBERON:0000925!3.22e-10!118;UBERON:0006595!3.22e-10!118;UBERON:0000926!2.54e-09!120;UBERON:0004120!2.54e-09!120;UBERON:0006603!2.54e-09!120;UBERON:0001048!3.25e-09!134;UBERON:0000153!7.46e-09!43;UBERON:0003929!1.71e-08!55;UBERON:0002368!5.10e-08!60;UBERON:0000475!1.11e-07!150;UBERON:0002530!6.31e-07!65
|tfbs_overrepresentation_for_novel_motifs=0.138811,0.000473445,0.122882,0.96166,0.493134,1.00127,0.240519,0.517797,0.548929,0.0803725,0.208344,1.22048,0.0278964,0.249744,0.53362,0,0.405853,0.820545,0.758457,0.0346275,0.6822,0.247808,0.249061,0.489432,0.400596,0.270807,0.233681,0.190063,0.0855806,0.535987,0.18034,0.493846,0.0591615,0.384407,0.0716204,0.0355512,0.0551797,0.228897,0.396493,0.332849,0.483482,0.183887,0.014039,0.538539,0.0465085,0.158598,0.339166,0.201138,0.162034,0.0870988,0.39102,0.291819,0.297906,0.621761,0.63782,0.255168,0.30656,0.222181,0.0858947,0.253617,0.476165,0.299289,0.323654,0.381514,0.26368,0.41591,0.765078,1.10104,0.472057,0.958179,0.111851,0.537191,0.0631898,0.66884,0.0802546,0.015297,0.19766,0.329879,2.03149,0.693097,0.541148,0.420719,0.298144,0.26638,0.563042,0.000337993,20.7434,0.012217,0.908536,1.25993,0.831175,0.56755,0.505205,0.870702,0.387366,0.348321,0.274301,0.507703,0.339375,0.00870948,0.779402,0.493598,0.605777,0.391523,0.390631,0.183584,0.44182,0.198293,0.346967,0.102757,0.418563,0.607409,0.69602,0.212058,0.837889,0.479203,0.000774063,0.168461,0.406964,1.1708,0.673855,0.363969,0.272218,0.877241,0.889642,0.464341,0.246642,0.499188,0.763646,0.239481,0.590261,0.161127,0.735806,0.265613,0.858504,0.850434,0.144091,0.184858,0.811653,1.62404,1.22863,0.769526,0.281588,0.50313,0.385159,0.541905,0.905286,1.58469,0.446755,0.0644667,0.0126545,0.00215267,0.623204,0.157644,0.264901,0.698893,0.795055,0.954207,3.3831,0.143914,0.820693,0.562267,0.464731,0.133047,0.382373,0.259222,0.0547089,1.89111,0.0109212
|tfbs_overrepresentation_jaspar=MA0003.1;0.00202058,MA0004.1;0.166273,MA0006.1;0.0693118,MA0007.1;0.156418,MA0009.1;0.517357,MA0014.1;0.000608625,MA0017.1;1.4762,MA0019.1;0.359884,MA0024.1;0.47854,MA0025.1;0.731571,MA0027.1;2.12059,MA0028.1;0.0742616,MA0029.1;0.459477,MA0030.1;1.17495,MA0031.1;0.434261,MA0038.1;0.270746,MA0040.1;0.528552,MA0041.1;2.45009,MA0042.1;3.79386,MA0043.1;0.604858,MA0046.1;0.549602,MA0048.1;0.00888801,MA0050.1;0.562435,MA0051.1;0.761088,MA0052.1;0.535783,MA0055.1;0.00346148,MA0056.1;0,MA0057.1;0.0382333,MA0058.1;0.107291,MA0059.1;0.114315,MA0060.1;0.145212,MA0061.1;0.0476315,MA0063.1;0,MA0066.1;0.725822,MA0067.1;0.836675,MA0068.1;0.0077798,MA0069.1;0.536088,MA0070.1;0.52739,MA0071.1;0.561031,MA0072.1;0.519805,MA0073.1;7.12429,MA0074.1;0.235223,MA0076.1;0.0921124,MA0077.1;0.500504,MA0078.1;0.820111,MA0081.1;0.800667,MA0083.1;0.604132,MA0084.1;1.15371,MA0087.1;0.564877,MA0088.1;0.137052,MA0089.1;0,MA0090.1;0.870232,MA0091.1;4.68715,MA0092.1;0.871078,MA0093.1;0.0783063,MA0095.1;0,MA0098.1;0,MA0100.1;0.226682,MA0101.1;0.119531,MA0103.1;0.295593,MA0105.1;0.0158657,MA0106.1;0.309901,MA0107.1;0.0845854,MA0108.2;0.378962,MA0109.1;0,MA0111.1;0.465601,MA0113.1;0.287528,MA0114.1;1.08747,MA0115.1;0.60742,MA0116.1;0.0692153,MA0117.1;0.577975,MA0119.1;0.119877,MA0122.1;0.596061,MA0124.1;0.786128,MA0125.1;0.716372,MA0130.1;0,MA0131.1;0.356119,MA0132.1;0,MA0133.1;0,MA0135.1;0.638323,MA0136.1;0.250125,MA0139.1;0.271406,MA0140.1;0.226598,MA0141.1;1.10531,MA0142.1;1.08106,MA0143.1;0.300449,MA0144.1;0.405604,MA0145.1;0.0220357,MA0146.1;0.00113485,MA0147.1;0.0528647,MA0148.1;2.27509,MA0149.1;0.12279,MA0062.2;0.0170313,MA0035.2;0.230058,MA0039.2;1.66561e-05,MA0138.2;0.349554,MA0002.2;0.514636,MA0137.2;0.0966473,MA0104.2;0.0319344,MA0047.2;2.09879,MA0112.2;0.287479,MA0065.2;0.156268,MA0150.1;0.473632,MA0151.1;0,MA0152.1;1.36519,MA0153.1;0.653688,MA0154.1;0.0439699,MA0155.1;0.00513446,MA0156.1;0.091654,MA0157.1;0.394402,MA0158.1;0,MA0159.1;0.208462,MA0160.1;0.529811,MA0161.1;0,MA0162.1;0.000212795,MA0163.1;0.000157225,MA0164.1;0.698382,MA0080.2;0.0850381,MA0018.2;0.257759,MA0099.2;0.344363,MA0079.2;1.36249e-09,MA0102.2;1.20505,MA0258.1;0.368189,MA0259.1;0.048545,MA0442.1;0
}}

Latest revision as of 15:12, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:33977266..33977288,+p@chr11:33977266..33977288
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Mm9::chr11:33977462..33977480,+p@chr11:33977462..33977480
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Mm9::chr11:34397162..34397173,-p@chr11:34397162..34397173
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Mm9::chr15:27591305..27591306,-p@chr15:27591305..27591306
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Mm9::chr17:57443295..57443306,+p@chr17:57443295..57443306
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Mm9::chr17:57443340..57443374,+p@chr17:57443340..57443374
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Mm9::chr17:57443389..57443400,+p@chr17:57443389..57443400
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Mm9::chr19:25222956..25222972,+p@chr19:25222956..25222972
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Mm9::chr1:139976772..139976784,-p@chr1:139976772..139976784
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Mm9::chr1:139976827..139976842,-p@chr1:139976827..139976842
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Mm9::chr1:140018017..140018043,-p@chr1:140018017..140018043
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Mm9::chr1:140018084..140018096,-p@chr1:140018084..140018096
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Mm9::chr1:140061843..140061864,-p@chr1:140061843..140061864
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Mm9::chr2:117162130..117162141,-p@chr2:117162130..117162141
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Mm9::chr2:44191440..44191453,+p@chr2:44191440..44191453
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Mm9::chr5:105459718..105459730,-p@chr5:105459718..105459730
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Mm9::chr5:136640912..136640928,-p@chr5:136640912..136640928
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Mm9::chr5:136641965..136641971,-p@chr5:136641965..136641971
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Mm9::chr6:146408662..146408666,-p@chr6:146408662..146408666
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Mm9::chr6:48690011..48690023,+p@chr6:48690011..48690023
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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
lymphoid lineage restricted progenitor cell2.28e-1012
hematopoietic lineage restricted progenitor cell2.29e-1025
mature alpha-beta T cell1.14e-099
alpha-beta T cell1.14e-099
immature T cell1.14e-099
mature T cell1.14e-099
immature alpha-beta T cell1.14e-099
T cell1.84e-0911
pro-T cell1.84e-0911
lymphocyte2.19e-0913
common lymphoid progenitor2.19e-0913
thymocyte1.49e-086
double negative thymocyte1.49e-086
naive T cell1.49e-086
double-positive, alpha-beta thymocyte1.49e-086
CD4-positive, alpha-beta thymocyte1.49e-086
naive thymus-derived CD4-positive, alpha-beta T cell1.49e-086
DN4 thymocyte1.49e-086
DN1 thymic pro-T cell1.49e-086
DN2 thymocyte1.49e-086
DN3 thymocyte1.49e-086
immature single positive thymocyte1.49e-086
early T lineage precursor1.49e-086
mature CD4 single-positive thymocyte1.49e-086
resting double-positive thymocyte1.49e-086
double-positive blast1.49e-086
CD69-positive double-positive thymocyte1.49e-086
CD69-positive, CD4-positive single-positive thymocyte1.49e-086
CD4-positive, CD8-intermediate double-positive thymocyte1.49e-086
CD24-positive, CD4 single-positive thymocyte1.49e-086
CD4-positive, alpha-beta T cell2.23e-088
leukocyte2.47e-0817
nongranular leukocyte2.47e-0817
hematopoietic cell3.21e-0732
hematopoietic oligopotent progenitor cell3.21e-0732
hematopoietic stem cell3.21e-0732
angioblastic mesenchymal cell3.21e-0732
hematopoietic multipotent progenitor cell3.21e-0732
nucleate cell3.44e-0716

Uber Anatomy
Ontology termp-valuen
hemopoietic organ6.45e-2729
immune organ6.45e-2729
hematopoietic system1.11e-2345
blood island1.11e-2345
hemolymphoid system1.97e-2348
immune system1.97e-2348
thymus1.33e-2123
neck1.33e-2123
respiratory system epithelium1.33e-2123
hemolymphoid system gland1.33e-2123
pharyngeal epithelium1.33e-2123
thymic region1.33e-2123
pharyngeal gland1.33e-2123
entire pharyngeal arch endoderm1.33e-2123
thymus primordium1.33e-2123
early pharyngeal endoderm1.33e-2123
respiratory tract3.15e-2141
mixed endoderm/mesoderm-derived structure5.80e-2135
respiratory system1.60e-2042
pharynx1.91e-2024
gland of gut1.91e-2024
upper respiratory tract1.91e-2024
chordate pharynx1.91e-2024
pharyngeal arch system1.91e-2024
pharyngeal region of foregut1.91e-2024
segment of respiratory tract1.70e-1727
foregut6.86e-1780
lateral plate mesoderm4.76e-1487
organ segment1.43e-1335
endo-epithelium1.61e-1269
craniocervical region1.18e-1136
subdivision of digestive tract5.86e-11114
digestive system1.40e-10116
digestive tract1.40e-10116
primitive gut1.40e-10116
endoderm-derived structure3.22e-10118
endoderm3.22e-10118
presumptive endoderm3.22e-10118
mesoderm2.54e-09120
mesoderm-derived structure2.54e-09120
presumptive mesoderm2.54e-09120
primordium3.25e-09134
anterior region of body7.46e-0943
gut epithelium1.71e-0855
endocrine gland5.10e-0860
organism subdivision1.11e-07150
gland6.31e-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)
MA0003.10.00202058
MA0004.10.166273
MA0006.10.0693118
MA0007.10.156418
MA0009.10.517357
MA0014.10.000608625
MA0017.11.4762
MA0019.10.359884
MA0024.10.47854
MA0025.10.731571
MA0027.12.12059
MA0028.10.0742616
MA0029.10.459477
MA0030.11.17495
MA0031.10.434261
MA0038.10.270746
MA0040.10.528552
MA0041.12.45009
MA0042.13.79386
MA0043.10.604858
MA0046.10.549602
MA0048.10.00888801
MA0050.10.562435
MA0051.10.761088
MA0052.10.535783
MA0055.10.00346148
MA0056.10
MA0057.10.0382333
MA0058.10.107291
MA0059.10.114315
MA0060.10.145212
MA0061.10.0476315
MA0063.10
MA0066.10.725822
MA0067.10.836675
MA0068.10.0077798
MA0069.10.536088
MA0070.10.52739
MA0071.10.561031
MA0072.10.519805
MA0073.17.12429
MA0074.10.235223
MA0076.10.0921124
MA0077.10.500504
MA0078.10.820111
MA0081.10.800667
MA0083.10.604132
MA0084.11.15371
MA0087.10.564877
MA0088.10.137052
MA0089.10
MA0090.10.870232
MA0091.14.68715
MA0092.10.871078
MA0093.10.0783063
MA0095.10
MA0098.10
MA0100.10.226682
MA0101.10.119531
MA0103.10.295593
MA0105.10.0158657
MA0106.10.309901
MA0107.10.0845854
MA0108.20.378962
MA0109.10
MA0111.10.465601
MA0113.10.287528
MA0114.11.08747
MA0115.10.60742
MA0116.10.0692153
MA0117.10.577975
MA0119.10.119877
MA0122.10.596061
MA0124.10.786128
MA0125.10.716372
MA0130.10
MA0131.10.356119
MA0132.10
MA0133.10
MA0135.10.638323
MA0136.10.250125
MA0139.10.271406
MA0140.10.226598
MA0141.11.10531
MA0142.11.08106
MA0143.10.300449
MA0144.10.405604
MA0145.10.0220357
MA0146.10.00113485
MA0147.10.0528647
MA0148.12.27509
MA0149.10.12279
MA0062.20.0170313
MA0035.20.230058
MA0039.21.66561e-05
MA0138.20.349554
MA0002.20.514636
MA0137.20.0966473
MA0104.20.0319344
MA0047.22.09879
MA0112.20.287479
MA0065.20.156268
MA0150.10.473632
MA0151.10
MA0152.11.36519
MA0153.10.653688
MA0154.10.0439699
MA0155.10.00513446
MA0156.10.091654
MA0157.10.394402
MA0158.10
MA0159.10.208462
MA0160.10.529811
MA0161.10
MA0162.10.000212795
MA0163.10.000157225
MA0164.10.698382
MA0080.20.0850381
MA0018.20.257759
MA0099.20.344363
MA0079.21.36249e-09
MA0102.21.20505
MA0258.10.368189
MA0259.10.048545
MA0442.10
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