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MCL coexpression mm9:1148: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0001968;fibronectin binding;0.0131481633363305;16401!GO:0007159;leukocyte adhesion;0.0289101108018125;16401!GO:0001974;blood vessel remodeling;0.0289101108018125;16401!GO:0007185;transmembrane receptor protein tyrosine phosphatase signaling pathway;0.0289101108018125;19265!GO:0007157;heterophilic cell adhesion;0.0289101108018125;16401!GO:0008305;integrin complex;0.0372204718592457;16401!
|ontology_enrichment_celltype=CL:0000988!8.25e-16!32;CL:0002032!8.25e-16!32;CL:0000037!8.25e-16!32;CL:0000566!8.25e-16!32;CL:0000837!8.25e-16!32;CL:0000838!5.58e-14!12;CL:0000084!6.49e-13!11;CL:0000827!6.49e-13!11;CL:0000542!1.50e-12!13;CL:0000051!1.50e-12!13;CL:0002031!5.03e-12!25;CL:0002242!6.92e-11!16;CL:0000791!8.56e-11!9;CL:0000789!8.56e-11!9;CL:0002420!8.56e-11!9;CL:0002419!8.56e-11!9;CL:0000790!8.56e-11!9;CL:0000624!9.01e-10!8;CL:0002320!3.28e-09!46;CL:0000134!3.28e-09!46;CL:0000738!1.43e-08!17;CL:0002087!1.43e-08!17;CL:0000893!1.51e-07!6;CL:0002489!1.51e-07!6;CL:0000898!1.51e-07!6;CL:0000809!1.51e-07!6;CL:0000810!1.51e-07!6;CL:0000895!1.51e-07!6;CL:0000808!1.51e-07!6;CL:0000894!1.51e-07!6;CL:0000806!1.51e-07!6;CL:0000807!1.51e-07!6;CL:0000805!1.51e-07!6;CL:0002425!1.51e-07!6;CL:0002436!1.51e-07!6;CL:0002427!1.51e-07!6;CL:0002428!1.51e-07!6;CL:0002429!1.51e-07!6;CL:0002433!1.51e-07!6;CL:0002431!1.51e-07!6;CL:0002432!1.51e-07!6;CL:0000219!3.31e-07!54
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!6.67e-21!48;UBERON:0002405!6.67e-21!48;UBERON:0002390!9.26e-19!45;UBERON:0003061!9.26e-19!45;UBERON:0004177!2.03e-18!29;UBERON:0005057!2.03e-18!29;UBERON:0000077!3.56e-16!35;UBERON:0002370!1.16e-15!23;UBERON:0000974!1.16e-15!23;UBERON:0004807!1.16e-15!23;UBERON:0005058!1.16e-15!23;UBERON:0003351!1.16e-15!23;UBERON:0009113!1.16e-15!23;UBERON:0003295!1.16e-15!23;UBERON:0009722!1.16e-15!23;UBERON:0005562!1.16e-15!23;UBERON:0007690!1.16e-15!23;UBERON:0006562!1.06e-14!24;UBERON:0003408!1.06e-14!24;UBERON:0001557!1.06e-14!24;UBERON:0001042!1.06e-14!24;UBERON:0008814!1.06e-14!24;UBERON:0009145!1.06e-14!24;UBERON:0000072!2.95e-12!27;UBERON:0000065!1.86e-11!41;UBERON:0001004!5.65e-11!42;UBERON:0001041!9.46e-11!80;UBERON:0005911!6.93e-10!69;UBERON:0003081!1.12e-09!87;UBERON:0003929!2.75e-09!55;UBERON:0002384!3.28e-09!46;UBERON:0004119!6.11e-09!118;UBERON:0000925!6.11e-09!118;UBERON:0006595!6.11e-09!118;UBERON:0001007!9.29e-09!116;UBERON:0001555!9.29e-09!116;UBERON:0007026!9.29e-09!116;UBERON:0000063!1.03e-08!35;UBERON:0004921!6.27e-08!114;UBERON:0002368!9.39e-08!60;UBERON:0000490!1.16e-07!66;UBERON:0007811!1.64e-07!36;UBERON:0002530!3.95e-07!65
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.369498,0.411716,1.20801,0.810002,0.495263,0.587291,0.206208,0.616096,0.219671,0.542749,0.575086,0.206435,0.599731,0.315771,0,0.795315,0.291368,0.561256,0.361892,0.374752,0.27937,0.598814,0.29769,1.07577,0.62766,0.542568,0.516511,0.911169,0.145661,0.50223,0.897561,0.78719,0.498917,0.316253,0.0235321,0.279977,0.57142,0.258564,0.230656,0.295233,0.507468,0.258106,0.317766,1.19315,0.469348,0.714592,0.532496,0.219744,0.917701,0.777641,0.654933,1.3744,1.04034,1.0579,0.606984,0.356236,0.56214,0.522357,0.604914,0.877332,0.664501,0.642748,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.21183,0.611537,1.09164,0.17012,0.482617,0.166511,0.703064,0.859987,0.98764,0.212973,0.812889,0.663039,0.200155,0.975495,0.339494,0.374181,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.668513,0.203879,0.913319,0.71485,0.399703,1.40122,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,0.430942,1.02459,2.63898,0.547992,1.27206,0.293461,0.187586,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.0806013,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.452587,1.38961,1.04192,0.243291,0.619892,1.12411,0.655955,0.327731,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,1.3969,0.573477,0.433127
|tfbs_overrepresentation_jaspar=MA0003.1;0.79075,MA0004.1;0.481116,MA0006.1;0.837454,MA0007.1;0.465969,MA0009.1;0.92425,MA0014.1;0.222567,MA0017.1;0.89657,MA0019.1;1.753,MA0024.1;0.880057,MA0025.1;1.15921,MA0027.1;2.57545,MA0028.1;0.860672,MA0029.1;0.858105,MA0030.1;0.864739,MA0031.1;0.828781,MA0038.1;0.62758,MA0040.1;0.936879,MA0041.1;0.404721,MA0042.1;0.391504,MA0043.1;1.02178,MA0046.1;0.960497,MA0048.1;0.128106,MA0050.1;0.520357,MA0051.1;0.636645,MA0052.1;0.945011,MA0055.1;1.92126,MA0056.1;0,MA0057.1;0.376102,MA0058.1;0.384683,MA0059.1;0.397033,MA0060.1;0.232592,MA0061.1;0.261749,MA0063.1;0,MA0066.1;0.616444,MA0067.1;1.27078,MA0068.1;0.771749,MA0069.1;0.945354,MA0070.1;0.93557,MA0071.1;0.519509,MA0072.1;0.927016,MA0073.1;0.0890846,MA0074.1;0.580087,MA0076.1;0.356883,MA0077.1;2.09251,MA0078.1;0.670113,MA0081.1;1.07783,MA0083.1;2.32874,MA0084.1;1.59945,MA0087.1;0.977537,MA0088.1;0.598004,MA0089.1;0,MA0090.1;0.446539,MA0091.1;0.494398,MA0092.1;0.446857,MA0093.1;0.329976,MA0095.1;0,MA0098.1;0,MA0100.1;0.568369,MA0101.1;0.406019,MA0103.1;0.920496,MA0105.1;0.488671,MA0106.1;0.677988,MA0107.1;0.342432,MA0108.2;0.763162,MA0109.1;0,MA0111.1;0.460823,MA0113.1;0.649407,MA0114.1;0.259463,MA0115.1;1.0246,MA0116.1;0.311187,MA0117.1;0.992087,MA0119.1;0.40661,MA0122.1;1.01209,MA0124.1;1.21735,MA0125.1;1.14291,MA0130.1;0,MA0131.1;0.735438,MA0132.1;0,MA0133.1;0,MA0135.1;1.05845,MA0136.1;1.46167,MA0139.1;0.202522,MA0140.1;0.568252,MA0141.1;0.368264,MA0142.1;0.814115,MA0143.1;0.665982,MA0144.1;0.262477,MA0145.1;0.631666,MA0146.1;0.264322,MA0147.1;0.274511,MA0148.1;0.49752,MA0149.1;0.411562,MA0062.2;0.167299,MA0035.2;0.573016,MA0039.2;0.219063,MA0138.2;0.727395,MA0002.2;0.205289,MA0137.2;0.365364,MA0104.2;0.218974,MA0047.2;0.626803,MA0112.2;0.304722,MA0065.2;0.0914071,MA0150.1;0.465855,MA0151.1;0,MA0152.1;0.626912,MA0153.1;1.07519,MA0154.1;0.792589,MA0155.1;0.336768,MA0156.1;0.356017,MA0157.1;0.781683,MA0158.1;0,MA0159.1;0.776527,MA0160.1;0.50056,MA0161.1;0,MA0162.1;0.878466,MA0163.1;0.28052,MA0164.1;0.600609,MA0080.2;0.908823,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;0.233827,MA0102.2;1.65195,MA0258.1;0.688848,MA0259.1;0.26402,MA0442.1;0
}}

Latest revision as of 16:28, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr16:49855630..49855685,-p@chr16:49855630..49855685
-
Mm9::chr18:32557234..32557249,+p@chr18:32557234..32557249
+
Mm9::chr19:4154620..4154629,+p2@Ptprcap
Mm9::chr19:4154640..4154668,+p1@Ptprcap
Mm9::chr19:4156100..4156111,+p@chr19:4156100..4156111
+
Mm9::chr19:46114855..46114867,-p@chr19:46114855..46114867
-
Mm9::chr2:79095076..79095083,+p12@Itga4


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:0001968fibronectin binding0.0131481633363305
GO:0007159leukocyte adhesion0.0289101108018125
GO:0001974blood vessel remodeling0.0289101108018125
GO:0007185transmembrane receptor protein tyrosine phosphatase signaling pathway0.0289101108018125
GO:0007157heterophilic cell adhesion0.0289101108018125
GO:0008305integrin complex0.0372204718592457



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
hematopoietic cell8.25e-1632
hematopoietic oligopotent progenitor cell8.25e-1632
hematopoietic stem cell8.25e-1632
angioblastic mesenchymal cell8.25e-1632
hematopoietic multipotent progenitor cell8.25e-1632
lymphoid lineage restricted progenitor cell5.58e-1412
T cell6.49e-1311
pro-T cell6.49e-1311
lymphocyte1.50e-1213
common lymphoid progenitor1.50e-1213
hematopoietic lineage restricted progenitor cell5.03e-1225
nucleate cell6.92e-1116
mature alpha-beta T cell8.56e-119
alpha-beta T cell8.56e-119
immature T cell8.56e-119
mature T cell8.56e-119
immature alpha-beta T cell8.56e-119
CD4-positive, alpha-beta T cell9.01e-108
connective tissue cell3.28e-0946
mesenchymal cell3.28e-0946
leukocyte1.43e-0817
nongranular leukocyte1.43e-0817
thymocyte1.51e-076
double negative thymocyte1.51e-076
naive T cell1.51e-076
double-positive, alpha-beta thymocyte1.51e-076
CD4-positive, alpha-beta thymocyte1.51e-076
naive thymus-derived CD4-positive, alpha-beta T cell1.51e-076
DN4 thymocyte1.51e-076
DN1 thymic pro-T cell1.51e-076
DN2 thymocyte1.51e-076
DN3 thymocyte1.51e-076
immature single positive thymocyte1.51e-076
early T lineage precursor1.51e-076
mature CD4 single-positive thymocyte1.51e-076
resting double-positive thymocyte1.51e-076
double-positive blast1.51e-076
CD69-positive double-positive thymocyte1.51e-076
CD69-positive, CD4-positive single-positive thymocyte1.51e-076
CD4-positive, CD8-intermediate double-positive thymocyte1.51e-076
CD24-positive, CD4 single-positive thymocyte1.51e-076
motile cell3.31e-0754

Uber Anatomy
Ontology termp-valuen
hemolymphoid system6.67e-2148
immune system6.67e-2148
hematopoietic system9.26e-1945
blood island9.26e-1945
hemopoietic organ2.03e-1829
immune organ2.03e-1829
mixed endoderm/mesoderm-derived structure3.56e-1635
thymus1.16e-1523
neck1.16e-1523
respiratory system epithelium1.16e-1523
hemolymphoid system gland1.16e-1523
pharyngeal epithelium1.16e-1523
thymic region1.16e-1523
pharyngeal gland1.16e-1523
entire pharyngeal arch endoderm1.16e-1523
thymus primordium1.16e-1523
early pharyngeal endoderm1.16e-1523
pharynx1.06e-1424
gland of gut1.06e-1424
upper respiratory tract1.06e-1424
chordate pharynx1.06e-1424
pharyngeal arch system1.06e-1424
pharyngeal region of foregut1.06e-1424
segment of respiratory tract2.95e-1227
respiratory tract1.86e-1141
respiratory system5.65e-1142
foregut9.46e-1180
endo-epithelium6.93e-1069
lateral plate mesoderm1.12e-0987
gut epithelium2.75e-0955
connective tissue3.28e-0946
endoderm-derived structure6.11e-09118
endoderm6.11e-09118
presumptive endoderm6.11e-09118
digestive system9.29e-09116
digestive tract9.29e-09116
primitive gut9.29e-09116
organ segment1.03e-0835
subdivision of digestive tract6.27e-08114
endocrine gland9.39e-0860
unilaminar epithelium1.16e-0766
craniocervical region1.64e-0736
gland3.95e-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)
MA0003.10.79075
MA0004.10.481116
MA0006.10.837454
MA0007.10.465969
MA0009.10.92425
MA0014.10.222567
MA0017.10.89657
MA0019.11.753
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.10.860672
MA0029.10.858105
MA0030.10.864739
MA0031.10.828781
MA0038.10.62758
MA0040.10.936879
MA0041.10.404721
MA0042.10.391504
MA0043.11.02178
MA0046.10.960497
MA0048.10.128106
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.11.92126
MA0056.10
MA0057.10.376102
MA0058.10.384683
MA0059.10.397033
MA0060.10.232592
MA0061.10.261749
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.771749
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.10.0890846
MA0074.10.580087
MA0076.10.356883
MA0077.12.09251
MA0078.10.670113
MA0081.11.07783
MA0083.12.32874
MA0084.11.59945
MA0087.10.977537
MA0088.10.598004
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.10.446857
MA0093.10.329976
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.10.920496
MA0105.10.488671
MA0106.10.677988
MA0107.10.342432
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.259463
MA0115.11.0246
MA0116.10.311187
MA0117.10.992087
MA0119.10.40661
MA0122.11.01209
MA0124.11.21735
MA0125.11.14291
MA0130.10
MA0131.10.735438
MA0132.10
MA0133.10
MA0135.11.05845
MA0136.11.46167
MA0139.10.202522
MA0140.10.568252
MA0141.10.368264
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.10.631666
MA0146.10.264322
MA0147.10.274511
MA0148.10.49752
MA0149.10.411562
MA0062.20.167299
MA0035.20.573016
MA0039.20.219063
MA0138.20.727395
MA0002.20.205289
MA0137.20.365364
MA0104.20.218974
MA0047.20.626803
MA0112.20.304722
MA0065.20.0914071
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.792589
MA0155.10.336768
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.10.776527
MA0160.10.50056
MA0161.10
MA0162.10.878466
MA0163.10.28052
MA0164.10.600609
MA0080.20.908823
MA0018.20.610433
MA0099.20.721008
MA0079.20.233827
MA0102.21.65195
MA0258.10.688848
MA0259.10.26402
MA0442.10
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