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MCL coexpression mm9:467: Difference between revisions

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{{MCL_coexpression_mm9
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side of plasma membrane;0.00912791783016858;22163,21936!GO:0009986;cell surface;0.00912791783016858;22163,21936!GO:0050710;negative regulation of cytokine secretion;0.00912791783016858;22163!GO:0050709;negative regulation of protein secretion;0.00912791783016858;22163!GO:0043120;tumor necrosis factor binding;0.00912791783016858;22163!GO:0008517;folic acid transporter activity;0.00912791783016858;64931!GO:0005031;tumor necrosis factor receptor activity;0.00912791783016858;22163!GO:0050707;regulation of cytokine secretion;0.00912791783016858;22163!GO:0005035;death receptor activity;0.00912791783016858;22163!GO:0050663;cytokine secretion;0.00985734105678631;22163!GO:0051183;vitamin transporter activity;0.0104538964262594;64931!GO:0051184;cofactor transporter activity;0.010950800927537;64931!GO:0005542;folic acid binding;0.0126334626276267;64931!GO:0051048;negative regulation of secretion;0.0140749730015192;22163!GO:0050708;regulation of protein secretion;0.0153235624722565;22163!GO:0006915;apoptosis;0.0261885469613398;22163,21936!GO:0012501;programmed cell death;0.0261885469613398;22163,21936!GO:0009306;protein secretion;0.0261885469613398;22163!GO:0008219;cell death;0.0261885469613398;22163,21936!GO:0016265;death;0.0261885469613398;22163,21936!GO:0051046;regulation of secretion;0.0405275446485512;22163!GO:0004872;receptor activity;0.0422874158580565;22163,64931,21936!GO:0019955;cytokine binding;0.0458356463213889;22163!GO:0060089;molecular transducer activity;0.0458356463213889;22163,64931,21936!GO:0004871;signal transducer 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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,1.1098064804006,0.835206546631728,0.850144310458138,0.736315040841768,0.670317592790424,0.226549106464441,0.291820866352936,0,0,0,0.0636076933539527,0.0558041721483835,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.546559098896642,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.24964188216007,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0662835200988411,0,0,0,0,0,0,0.0685090053637401,0,0,0,0.08030228141145,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.119259559192106,0,0,0.0265240061007451,0.0357618192777494,0.0393518750139388,0.0935585710841254,0.0861106445527604,0.0798802230592418,0.0467520571956962,0.0797788474440915,0.15767882076776,0.125766004618015,0.183220474851329,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=GO:0009897;external side of plasma membrane;0.00912791783016858;22163,21936!GO:0009986;cell surface;0.00912791783016858;22163,21936!GO:0050710;negative regulation of cytokine secretion;0.00912791783016858;22163!GO:0050709;negative regulation of protein secretion;0.00912791783016858;22163!GO:0043120;tumor necrosis factor binding;0.00912791783016858;22163!GO:0008517;folic acid transporter activity;0.00912791783016858;64931!GO:0005031;tumor necrosis factor receptor activity;0.00912791783016858;22163!GO:0050707;regulation of cytokine secretion;0.00912791783016858;22163!GO:0005035;death receptor activity;0.00912791783016858;22163!GO:0050663;cytokine secretion;0.00985734105678631;22163!GO:0051183;vitamin transporter activity;0.0104538964262594;64931!GO:0051184;cofactor transporter activity;0.010950800927537;64931!GO:0005542;folic acid binding;0.0126334626276267;64931!GO:0051048;negative regulation of secretion;0.0140749730015192;22163!GO:0050708;regulation of protein secretion;0.0153235624722565;22163!GO:0006915;apoptosis;0.0261885469613398;22163,21936!GO:0012501;programmed cell death;0.0261885469613398;22163,21936!GO:0009306;protein secretion;0.0261885469613398;22163!GO:0008219;cell death;0.0261885469613398;22163,21936!GO:0016265;death;0.0261885469613398;22163,21936!GO:0051046;regulation of secretion;0.0405275446485512;22163!GO:0004872;receptor activity;0.0422874158580565;22163,64931,21936!GO:0019955;cytokine binding;0.0458356463213889;22163!GO:0060089;molecular transducer activity;0.0458356463213889;22163,64931,21936!GO:0004871;signal transducer activity;0.0458356463213889;22163,64931,21936!
}}

Latest revision as of 15:21, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:105078012..105078042,+p4@Adamts6
Mm9::chr13:105412781..105412798,+p@chr13:105412781..105412798
+
Mm9::chr19:10800783..10800787,-p@chr19:10800783..10800787
-
Mm9::chr2:153104456..153104461,+p@chr2:153104456..153104461
+
Mm9::chr4:155387944..155387958,+p1@Tnfrsf4
Mm9::chr4:155387967..155387981,+p2@Tnfrsf4
Mm9::chr4:155388007..155388018,+p3@Tnfrsf4
Mm9::chr4:155400315..155400334,-p@chr4:155400315..155400334
-
Mm9::chr4:155400413..155400480,+p1@Tnfrsf18
Mm9::chr6:129189762..129189789,-p@chr6:129189762..129189789
-
Mm9::chr6:129189813..129189824,-p@chr6:129189813..129189824
-
Mm9::chr6:129189844..129189851,-p@chr6:129189844..129189851
-
Mm9::chr8:84290231..84290238,+p@chr8:84290231..84290238
+
Mm9::chr9:107200546..107200558,-p@chr9:107200546..107200558
-
Mm9::chr9:107200687..107200702,+p@chr9:107200687..107200702
+
Mm9::chr9:14708434..14708444,-p8@Folr4


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:0009897external side of plasma membrane0.00912791783016858
GO:0009986cell surface0.00912791783016858
GO:0050710negative regulation of cytokine secretion0.00912791783016858
GO:0050709negative regulation of protein secretion0.00912791783016858
GO:0043120tumor necrosis factor binding0.00912791783016858
GO:0008517folic acid transporter activity0.00912791783016858
GO:0005031tumor necrosis factor receptor activity0.00912791783016858
GO:0050707regulation of cytokine secretion0.00912791783016858
GO:0005035death receptor activity0.00912791783016858
GO:0050663cytokine secretion0.00985734105678631
GO:0051183vitamin transporter activity0.0104538964262594
GO:0051184cofactor transporter activity0.010950800927537
GO:0005542folic acid binding0.0126334626276267
GO:0051048negative regulation of secretion0.0140749730015192
GO:0050708regulation of protein secretion0.0153235624722565
GO:0006915apoptosis0.0261885469613398
GO:0012501programmed cell death0.0261885469613398
GO:0009306protein secretion0.0261885469613398
GO:0008219cell death0.0261885469613398
GO:0016265death0.0261885469613398
GO:0051046regulation of secretion0.0405275446485512
GO:0004872receptor activity0.0422874158580565
GO:0019955cytokine binding0.0458356463213889
GO:0060089molecular transducer activity0.0458356463213889
GO:0004871signal transducer activity0.0458356463213889



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 cell2.73e-298
mature alpha-beta T cell6.68e-269
alpha-beta T cell6.68e-269
immature T cell6.68e-269
mature T cell6.68e-269
immature alpha-beta T cell6.68e-269
thymocyte2.94e-226
double negative thymocyte2.94e-226
naive T cell2.94e-226
double-positive, alpha-beta thymocyte2.94e-226
CD4-positive, alpha-beta thymocyte2.94e-226
naive thymus-derived CD4-positive, alpha-beta T cell2.94e-226
DN4 thymocyte2.94e-226
DN1 thymic pro-T cell2.94e-226
DN2 thymocyte2.94e-226
DN3 thymocyte2.94e-226
immature single positive thymocyte2.94e-226
early T lineage precursor2.94e-226
mature CD4 single-positive thymocyte2.94e-226
resting double-positive thymocyte2.94e-226
double-positive blast2.94e-226
CD69-positive double-positive thymocyte2.94e-226
CD69-positive, CD4-positive single-positive thymocyte2.94e-226
CD4-positive, CD8-intermediate double-positive thymocyte2.94e-226
CD24-positive, CD4 single-positive thymocyte2.94e-226
T cell5.71e-2111
pro-T cell5.71e-2111
lymphoid lineage restricted progenitor cell4.05e-1912
lymphocyte1.49e-1713
common lymphoid progenitor1.49e-1713
nucleate cell5.03e-1416
leukocyte3.99e-1317
nongranular leukocyte3.99e-1317
hematopoietic lineage restricted progenitor cell5.70e-1325
hematopoietic cell9.68e-1032
hematopoietic oligopotent progenitor cell9.68e-1032
hematopoietic stem cell9.68e-1032
angioblastic mesenchymal cell9.68e-1032
hematopoietic multipotent progenitor cell9.68e-1032

Uber Anatomy
Ontology termp-valuen
thymus8.01e-4623
neck8.01e-4623
respiratory system epithelium8.01e-4623
hemolymphoid system gland8.01e-4623
pharyngeal epithelium8.01e-4623
thymic region8.01e-4623
pharyngeal gland8.01e-4623
entire pharyngeal arch endoderm8.01e-4623
thymus primordium8.01e-4623
early pharyngeal endoderm8.01e-4623
hemopoietic organ2.49e-4429
immune organ2.49e-4429
pharynx8.97e-4424
gland of gut8.97e-4424
upper respiratory tract8.97e-4424
chordate pharynx8.97e-4424
pharyngeal arch system8.97e-4424
pharyngeal region of foregut8.97e-4424
segment of respiratory tract1.55e-3827
mixed endoderm/mesoderm-derived structure4.16e-3635
hemolymphoid system2.96e-3448
immune system2.96e-3448
hematopoietic system2.66e-3345
blood island2.66e-3345
organ segment5.97e-2935
craniocervical region4.73e-2836
respiratory tract3.28e-2441
respiratory system1.49e-2342
anterior region of body6.34e-2343
gut epithelium3.64e-1755
endocrine gland1.92e-1560
lateral plate mesoderm2.63e-1587
gland5.50e-1465
unilaminar epithelium1.01e-1366
foregut1.10e-1380
organ part4.53e-1399
endo-epithelium5.68e-1369
endocrine system2.76e-1272
mesoderm5.72e-10120
mesoderm-derived structure5.72e-10120
presumptive mesoderm5.72e-10120
subdivision of digestive tract1.87e-08114
digestive system3.05e-08116
digestive tract3.05e-08116
primitive gut3.05e-08116
endoderm-derived structure4.90e-08118
endoderm4.90e-08118
presumptive endoderm4.90e-08118
organism subdivision3.27e-07150


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)
MA0003.11.68224e-05
MA0004.10.631712
MA0006.10.701162
MA0007.10.210531
MA0009.10.599391
MA0014.10.000362989
MA0017.10.387005
MA0019.10.434009
MA0024.10.558971
MA0025.10.819843
MA0027.12.21717
MA0028.10.360944
MA0029.11.33253
MA0030.10.545058
MA0031.10.512616
MA0038.10.33811
MA0040.10.611015
MA0041.10.166538
MA0042.10.15744
MA0043.10.689898
MA0046.10.632833
MA0048.10.087253
MA0050.10.251816
MA0051.10.345658
MA0052.10.618515
MA0055.10.0395234
MA0056.10
MA0057.10.381022
MA0058.10.152805
MA0059.10.161227
MA0060.10.0623353
MA0061.10.267107
MA0063.10
MA0066.11.57697
MA0067.10.92691
MA0068.10.0798662
MA0069.10.618831
MA0070.10.609808
MA0071.11.29438
MA0072.10.601934
MA0073.10.150046
MA0074.10.299171
MA0076.10.134359
MA0077.10.581866
MA0078.10.976277
MA0081.10.525479
MA0083.10.68915
MA0084.11.24749
MA0087.10.648637
MA0088.10.251567
MA0089.10
MA0090.10.196267
MA0091.10.231874
MA0092.10.571528
MA0093.10.374263
MA0095.10
MA0098.10
MA0100.10.289731
MA0101.12.20176
MA0103.10.404646
MA0105.10.128193
MA0106.10.380511
MA0107.10.787845
MA0108.20.454274
MA0109.10
MA0111.11.12477
MA0113.10.356344
MA0114.10.263654
MA0115.10.692537
MA0116.10.105729
MA0117.10.662171
MA0119.10.16785
MA0122.10.680832
MA0124.10.875485
MA0125.10.804312
MA0130.10
MA0131.10.43
MA0132.10
MA0133.10
MA0135.10.724328
MA0136.10.84684
MA0139.10.406429
MA0140.11.43615
MA0141.10.141822
MA0142.10.499475
MA0143.10.37032
MA0144.10.0778672
MA0145.10.0491125
MA0146.10.000633445
MA0147.10.286569
MA0148.10.23425
MA0149.10.171305
MA0062.20.134374
MA0035.21.45004
MA0039.20.493706
MA0138.20.423003
MA0002.22.09532
MA0137.20.432446
MA0104.20.0556953
MA0047.20.337465
MA0112.20.135501
MA0065.20.0494003
MA0150.10.210447
MA0151.10
MA0152.11.60763
MA0153.10.740107
MA0154.10.413095
MA0155.10.0125946
MA0156.10.133796
MA0157.10.47062
MA0158.10
MA0159.10.301936
MA0160.10.23657
MA0161.10
MA0162.10.000977979
MA0163.10.120454
MA0164.10.315868
MA0080.20.396013
MA0018.20.323932
MA0099.20.417463
MA0079.20.00714859
MA0102.21.29919
MA0258.10.893749
MA0259.10.570812
MA0442.10
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