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MCL coexpression mm9:319: Difference between revisions

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{{MCL_coexpression_mm9
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secretion;0.034478015562577;16534!GO:0050714;positive regulation of protein secretion;0.034478015562577;16534!GO:0051047;positive regulation of secretion;0.034478015562577;16534!GO:0007589;fluid secretion;0.034478015562577;16534!GO:0015269;calcium-activated potassium channel activity;0.034478015562577;16534!GO:0051085;chaperone cofactor-dependent protein folding;0.034478015562577;15481!GO:0022600;digestive system process;0.034478015562577;16534!GO:0022839;ion gated channel activity;0.034478015562577;16534!GO:0005227;calcium activated cation channel activity;0.034478015562577;16534!GO:0051084;'de novo' posttranslational protein folding;0.034478015562577;15481!GO:0050708;regulation of protein secretion;0.034478015562577;16534!GO:0006458;'de novo' protein folding;0.034478015562577;15481!GO:0042612;MHC class I protein complex;0.0358764336457484;15019!GO:0004709;MAP kinase kinase kinase activity;0.0358764336457484;53859!GO:0002474;antigen processing and presentation of peptide antigen via MHC class I;0.0374178926128342;15019!GO:0042611;MHC protein complex;0.049189570075961;15019!GO:0009408;response to heat;0.049189570075961;15481!GO:0009306;protein 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|gostat_on_MCL_coexpression=GO:0046541;saliva secretion;0.034478015562577;16534!GO:0050714;positive regulation of protein secretion;0.034478015562577;16534!GO:0051047;positive regulation of secretion;0.034478015562577;16534!GO:0007589;fluid secretion;0.034478015562577;16534!GO:0015269;calcium-activated potassium channel activity;0.034478015562577;16534!GO:0051085;chaperone cofactor-dependent protein folding;0.034478015562577;15481!GO:0022600;digestive system process;0.034478015562577;16534!GO:0022839;ion gated channel activity;0.034478015562577;16534!GO:0005227;calcium activated cation channel activity;0.034478015562577;16534!GO:0051084;'de novo' posttranslational protein folding;0.034478015562577;15481!GO:0050708;regulation of protein secretion;0.034478015562577;16534!GO:0006458;'de novo' protein folding;0.034478015562577;15481!GO:0042612;MHC class I protein complex;0.0358764336457484;15019!GO:0004709;MAP kinase kinase kinase activity;0.0358764336457484;53859!GO:0002474;antigen processing and presentation of peptide antigen via MHC class I;0.0374178926128342;15019!GO:0042611;MHC protein complex;0.049189570075961;15019!GO:0009408;response to heat;0.049189570075961;15481!GO:0009306;protein secretion;0.049189570075961;16534!
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|ontology_enrichment_uberon=UBERON:0002384!5.52e-17!46;UBERON:0002370!3.66e-14!23;UBERON:0000974!3.66e-14!23;UBERON:0004807!3.66e-14!23;UBERON:0005058!3.66e-14!23;UBERON:0003351!3.66e-14!23;UBERON:0009113!3.66e-14!23;UBERON:0003295!3.66e-14!23;UBERON:0009722!3.66e-14!23;UBERON:0005562!3.66e-14!23;UBERON:0007690!3.66e-14!23;UBERON:0006562!1.49e-13!24;UBERON:0003408!1.49e-13!24;UBERON:0001557!1.49e-13!24;UBERON:0001042!1.49e-13!24;UBERON:0008814!1.49e-13!24;UBERON:0009145!1.49e-13!24;UBERON:0002193!3.84e-13!48;UBERON:0002405!3.84e-13!48;UBERON:0000072!5.40e-12!27;UBERON:0002390!2.19e-11!45;UBERON:0003061!2.19e-11!45;UBERON:0004177!3.92e-11!29;UBERON:0005057!3.92e-11!29;UBERON:0000077!3.91e-09!35;UBERON:0000063!3.91e-09!35;UBERON:0007811!7.26e-09!36;UBERON:0000065!1.02e-07!41;UBERON:0001004!1.61e-07!42;UBERON:0000153!2.48e-07!43
|tfbs_overrepresentation_for_novel_motifs=0.317337,0.318152,0.282026,0.376992,0.619074,0.398187,0.538273,0.171073,0.185974,0.705243,0.154519,0.997828,0.569961,0.19087,0.377417,0,0.333505,0.594091,0.512249,0.112549,0.0661203,0.059033,0.190264,0.614199,0.292091,0.209658,0.280346,0.429523,0.198293,0.332722,0.408389,0.416414,0.137902,0.411336,0.166509,0.085061,0.0315753,0.172462,0.263333,0.0838724,0.950664,0.133472,0.189459,0.381604,0.270146,0.360889,0.271716,0.45352,1.18007,0.201733,0.319672,0.228569,1.01744,0.538915,0.554419,0.195691,0.464683,0.166575,0.258637,0.566281,0.39965,0.235329,0.205288,0.310832,0.20328,0.90792,0.678037,1.00855,1.02441,0.867464,0.0740354,0.354986,0.00699494,0.584436,0.116124,0.102175,0.111084,0.263199,0.38541,0.0679477,0.358206,0.347414,0.660928,0.544327,0.48244,0.103202,0.0717289,0.531868,0.275409,1.16606,0.74267,0.486763,0.427209,0.355202,0.104653,0.224705,0.0630984,0.429584,0.271907,0.436104,0.304757,0.416179,0.523506,0.320141,0.31931,0.415447,0.367229,0.877651,0.246199,0.237049,0.636848,0.525078,0.518312,0.927728,0.749248,0.600735,0.0064379,1.25321,0.334542,0.297443,1.43865,0.294572,0.605922,0.726359,0.800032,0.388466,0.188119,0.421488,0.67664,0.361313,0.508573,0.366432,0.649498,0.205008,0.769462,0.516848,0.328991,0.418217,0.723554,1.52843,1.13499,0.682379,0.625834,0.425235,0.31422,0.416785,0.274066,1.4892,0.332285,0.150113,0.189028,0.0172266,0.540306,1.06407,0.204372,0.613593,0.229288,1.0962,0.647931,0.328601,0.732404,0.481698,0.388835,0.0910449,0.311631,0.199302,0.127618,2.24967,0.0680705
|tfbs_overrepresentation_jaspar=MA0003.1;0.0370755,MA0004.1;0.118549,MA0006.1;0.368273,MA0007.1;0.356106,MA0009.1;0.438777,MA0014.1;0.00202333,MA0017.1;0.0511807,MA0019.1;0.290797,MA0024.1;0.401898,MA0025.1;0.645374,MA0027.1;2.02409,MA0028.1;0.172544,MA0029.1;0.383872,MA0030.1;0.389298,MA0031.1;0.360121,MA0038.1;0.602791,MA0040.1;1.99238,MA0041.1;0.0795363,MA0042.1;0.255859,MA0043.1;0.522621,MA0046.1;0.469568,MA0048.1;0.0199474,MA0050.1;0.435264,MA0051.1;0.215828,MA0052.1;0.456356,MA0055.1;0.0121237,MA0056.1;0,MA0057.1;0.0526414,MA0058.1;0.0704409,MA0059.1;0.0759876,MA0060.1;0.414568,MA0061.1;1.16864,MA0063.1;0,MA0066.1;0.584787,MA0067.1;0.748059,MA0068.1;0.861798,MA0069.1;1.1565,MA0070.1;0.448343,MA0071.1;0.433998,MA0072.1;0.44111,MA0073.1;0.489257,MA0074.1;0.526923,MA0076.1;0.808369,MA0077.1;0.422739,MA0078.1;0.672666,MA0081.1;0.611511,MA0083.1;1.29616,MA0084.1;1.0607,MA0087.1;0.484199,MA0088.1;0.370727,MA0089.1;0,MA0090.1;0.32897,MA0091.1;0.396925,MA0092.1;0.329408,MA0093.1;0.181765,MA0095.1;0,MA0098.1;0,MA0100.1;0.170518,MA0101.1;0.976183,MA0103.1;0.203213,MA0105.1;0.395414,MA0106.1;0.685785,MA0107.1;1.16283,MA0108.2;0.830865,MA0109.1;0,MA0111.1;0.107549,MA0113.1;1.19424,MA0114.1;0.109084,MA0115.1;0.525089,MA0116.1;0.0415661,MA0117.1;0.496768,MA0119.1;0.0804194,MA0122.1;0.514153,MA0124.1;0.698593,MA0125.1;0.630583,MA0130.1;0,MA0131.1;0.287321,MA0132.1;0,MA0133.1;0,MA0135.1;0.554905,MA0136.1;0.191208,MA0139.1;0.329061,MA0140.1;0.170444,MA0141.1;0.226841,MA0142.1;0.920091,MA0143.1;0.236381,MA0144.1;0.270735,MA0145.1;0.0289231,MA0146.1;0.0544088,MA0147.1;0.293895,MA0148.1;0.401483,MA0149.1;0.0827548,MA0062.2;0.414115,MA0035.2;0.515842,MA0039.2;0.0298145,MA0138.2;0.281269,MA0002.2;0.565269,MA0137.2;0.062153,MA0104.2;0.0744814,MA0047.2;0.209072,MA0112.2;0.150183,MA0065.2;0.151106,MA0150.1;0.355945,MA0151.1;0,MA0152.1;0.209147,MA0153.1;0.569763,MA0154.1;0.140391,MA0155.1;0.0386081,MA0156.1;0.805459,MA0157.1;0.322822,MA0158.1;0,MA0159.1;0.572269,MA0160.1;0.807296,MA0161.1;0,MA0162.1;0.00637695,MA0163.1;0.0318757,MA0164.1;0.559407,MA0080.2;1.16684,MA0018.2;0.575122,MA0099.2;0.758369,MA0079.2;0.00630905,MA0102.2;1.11159,MA0258.1;0.455063,MA0259.1;0.113327,MA0442.1;0
}}

Latest revision as of 15:05, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:13768074..13768075,+p@chr10:13768074..13768075
+
Mm9::chr11:103128707..103128718,-p2@Map3k14
Mm9::chr14:122277963..122277972,+p3@Ubac2
Mm9::chr14:122278717..122278745,-p2@uc007van.1
Mm9::chr14:122278753..122278760,-p8@uc007van.1
Mm9::chr15:44451456..44451458,-p@chr15:44451456..44451458
-
Mm9::chr16:45224642..45224647,-p@chr16:45224642..45224647
-
Mm9::chr17:31927580..31927601,-p@chr17:31927580..31927601
-
Mm9::chr17:35531042..35531044,+p2@H2-Q8
Mm9::chr17:52301956..52301965,-p@chr17:52301956..52301965
-
Mm9::chr19:57552033..57552048,+p@chr19:57552033..57552048
+
Mm9::chr2:11181142..11181148,-p@chr2:11181142..11181148
-
Mm9::chr4:129249619..129249629,-p@chr4:129249619..129249629
-
Mm9::chr4:129250814..129250842,-p3@Lck
Mm9::chr4:129498481..129498506,+p@chr4:129498481..129498506
+
Mm9::chr4:154310249..154310259,+p@chr4:154310249..154310259
+
Mm9::chr4:154311259..154311277,+p@chr4:154311259..154311277
+
Mm9::chr4:154311294..154311308,+p@chr4:154311294..154311308
+
Mm9::chr4:154317073..154317087,+p@chr4:154317073..154317087
+
Mm9::chr4:154318286..154318297,-p@chr4:154318286..154318297
-
Mm9::chr5:105565106..105565127,-p@chr5:105565106..105565127
-
Mm9::chr7:25155103..25155112,+p10@Kcnn4
Mm9::chr8:125074551..125074598,+p@chr8:125074551..125074598
+
Mm9::chr8:86558320..86558323,-p@chr8:86558320..86558323
-
Mm9::chr9:40610449..40610452,+p2@Hspa8


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:0046541saliva secretion0.034478015562577
GO:0050714positive regulation of protein secretion0.034478015562577
GO:0051047positive regulation of secretion0.034478015562577
GO:0007589fluid secretion0.034478015562577
GO:0015269calcium-activated potassium channel activity0.034478015562577
GO:0051085chaperone cofactor-dependent protein folding0.034478015562577
GO:0022600digestive system process0.034478015562577
GO:0022839ion gated channel activity0.034478015562577
GO:0005227calcium activated cation channel activity0.034478015562577
GO:0051084'de novo' posttranslational protein folding0.034478015562577
GO:0050708regulation of protein secretion0.034478015562577
GO:0006458'de novo' protein folding0.034478015562577
GO:0042612MHC class I protein complex0.0358764336457484
GO:0004709MAP kinase kinase kinase activity0.0358764336457484
GO:0002474antigen processing and presentation of peptide antigen via MHC class I0.0374178926128342
GO:0042611MHC protein complex0.049189570075961
GO:0009408response to heat0.049189570075961
GO:0009306protein secretion0.049189570075961



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
mature alpha-beta T cell3.09e-619
alpha-beta T cell3.09e-619
immature T cell3.09e-619
mature T cell3.09e-619
immature alpha-beta T cell3.09e-619
CD4-positive, alpha-beta T cell1.35e-548
T cell5.27e-5011
pro-T cell5.27e-5011
lymphoid lineage restricted progenitor cell8.65e-4612
lymphocyte3.19e-4213
common lymphoid progenitor3.19e-4213
thymocyte2.88e-416
double negative thymocyte2.88e-416
naive T cell2.88e-416
double-positive, alpha-beta thymocyte2.88e-416
CD4-positive, alpha-beta thymocyte2.88e-416
naive thymus-derived CD4-positive, alpha-beta T cell2.88e-416
DN4 thymocyte2.88e-416
DN1 thymic pro-T cell2.88e-416
DN2 thymocyte2.88e-416
DN3 thymocyte2.88e-416
immature single positive thymocyte2.88e-416
early T lineage precursor2.88e-416
mature CD4 single-positive thymocyte2.88e-416
resting double-positive thymocyte2.88e-416
double-positive blast2.88e-416
CD69-positive double-positive thymocyte2.88e-416
CD69-positive, CD4-positive single-positive thymocyte2.88e-416
CD4-positive, CD8-intermediate double-positive thymocyte2.88e-416
CD24-positive, CD4 single-positive thymocyte2.88e-416
nucleate cell3.45e-3416
leukocyte3.87e-3217
nongranular leukocyte3.87e-3217
hematopoietic lineage restricted progenitor cell4.69e-3225
hematopoietic cell7.61e-2532
hematopoietic oligopotent progenitor cell7.61e-2532
hematopoietic stem cell7.61e-2532
angioblastic mesenchymal cell7.61e-2532
hematopoietic multipotent progenitor cell7.61e-2532
connective tissue cell5.52e-1746
mesenchymal cell5.52e-1746
motile cell2.59e-1454
regulatory T cell1.84e-081
CD4-positive, CD25-positive, alpha-beta regulatory T cell1.84e-081
CD8-positive, alpha-beta T cell3.50e-081
somatic stem cell5.05e-0891
multi fate stem cell5.05e-0891
stem cell1.89e-0797

Uber Anatomy
Ontology termp-valuen
connective tissue5.52e-1746
thymus3.66e-1423
neck3.66e-1423
respiratory system epithelium3.66e-1423
hemolymphoid system gland3.66e-1423
pharyngeal epithelium3.66e-1423
thymic region3.66e-1423
pharyngeal gland3.66e-1423
entire pharyngeal arch endoderm3.66e-1423
thymus primordium3.66e-1423
early pharyngeal endoderm3.66e-1423
pharynx1.49e-1324
gland of gut1.49e-1324
upper respiratory tract1.49e-1324
chordate pharynx1.49e-1324
pharyngeal arch system1.49e-1324
pharyngeal region of foregut1.49e-1324
hemolymphoid system3.84e-1348
immune system3.84e-1348
segment of respiratory tract5.40e-1227
hematopoietic system2.19e-1145
blood island2.19e-1145
hemopoietic organ3.92e-1129
immune organ3.92e-1129
mixed endoderm/mesoderm-derived structure3.91e-0935
organ segment3.91e-0935
craniocervical region7.26e-0936
respiratory tract1.02e-0741
respiratory system1.61e-0742
anterior region of body2.48e-0743


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)
MA0003.10.0370755
MA0004.10.118549
MA0006.10.368273
MA0007.10.356106
MA0009.10.438777
MA0014.10.00202333
MA0017.10.0511807
MA0019.10.290797
MA0024.10.401898
MA0025.10.645374
MA0027.12.02409
MA0028.10.172544
MA0029.10.383872
MA0030.10.389298
MA0031.10.360121
MA0038.10.602791
MA0040.11.99238
MA0041.10.0795363
MA0042.10.255859
MA0043.10.522621
MA0046.10.469568
MA0048.10.0199474
MA0050.10.435264
MA0051.10.215828
MA0052.10.456356
MA0055.10.0121237
MA0056.10
MA0057.10.0526414
MA0058.10.0704409
MA0059.10.0759876
MA0060.10.414568
MA0061.11.16864
MA0063.10
MA0066.10.584787
MA0067.10.748059
MA0068.10.861798
MA0069.11.1565
MA0070.10.448343
MA0071.10.433998
MA0072.10.44111
MA0073.10.489257
MA0074.10.526923
MA0076.10.808369
MA0077.10.422739
MA0078.10.672666
MA0081.10.611511
MA0083.11.29616
MA0084.11.0607
MA0087.10.484199
MA0088.10.370727
MA0089.10
MA0090.10.32897
MA0091.10.396925
MA0092.10.329408
MA0093.10.181765
MA0095.10
MA0098.10
MA0100.10.170518
MA0101.10.976183
MA0103.10.203213
MA0105.10.395414
MA0106.10.685785
MA0107.11.16283
MA0108.20.830865
MA0109.10
MA0111.10.107549
MA0113.11.19424
MA0114.10.109084
MA0115.10.525089
MA0116.10.0415661
MA0117.10.496768
MA0119.10.0804194
MA0122.10.514153
MA0124.10.698593
MA0125.10.630583
MA0130.10
MA0131.10.287321
MA0132.10
MA0133.10
MA0135.10.554905
MA0136.10.191208
MA0139.10.329061
MA0140.10.170444
MA0141.10.226841
MA0142.10.920091
MA0143.10.236381
MA0144.10.270735
MA0145.10.0289231
MA0146.10.0544088
MA0147.10.293895
MA0148.10.401483
MA0149.10.0827548
MA0062.20.414115
MA0035.20.515842
MA0039.20.0298145
MA0138.20.281269
MA0002.20.565269
MA0137.20.062153
MA0104.20.0744814
MA0047.20.209072
MA0112.20.150183
MA0065.20.151106
MA0150.10.355945
MA0151.10
MA0152.10.209147
MA0153.10.569763
MA0154.10.140391
MA0155.10.0386081
MA0156.10.805459
MA0157.10.322822
MA0158.10
MA0159.10.572269
MA0160.10.807296
MA0161.10
MA0162.10.00637695
MA0163.10.0318757
MA0164.10.559407
MA0080.21.16684
MA0018.20.575122
MA0099.20.758369
MA0079.20.00630905
MA0102.21.11159
MA0258.10.455063
MA0259.10.113327
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:319&oldid=3072318"