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MCL coexpression mm9:433: Difference between revisions

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{{MCL_coexpression_mm9
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secretion;0.0456920771900011;16534!GO:0050714;positive regulation of protein secretion;0.0456920771900011;16534!GO:0042069;regulation of catecholamine metabolic process;0.0456920771900011;18227!GO:0042053;regulation of dopamine metabolic process;0.0456920771900011;18227!GO:0051047;positive regulation of secretion;0.0456920771900011;16534!GO:0007589;fluid secretion;0.0456920771900011;16534!GO:0015269;calcium-activated potassium channel activity;0.0456920771900011;16534!GO:0022600;digestive system process;0.0456920771900011;16534!GO:0022839;ion gated channel activity;0.0456920771900011;16534!GO:0005227;calcium activated cation channel activity;0.0456920771900011;16534!GO:0050708;regulation of protein 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|gostat_on_MCL_coexpression=GO:0046541;saliva secretion;0.0456920771900011;16534!GO:0050714;positive regulation of protein secretion;0.0456920771900011;16534!GO:0042069;regulation of catecholamine metabolic process;0.0456920771900011;18227!GO:0042053;regulation of dopamine metabolic process;0.0456920771900011;18227!GO:0051047;positive regulation of secretion;0.0456920771900011;16534!GO:0007589;fluid secretion;0.0456920771900011;16534!GO:0015269;calcium-activated potassium channel activity;0.0456920771900011;16534!GO:0022600;digestive system process;0.0456920771900011;16534!GO:0022839;ion gated channel activity;0.0456920771900011;16534!GO:0005227;calcium activated cation channel activity;0.0456920771900011;16534!GO:0050708;regulation of protein secretion;0.0456920771900011;16534!
|ontology_enrichment_celltype=CL:0000988!5.50e-30!32;CL:0002032!5.50e-30!32;CL:0000037!5.50e-30!32;CL:0000566!5.50e-30!32;CL:0000837!5.50e-30!32;CL:0000838!5.82e-30!12;CL:0000542!1.83e-27!13;CL:0000051!1.83e-27!13;CL:0000084!1.86e-27!11;CL:0000827!1.86e-27!11;CL:0000791!3.91e-23!9;CL:0000789!3.91e-23!9;CL:0002420!3.91e-23!9;CL:0002419!3.91e-23!9;CL:0000790!3.91e-23!9;CL:0002242!7.68e-22!16;CL:0002320!8.89e-22!46;CL:0000134!8.89e-22!46;CL:0000219!1.18e-21!54;CL:0000624!9.72e-21!8;CL:0000738!2.08e-20!17;CL:0002087!2.08e-20!17;CL:0002031!7.06e-18!25;CL:0000034!1.21e-16!97;CL:0000893!6.40e-16!6;CL:0002489!6.40e-16!6;CL:0000898!6.40e-16!6;CL:0000809!6.40e-16!6;CL:0000810!6.40e-16!6;CL:0000895!6.40e-16!6;CL:0000808!6.40e-16!6;CL:0000894!6.40e-16!6;CL:0000806!6.40e-16!6;CL:0000807!6.40e-16!6;CL:0000805!6.40e-16!6;CL:0002425!6.40e-16!6;CL:0002436!6.40e-16!6;CL:0002427!6.40e-16!6;CL:0002428!6.40e-16!6;CL:0002429!6.40e-16!6;CL:0002433!6.40e-16!6;CL:0002431!6.40e-16!6;CL:0002432!6.40e-16!6;CL:0000723!2.14e-13!91;CL:0000048!2.14e-13!91;CL:0002371!3.66e-12!118;CL:0000548!2.69e-09!115;CL:0000255!2.69e-09!115;CL:0000049!2.95e-08!19;CL:0000215!4.38e-08!3
|ontology_enrichment_disease=DOID:0060100!1.34e-08!3;DOID:4045!1.34e-08!3
|ontology_enrichment_uberon=UBERON:0002384!8.89e-22!46
|tfbs_overrepresentation_for_novel_motifs=1.00028,0.0322544,0.476315,0.205657,0.0882392,0.216369,0.286882,0.165361,0.177198,0.896006,0.252112,0.760086,0.165655,0.296787,0.322172,0,0.46143,0.596872,0.147449,0.53564,0.415519,1.15861,0.296055,1.02912,0.16256,0.319311,0.13779,0.232181,0.366819,0.230852,0.630968,0.552579,0.281806,0.279585,0.322914,0.144175,0.268195,0.753507,0.0668978,0.0536011,0.290922,0.640129,0.528785,0.325245,0.434967,0.197508,0.391673,0.244272,0.64057,0.37148,0.445973,0.341665,0.217128,0.683824,0.700221,0.302599,0.385691,0.26711,0.554816,0.300938,0.534331,0.349585,0.427506,0.43605,0.311703,0.471894,0.829699,1.16897,0.530087,1.02503,0.444898,0.390307,0.623456,0.731855,0.531778,0.263994,0.027847,0.994033,1.28944,0.422405,0.696815,0.476893,0.920052,1.00736,0.623727,0.572181,0.288683,0.0927017,0.395899,1.32869,0.896685,0.62835,2.37195,0.0914951,1.29816,0.207461,0.370414,0.56686,0.391893,0.614116,0.959508,0.552324,0.667487,0.446498,0.445567,0.639347,0.498793,0.241171,0.848883,0.134388,0.50853,0.669156,0.136675,0.711663,0.903482,0.085085,0.529599,0.208431,0.462587,0.944825,0.736964,0.4177,0.320815,0.381122,0.955823,0.522111,0.293459,0.558086,0.828246,0.093155,0.651613,0.200314,0.799981,0.313768,0.92434,0.204108,0.181334,1.20107,0.876916,1.69384,1.29725,0.834212,1.58373,0.562149,1.12026,0.225756,0.394362,1.65442,0.183006,0.299565,0.447655,0.767951,0.685297,0.215456,0.313008,0.762455,0.342508,1.68492,0.993295,0.181136,0.886073,0.622933,1.29742,0.168927,1.11397,1.49864,0.0772819,0.275979,0.478093
}}

Latest revision as of 15:17, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:120416369..120416378,-p@chr10:120416369..120416378
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Mm9::chr12:4925036..4925055,-p@chr12:4925036..4925055
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Mm9::chr16:17722647..17722693,+p@chr16:17722647..17722693
+
Mm9::chr17:17511579..17511588,+p@chr17:17511579..17511588
+
Mm9::chr17:29626018..29626030,-p@chr17:29626018..29626030
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Mm9::chr17:29626283..29626293,+p@chr17:29626283..29626293
+
Mm9::chr19:36423777..36423809,-p@chr19:36423777..36423809
-
Mm9::chr2:56976467..56976482,-p4@Nr4a2
Mm9::chr4:102244812..102244831,-p@chr4:102244812..102244831
-
Mm9::chr4:102244969..102244982,+p@chr4:102244969..102244982
+
Mm9::chr7:25155202..25155218,+p8@Kcnn4
Mm9::chr7:26465861..26465880,+p2@B9d2
Mm9::chr7:87546167..87546184,+p@chr7:87546167..87546184
+
Mm9::chr9:75255861..75255886,+p@chr9:75255861..75255886
+
Mm9::chr9:75255893..75255906,+p@chr9:75255893..75255906
+
Mm9::chr9:75256131..75256135,+p@chr9:75256131..75256135
+
Mm9::chrX:101176473..101176487,-p3@Rlim


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 secretion0.0456920771900011
GO:0050714positive regulation of protein secretion0.0456920771900011
GO:0042069regulation of catecholamine metabolic process0.0456920771900011
GO:0042053regulation of dopamine metabolic process0.0456920771900011
GO:0051047positive regulation of secretion0.0456920771900011
GO:0007589fluid secretion0.0456920771900011
GO:0015269calcium-activated potassium channel activity0.0456920771900011
GO:0022600digestive system process0.0456920771900011
GO:0022839ion gated channel activity0.0456920771900011
GO:0005227calcium activated cation channel activity0.0456920771900011
GO:0050708regulation of protein secretion0.0456920771900011



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>disease_data<br>

Cell Type
Ontology termp-valuen
hematopoietic cell5.50e-3032
hematopoietic oligopotent progenitor cell5.50e-3032
hematopoietic stem cell5.50e-3032
angioblastic mesenchymal cell5.50e-3032
hematopoietic multipotent progenitor cell5.50e-3032
lymphoid lineage restricted progenitor cell5.82e-3012
lymphocyte1.83e-2713
common lymphoid progenitor1.83e-2713
T cell1.86e-2711
pro-T cell1.86e-2711
mature alpha-beta T cell3.91e-239
alpha-beta T cell3.91e-239
immature T cell3.91e-239
mature T cell3.91e-239
immature alpha-beta T cell3.91e-239
nucleate cell7.68e-2216
connective tissue cell8.89e-2246
mesenchymal cell8.89e-2246
motile cell1.18e-2154
CD4-positive, alpha-beta T cell9.72e-218
leukocyte2.08e-2017
nongranular leukocyte2.08e-2017
hematopoietic lineage restricted progenitor cell7.06e-1825
stem cell1.21e-1697
thymocyte6.40e-166
double negative thymocyte6.40e-166
naive T cell6.40e-166
double-positive, alpha-beta thymocyte6.40e-166
CD4-positive, alpha-beta thymocyte6.40e-166
naive thymus-derived CD4-positive, alpha-beta T cell6.40e-166
DN4 thymocyte6.40e-166
DN1 thymic pro-T cell6.40e-166
DN2 thymocyte6.40e-166
DN3 thymocyte6.40e-166
immature single positive thymocyte6.40e-166
early T lineage precursor6.40e-166
mature CD4 single-positive thymocyte6.40e-166
resting double-positive thymocyte6.40e-166
double-positive blast6.40e-166
CD69-positive double-positive thymocyte6.40e-166
CD69-positive, CD4-positive single-positive thymocyte6.40e-166
CD4-positive, CD8-intermediate double-positive thymocyte6.40e-166
CD24-positive, CD4 single-positive thymocyte6.40e-166
somatic stem cell2.14e-1391
multi fate stem cell2.14e-1391
somatic cell3.66e-12118
animal cell2.69e-09115
eukaryotic cell2.69e-09115
common myeloid progenitor2.95e-0819
barrier cell4.38e-083

Uber Anatomy
Ontology termp-valuen
connective tissue8.89e-2246

Disease
Ontology termp-valuen
musculoskeletal system cancer1.34e-083
muscle cancer1.34e-083


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)
MA0003.10.40217
MA0004.10.594255
MA0006.11.0833
MA0007.10.56814
MA0009.10.576798
MA0014.10.203425
MA0017.10.110433
MA0019.10.413421
MA0024.10.536784
MA0025.13.10977
MA0027.12.19092
MA0028.10.100975
MA0029.10.51708
MA0030.10.523021
MA0031.10.490954
MA0038.11.54269
MA0040.10.588314
MA0041.10.464691
MA0042.10.144042
MA0043.10.666547
MA0046.10.609938
MA0048.10.373835
MA0050.10.662757
MA0051.10.326637
MA0052.10.595747
MA0055.10.855686
MA0056.10
MA0057.10.0640642
MA0058.10.851133
MA0059.10.885442
MA0060.10.200642
MA0061.11.85379
MA0063.10
MA0066.10.834818
MA0067.10.902253
MA0068.10.876728
MA0069.10.59606
MA0070.10.587119
MA0071.10.234437
MA0072.10.579318
MA0073.10.596603
MA0074.10.281183
MA0076.10.122031
MA0077.10.559443
MA0078.10.354249
MA0081.10.163204
MA0083.10.665805
MA0084.11.22195
MA0087.10.625609
MA0088.10.602878
MA0089.10
MA0090.10.181323
MA0091.10.617309
MA0092.10.535473
MA0093.10.700866
MA0095.10
MA0098.10
MA0100.10.271974
MA0101.10.466845
MA0103.10.116929
MA0105.10.269753
MA0106.10.360817
MA0107.10.363753
MA0108.20.433384
MA0109.10
MA0111.10.191411
MA0113.10.337108
MA0114.10.238352
MA0115.10.669167
MA0116.10.650012
MA0117.12.61342
MA0119.11.46173
MA0122.10.657549
MA0124.10.851049
MA0125.10.780232
MA0130.10
MA0131.10.409473
MA0132.10
MA0133.10
MA0135.10.700734
MA0136.10.805431
MA0139.10.656302
MA0140.10.271883
MA0141.10.129134
MA0142.10.477975
MA0143.10.350815
MA0144.10.0688535
MA0145.10.114551
MA0146.10.406458
MA0147.11.40375
MA0148.10.218033
MA0149.10.157322
MA0062.20.117092
MA0035.20.756371
MA0039.20.0868588
MA0138.20.402586
MA0002.20.667016
MA0137.20.127311
MA0104.20.720139
MA0047.20.318614
MA0112.20.0402239
MA0065.20.00774345
MA0150.10.567944
MA0151.10
MA0152.10.318703
MA0153.10.716409
MA0154.11.26673
MA0155.10.138235
MA0156.10.77202
MA0157.10.4495
MA0158.10
MA0159.10.274824
MA0160.10.220282
MA0161.10
MA0162.10.111327
MA0163.10.0961118
MA0164.10.806095
MA0080.20.737223
MA0018.20.305372
MA0099.22.71926
MA0079.20.0053623
MA0102.21.27355
MA0258.10.0609037
MA0259.10.524511
MA0442.10
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