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MCL coexpression mm9:805: Difference between revisions

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{{MCL_coexpression_mm9
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chloride channel activity;0.0320372344834076;12724!GO:0022844;voltage-gated anion channel activity;0.0320372344834076;12724!GO:0043168;anion binding;0.0365688293700127;12724!GO:0031404;chloride ion binding;0.0365688293700127;12724!GO:0005254;chloride channel activity;0.0365688293700127;12724!GO:0006821;chloride transport;0.0365688293700127;12724!GO:0005253;anion channel activity;0.0365688293700127;12724!|ontology_enrichment_celltype=CL:0000791!1.51e-26!9;CL:0000789!1.51e-26!9;CL:0002420!1.51e-26!9;CL:0002419!1.51e-26!9;CL:0000790!1.51e-26!9;CL:0000838!4.89e-24!12;CL:0000624!1.19e-23!8;CL:0000542!4.80e-22!13;CL:0000051!4.80e-22!13;CL:0000988!1.17e-21!32;CL:0002032!1.17e-21!32;CL:0000037!1.17e-21!32;CL:0000566!1.17e-21!32;CL:0000837!1.17e-21!32;CL:0000084!1.94e-21!11;CL:0000827!1.94e-21!11;CL:0000893!7.23e-18!6;CL:0002489!7.23e-18!6;CL:0000898!7.23e-18!6;CL:0000809!7.23e-18!6;CL:0000810!7.23e-18!6;CL:0000895!7.23e-18!6;CL:0000808!7.23e-18!6;CL:0000894!7.23e-18!6;CL:0000806!7.23e-18!6;CL:0000807!7.23e-18!6;CL:0000805!7.23e-18!6;CL:0002425!7.23e-18!6;CL:0002436!7.23e-18!6;CL:0002427!7.23e-18!6;CL:0002428!7.23e-18!6;CL:0002429!7.23e-18!6;CL:0002433!7.23e-18!6;CL:0002431!7.23e-18!6;CL:0002432!7.23e-18!6;CL:0002242!1.45e-17!16;CL:0000738!2.02e-16!17;CL:0002087!2.02e-16!17;CL:0002320!3.49e-16!46;CL:0000134!3.49e-16!46;CL:0000219!6.04e-15!54;CL:0000034!2.99e-11!97;CL:0002031!1.43e-10!25;CL:0000723!2.19e-08!91;CL:0000048!2.19e-08!91|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0002384!3.49e-16!46|tfbs_overrepresentation_for_novel_motifs=0.354643,0.433653,0.330161,0.394491,1.20555,0.40827,0.495658,0.146465,0.912659,0.314043,0.453212,0.484001,0.88117,0.507558,0.680035,0,0.696644,0.22065,0.829774,0.528436,0.296085,0.179861,0.50668,0.226287,0.337218,0.534339,0.128175,0.428336,0.268347,0.656973,0.414842,0.796599,0.624261,0.364174,0.242923,0.137663,0.210533,1.20775,0.191662,0.167387,0.224094,0.419787,0.163087,0.244285,0.158271,0.383899,0.618203,0.443479,0.314152,0.271021,0.679429,0.560572,0.633942,0.937018,0.954342,0.514504,0.279148,0.471658,1.25881,0.512521,0.776777,0.569793,0.163832,0.668331,0.525334,0.708248,1.08987,1.43807,1.81937,1.29123,0.31262,0.460931,1.14319,0.987652,0.371787,0.349958,0.364033,0.607043,0.759798,0.299972,0.463363,0.713779,1.39458,0.436063,0.873141,0.651261,0.0211263,0.657454,0.623015,1.60001,1.15927,0.878077,0.809272,0.657661,1.66008,0.17334,0.871972,0.812053,0.618454,0.278788,0.210602,0.796322,0.919715,0.680015,0.678976,0.419366,0.737915,0.439611,0.821842,0.297733,0.348012,0.921485,1.47733,0.458194,1.16629,0.633313,0.496288,1.02946,0.697928,0.207304,0.993019,0.647706,0.536114,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,0.235546,0.90286,1.00644,1.05894,0.527782,1.18781,0.177062,0.362565,0.421136,1.13883,1.96797,1.5682,1.09456,1.35119,0.806961,0.672593,0.420221,0.621266,1.92834,0.364791,0.229209,0.098204,0.041769,0.938577,0.178329,0.526881,1.01974,0.561556,0.705025,0.352329,0.950885,1.1483,0.872292,0.763895,0.345891,0.669337,1.29138,0.602679,0.482466,0.254444|tfbs_overrepresentation_jaspar=MA0003.1;0.294637,MA0004.1;0.394951,MA0006.1;0.238555,MA0007.1;0.38073,MA0009.1;0.82278,MA0014.1;0.248772,MA0017.1;1.3362,MA0019.1;0.642876,MA0024.1;0.779446,MA0025.1;1.05446,MA0027.1;2.46647,MA0028.1;0.692501,MA0029.1;0.757957,MA0030.1;0.764448,MA0031.1;0.729293,MA0038.1;0.534262,MA0040.1;0.835181,MA0041.1;0.323687,MA0042.1;0.837668,MA0043.1;0.918718,MA0046.1;0.858391,MA0048.1;0.281053,MA0050.1;0.431976,MA0051.1;0.542972,MA0052.1;0.84317,MA0055.1;0.424109,MA0056.1;0,MA0057.1;0.549903,MA0058.1;0.305206,MA0059.1;0.316585,MA0060.1;0.505012,MA0061.1;2.40227,MA0063.1;0,MA0066.1;0.523573,MA0067.1;1.16502,MA0068.1;0.077274,MA0069.1;0.843506,MA0070.1;0.833895,MA0071.1;0.431174,MA0072.1;0.825495,MA0073.1;0.000250057,MA0074.1;0.488775,MA0076.1;1.40007,MA0077.1;0.804033,MA0078.1;0.575205,MA0081.1;0.338098,MA0083.1;0.917931,MA0084.1;1.49188,MA0087.1;0.87515,MA0088.1;0.18495,MA0089.1;0,MA0090.1;0.362551,MA0091.1;0.407455,MA0092.1;0.95209,MA0093.1;0.2553,MA0095.1;0,MA0098.1;0,MA0100.1;0.477594,MA0101.1;3.27482,MA0103.1;0.272167,MA0105.1;1.73381,MA0106.1;0.582805,MA0107.1;3.79511,MA0108.2;0.665343,MA0109.1;0,MA0111.1;0.375908,MA0113.1;0.555251,MA0114.1;0.561811,MA0115.1;0.921497,MA0116.1;0.238371,MA0117.1;0.88947,MA0119.1;0.325434,MA0122.1;0.909168,MA0124.1;1.11203,MA0125.1;1.03833,MA0130.1;0,MA0131.1;0.638414,MA0132.1;0,MA0133.1;0,MA0135.1;0.954884,MA0136.1;0.508047,MA0139.1;0.867077,MA0140.1;0.477483,MA0141.1;0.29014,MA0142.1;0.714976,MA0143.1;0.571221,MA0144.1;0.195095,MA0145.1;1.65394,MA0146.1;0.0548413,MA0147.1;0.593505,MA0148.1;1.05634,MA0149.1;0.330018,MA0062.2;1.21132,MA0035.2;0.482026,MA0039.2;0.0156581,MA0138.2;0.630612,MA0002.2;0.145685,MA0137.2;0.287486,MA0104.2;0.476119,MA0047.2;0.533516,MA0112.2;0.200175,MA0065.2;0.773848,MA0150.1;0.991233,MA0151.1;0,MA0152.1;1.32101,MA0153.1;0.971406,MA0154.1;1.46345,MA0155.1;0.0631765,MA0156.1;0.763978,MA0157.1;0.683365,MA0158.1;0,MA0159.1;0.214506,MA0160.1;0.413266,MA0161.1;0,MA0162.1;0.0672805,MA0163.1;0.0600297,MA0164.1;0.508398,MA0080.2;0.737531,MA0018.2;1.28741,MA0099.2;0.624421,MA0079.2;0.000746166,MA0102.2;1.5442,MA0258.1;0.533988,MA0259.1;0.196451,MA0442.1;0}}
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|gostat_on_MCL_coexpression=GO:0005247;voltage-gated chloride channel activity;0.0320372344834076;12724!GO:0022844;voltage-gated anion channel activity;0.0320372344834076;12724!GO:0043168;anion binding;0.0365688293700127;12724!GO:0031404;chloride ion binding;0.0365688293700127;12724!GO:0005254;chloride channel activity;0.0365688293700127;12724!GO:0006821;chloride transport;0.0365688293700127;12724!GO:0005253;anion channel activity;0.0365688293700127;12724!
}}

Latest revision as of 15:55, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:17514007..17514018,-p@chr12:17514007..17514018
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Mm9::chr12:17514022..17514031,-p@chr12:17514022..17514031
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Mm9::chr13:38129788..38129801,-p@chr13:38129788..38129801
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Mm9::chr15:59430663..59430691,+p@chr15:59430663..59430691
+
Mm9::chr16:20717297..20717309,-p9@Clcn2
Mm9::chr2:31326367..31326373,-p@chr2:31326367..31326373
-
Mm9::chr3:52001982..52001995,-p@chr3:52001982..52001995
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Mm9::chr4:108520502..108520530,+p@chr4:108520502..108520530
+
Mm9::chr6:113026311..113026321,-p@chr6:113026311..113026321
-


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:0005247voltage-gated chloride channel activity0.0320372344834076
GO:0022844voltage-gated anion channel activity0.0320372344834076
GO:0043168anion binding0.0365688293700127
GO:0031404chloride ion binding0.0365688293700127
GO:0005254chloride channel activity0.0365688293700127
GO:0006821chloride transport0.0365688293700127
GO:0005253anion channel activity0.0365688293700127



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 cell1.51e-269
alpha-beta T cell1.51e-269
immature T cell1.51e-269
mature T cell1.51e-269
immature alpha-beta T cell1.51e-269
lymphoid lineage restricted progenitor cell4.89e-2412
CD4-positive, alpha-beta T cell1.19e-238
lymphocyte4.80e-2213
common lymphoid progenitor4.80e-2213
hematopoietic cell1.17e-2132
hematopoietic oligopotent progenitor cell1.17e-2132
hematopoietic stem cell1.17e-2132
angioblastic mesenchymal cell1.17e-2132
hematopoietic multipotent progenitor cell1.17e-2132
T cell1.94e-2111
pro-T cell1.94e-2111
thymocyte7.23e-186
double negative thymocyte7.23e-186
naive T cell7.23e-186
double-positive, alpha-beta thymocyte7.23e-186
CD4-positive, alpha-beta thymocyte7.23e-186
naive thymus-derived CD4-positive, alpha-beta T cell7.23e-186
DN4 thymocyte7.23e-186
DN1 thymic pro-T cell7.23e-186
DN2 thymocyte7.23e-186
DN3 thymocyte7.23e-186
immature single positive thymocyte7.23e-186
early T lineage precursor7.23e-186
mature CD4 single-positive thymocyte7.23e-186
resting double-positive thymocyte7.23e-186
double-positive blast7.23e-186
CD69-positive double-positive thymocyte7.23e-186
CD69-positive, CD4-positive single-positive thymocyte7.23e-186
CD4-positive, CD8-intermediate double-positive thymocyte7.23e-186
CD24-positive, CD4 single-positive thymocyte7.23e-186
nucleate cell1.45e-1716
leukocyte2.02e-1617
nongranular leukocyte2.02e-1617
connective tissue cell3.49e-1646
mesenchymal cell3.49e-1646
motile cell6.04e-1554
stem cell2.99e-1197
hematopoietic lineage restricted progenitor cell1.43e-1025
somatic stem cell2.19e-0891
multi fate stem cell2.19e-0891

Uber Anatomy
Ontology termp-valuen
connective tissue3.49e-1646


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)
MA0003.10.294637
MA0004.10.394951
MA0006.10.238555
MA0007.10.38073
MA0009.10.82278
MA0014.10.248772
MA0017.11.3362
MA0019.10.642876
MA0024.10.779446
MA0025.11.05446
MA0027.12.46647
MA0028.10.692501
MA0029.10.757957
MA0030.10.764448
MA0031.10.729293
MA0038.10.534262
MA0040.10.835181
MA0041.10.323687
MA0042.10.837668
MA0043.10.918718
MA0046.10.858391
MA0048.10.281053
MA0050.10.431976
MA0051.10.542972
MA0052.10.84317
MA0055.10.424109
MA0056.10
MA0057.10.549903
MA0058.10.305206
MA0059.10.316585
MA0060.10.505012
MA0061.12.40227
MA0063.10
MA0066.10.523573
MA0067.11.16502
MA0068.10.077274
MA0069.10.843506
MA0070.10.833895
MA0071.10.431174
MA0072.10.825495
MA0073.10.000250057
MA0074.10.488775
MA0076.11.40007
MA0077.10.804033
MA0078.10.575205
MA0081.10.338098
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.10.18495
MA0089.10
MA0090.10.362551
MA0091.10.407455
MA0092.10.95209
MA0093.10.2553
MA0095.10
MA0098.10
MA0100.10.477594
MA0101.13.27482
MA0103.10.272167
MA0105.11.73381
MA0106.10.582805
MA0107.13.79511
MA0108.20.665343
MA0109.10
MA0111.10.375908
MA0113.10.555251
MA0114.10.561811
MA0115.10.921497
MA0116.10.238371
MA0117.10.88947
MA0119.10.325434
MA0122.10.909168
MA0124.11.11203
MA0125.11.03833
MA0130.10
MA0131.10.638414
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.10.508047
MA0139.10.867077
MA0140.10.477483
MA0141.10.29014
MA0142.10.714976
MA0143.10.571221
MA0144.10.195095
MA0145.11.65394
MA0146.10.0548413
MA0147.10.593505
MA0148.11.05634
MA0149.10.330018
MA0062.21.21132
MA0035.20.482026
MA0039.20.0156581
MA0138.20.630612
MA0002.20.145685
MA0137.20.287486
MA0104.20.476119
MA0047.20.533516
MA0112.20.200175
MA0065.20.773848
MA0150.10.991233
MA0151.10
MA0152.11.32101
MA0153.10.971406
MA0154.11.46345
MA0155.10.0631765
MA0156.10.763978
MA0157.10.683365
MA0158.10
MA0159.10.214506
MA0160.10.413266
MA0161.10
MA0162.10.0672805
MA0163.10.0600297
MA0164.10.508398
MA0080.20.737531
MA0018.21.28741
MA0099.20.624421
MA0079.20.000746166
MA0102.21.5442
MA0258.10.533988
MA0259.10.196451
MA0442.10
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