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MCL coexpression mm9:434: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002384!4.81e-17!46
|ontology_enrichment_uberon=UBERON:0002384!4.81e-17!46
|tfbs_overrepresentation_for_novel_motifs=0.175413,0.0809701,0.476315,0.593409,0.296927,0.216369,0.286882,0.0429524,0.398834,0.0604331,0.252112,0.277243,0.165655,0.296787,0.662379,0,0.46143,0.083948,0.147449,0.316699,0.133242,0.208446,0.296055,1.02912,0.16256,0.319311,0.0343308,0.232181,0.114379,0.439213,0.22152,0.552579,0.281806,0.279585,0.66368,0.144175,0.268195,0.753507,0.237064,0.43804,1.01941,0.225414,0.33101,0.325245,0.0430977,0.197508,1.01546,0.244272,0.138979,0.116163,0.445973,0.341665,0.217128,0.683824,0.700221,0.302599,0.77262,0.26711,0.127634,0.300938,0.534331,0.349585,0.0517361,0.43605,0.838156,0.471894,0.829699,1.16897,0.530087,1.02503,0.144846,0.17272,0.22592,0.731855,0.0291015,0.263994,0.027847,0.381898,0.518764,0.835355,0.174228,0.476893,0.348372,1.00736,0.623727,1.04624,0.00938132,1.05183,0.395899,1.32869,0.896685,0.62835,1.38593,0.0914951,0.231442,0.455703,1.02731,0.56686,0.391893,0.1892,0.26831,0.552324,1.60236,0.446498,0.445567,0.225081,0.498793,0.241171,0.43037,0.828607,0.50853,0.669156,0.136675,0.256145,0.903482,0.288262,1.32018,0.208431,0.462587,0.0759495,0.736964,0.4177,0.320815,0.381122,0.955823,0.522111,0.293459,0.558086,0.828246,0.093155,0.651613,0.580662,0.799981,0.313768,0.92434,0.0320829,0.181334,0.64263,0.876916,1.69384,1.29725,0.834212,0.330794,0.562149,0.439856,0.225756,0.394362,1.65442,0.539014,0.622526,0.236,0.767951,0.685297,0.215456,0.313008,0.762455,0.342508,0.340691,0.173692,0.181136,0.886073,0.622933,3.29266,0.50469,0.436947,0.827428,0.266569,0.757197,0.328329
|tfbs_overrepresentation_for_novel_motifs=0.175413,0.0809701,0.476315,0.593409,0.296927,0.216369,0.286882,0.0429524,0.398834,0.0604331,0.252112,0.277243,0.165655,0.296787,0.662379,0,0.46143,0.083948,0.147449,0.316699,0.133242,0.208446,0.296055,1.02912,0.16256,0.319311,0.0343308,0.232181,0.114379,0.439213,0.22152,0.552579,0.281806,0.279585,0.66368,0.144175,0.268195,0.753507,0.237064,0.43804,1.01941,0.225414,0.33101,0.325245,0.0430977,0.197508,1.01546,0.244272,0.138979,0.116163,0.445973,0.341665,0.217128,0.683824,0.700221,0.302599,0.77262,0.26711,0.127634,0.300938,0.534331,0.349585,0.0517361,0.43605,0.838156,0.471894,0.829699,1.16897,0.530087,1.02503,0.144846,0.17272,0.22592,0.731855,0.0291015,0.263994,0.027847,0.381898,0.518764,0.835355,0.174228,0.476893,0.348372,1.00736,0.623727,1.04624,0.00938132,1.05183,0.395899,1.32869,0.896685,0.62835,1.38593,0.0914951,0.231442,0.455703,1.02731,0.56686,0.391893,0.1892,0.26831,0.552324,1.60236,0.446498,0.445567,0.225081,0.498793,0.241171,0.43037,0.828607,0.50853,0.669156,0.136675,0.256145,0.903482,0.288262,1.32018,0.208431,0.462587,0.0759495,0.736964,0.4177,0.320815,0.381122,0.955823,0.522111,0.293459,0.558086,0.828246,0.093155,0.651613,0.580662,0.799981,0.313768,0.92434,0.0320829,0.181334,0.64263,0.876916,1.69384,1.29725,0.834212,0.330794,0.562149,0.439856,0.225756,0.394362,1.65442,0.539014,0.622526,0.236,0.767951,0.685297,0.215456,0.313008,0.762455,0.342508,0.340691,0.173692,0.181136,0.886073,0.622933,3.29266,0.50469,0.436947,0.827428,0.266569,0.757197,0.328329
|tfbs_overrepresentation_jaspar=MA0003.1;0.539169,MA0004.1;0.206012,MA0006.1;0.650564,MA0007.1;1.69862,MA0009.1;0.576798,MA0014.1;3.93274,MA0017.1;0.110433,MA0019.1;0.413421,MA0024.1;2.28211,MA0025.1;0.795679,MA0027.1;2.19092,MA0028.1;0.100975,MA0029.1;0.51708,MA0030.1;0.523021,MA0031.1;0.490954,MA0038.1;0.319246,MA0040.1;0.588314,MA0041.1;1.4542,MA0042.1;0.442876,MA0043.1;1.6004,MA0046.1;0.609938,MA0048.1;0.0741002,MA0050.1;1.23381,MA0051.1;0.871644,MA0052.1;0.595747,MA0055.1;0.00852128,MA0056.1;0,MA0057.1;0.851334,MA0058.1;0.139612,MA0059.1;0.147666,MA0060.1;0.773219,MA0061.1;0.887454,MA0063.1;0,MA0066.1;0.310219,MA0067.1;0.902253,MA0068.1;0.58378,MA0069.1;0.59606,MA0070.1;0.587119,MA0071.1;0.234437,MA0072.1;0.579318,MA0073.1;0.596603,MA0074.1;0.281183,MA0076.1;0.122031,MA0077.1;2.35617,MA0078.1;0.354249,MA0081.1;0.163204,MA0083.1;0.665805,MA0084.1;1.22195,MA0087.1;0.625609,MA0088.1;0.216372,MA0089.1;0,MA0090.1;0.181323,MA0091.1;0.215731,MA0092.1;0.535473,MA0093.1;0.105788,MA0095.1;0,MA0098.1;0,MA0100.1;1.37158,MA0101.1;0.466845,MA0103.1;0.373479,MA0105.1;2.585,MA0106.1;0.360817,MA0107.1;0.363753,MA0108.2;1.10626,MA0109.1;0,MA0111.1;0.559312,MA0113.1;0.895012,MA0114.1;0.238352,MA0115.1;1.60586,MA0116.1;0.0949327,MA0117.1;0.639033,MA0119.1;1.46173,MA0122.1;0.657549,MA0124.1;0.851049,MA0125.1;0.780232,MA0130.1;0,MA0131.1;0.409473,MA0132.1;0,MA0133.1;0,MA0135.1;0.700734,MA0136.1;0.297196,MA0139.1;0.367034,MA0140.1;0.271883,MA0141.1;0.405018,MA0142.1;0.477975,MA0143.1;0.350815,MA0144.1;0.890316,MA0145.1;0.0402268,MA0146.1;0.0854498,MA0147.1;0.0750034,MA0148.1;0.218033,MA0149.1;0.476058,MA0062.2;0.0281188,MA0035.2;0.275617,MA0039.2;1.01082,MA0138.2;1.03931,MA0002.2;0.164166,MA0137.2;0.797731,MA0104.2;0.1822,MA0047.2;0.853678,MA0112.2;0.420656,MA0065.2;0.941441,MA0150.1;0.567944,MA0151.1;0,MA0152.1;0.853876,MA0153.1;0.716409,MA0154.1;0.0721234,MA0155.1;0.742144,MA0156.1;0.77202,MA0157.1;0.4495,MA0158.1;0,MA0159.1;0.976867,MA0160.1;0.220282,MA0161.1;0,MA0162.1;2.16067,MA0163.1;0.441382,MA0164.1;0.806095,MA0080.2;0.113741,MA0018.2;3.15148,MA0099.2;1.81477,MA0079.2;2.97298,MA0102.2;1.27355,MA0258.1;0.219649,MA0259.1;0.524511,MA0442.1;0
}}
}}

Revision as of 11:44, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:13589556..13589587,-p@chr10:13589556..13589587
-
Mm9::chr11:23646730..23646750,-p@chr11:23646730..23646750
-
Mm9::chr11:23648455..23648462,-p@chr11:23648455..23648462
-
Mm9::chr17:34256262..34256285,-p@chr17:34256262..34256285
-
Mm9::chr17:71200529..71200556,-p1@Tgif1
Mm9::chr17:71200558..71200572,-p4@Tgif1
Mm9::chr17:71200676..71200704,+p@chr17:71200676..71200704
+
Mm9::chr17:71201050..71201078,-p9@Tgif1
Mm9::chr18:3281015..3281028,-p18@Crem
Mm9::chr18:3281725..3281740,-p3@Crem
Mm9::chr18:3281750..3281776,-p2@Crem
Mm9::chr1:173848007..173848014,+p@chr1:173848007..173848014
+
Mm9::chr3:21852105..21852114,+p@chr3:21852105..21852114
+
Mm9::chr3:30993641..30993651,+p7@Skil
Mm9::chr4:32337706..32337718,-p@chr4:32337706..32337718
-
Mm9::chr6:122290517..122290528,-p15@Phc1
Mm9::chr9:44413016..44413033,+p3@Ddx6


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:0044451nucleoplasm part0.0220916838479725
GO:0005654nucleoplasm0.0220916838479725
GO:0008432JUN kinase binding0.0220916838479725
GO:0031981nuclear lumen0.0220916838479725
GO:0031974membrane-enclosed lumen0.0220916838479725
GO:0043233organelle lumen0.0220916838479725
GO:0007283spermatogenesis0.0233882010690361
GO:0048232male gamete generation0.0233882010690361
GO:0005634nucleus0.0277644688566074
GO:0044428nuclear part0.0277644688566074
GO:0007276gamete generation0.0277644688566074
GO:0019953sexual reproduction0.03423568125556
GO:0001739sex chromatin0.03423568125556
GO:0000803sex chromosome0.0344347483300447
GO:0003724RNA helicase activity0.0346065965449581
GO:0003676nucleic acid binding0.0403273692115077
GO:0005667transcription factor complex0.0436719040086291
GO:0000003reproduction0.0436719040086291
GO:0005720nuclear heterochromatin0.0436719040086291
GO:0043565sequence-specific DNA binding0.0436719040086291



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 cell9.86e-2532
hematopoietic oligopotent progenitor cell9.86e-2532
hematopoietic stem cell9.86e-2532
angioblastic mesenchymal cell9.86e-2532
hematopoietic multipotent progenitor cell9.86e-2532
lymphoid lineage restricted progenitor cell1.44e-2212
T cell1.33e-2011
pro-T cell1.33e-2011
lymphocyte1.39e-2013
common lymphoid progenitor1.39e-2013
mature alpha-beta T cell5.48e-189
alpha-beta T cell5.48e-189
immature T cell5.48e-189
mature T cell5.48e-189
immature alpha-beta T cell5.48e-189
leukocyte2.03e-1717
nongranular leukocyte2.03e-1717
connective tissue cell4.81e-1746
mesenchymal cell4.81e-1746
hematopoietic lineage restricted progenitor cell5.55e-1725
motile cell2.24e-1654
nucleate cell4.00e-1616
CD4-positive, alpha-beta T cell4.43e-168
thymocyte2.66e-126
double negative thymocyte2.66e-126
naive T cell2.66e-126
double-positive, alpha-beta thymocyte2.66e-126
CD4-positive, alpha-beta thymocyte2.66e-126
naive thymus-derived CD4-positive, alpha-beta T cell2.66e-126
DN4 thymocyte2.66e-126
DN1 thymic pro-T cell2.66e-126
DN2 thymocyte2.66e-126
DN3 thymocyte2.66e-126
immature single positive thymocyte2.66e-126
early T lineage precursor2.66e-126
mature CD4 single-positive thymocyte2.66e-126
resting double-positive thymocyte2.66e-126
double-positive blast2.66e-126
CD69-positive double-positive thymocyte2.66e-126
CD69-positive, CD4-positive single-positive thymocyte2.66e-126
CD4-positive, CD8-intermediate double-positive thymocyte2.66e-126
CD24-positive, CD4 single-positive thymocyte2.66e-126
stem cell8.45e-1097
animal cell3.20e-08115
eukaryotic cell3.20e-08115
common myeloid progenitor5.55e-0819
somatic stem cell6.61e-0891
multi fate stem cell6.61e-0891
somatic cell8.04e-08118

Uber Anatomy
Ontology termp-valuen
connective tissue4.81e-1746


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)
MA0003.10.539169
MA0004.10.206012
MA0006.10.650564
MA0007.11.69862
MA0009.10.576798
MA0014.13.93274
MA0017.10.110433
MA0019.10.413421
MA0024.12.28211
MA0025.10.795679
MA0027.12.19092
MA0028.10.100975
MA0029.10.51708
MA0030.10.523021
MA0031.10.490954
MA0038.10.319246
MA0040.10.588314
MA0041.11.4542
MA0042.10.442876
MA0043.11.6004
MA0046.10.609938
MA0048.10.0741002
MA0050.11.23381
MA0051.10.871644
MA0052.10.595747
MA0055.10.00852128
MA0056.10
MA0057.10.851334
MA0058.10.139612
MA0059.10.147666
MA0060.10.773219
MA0061.10.887454
MA0063.10
MA0066.10.310219
MA0067.10.902253
MA0068.10.58378
MA0069.10.59606
MA0070.10.587119
MA0071.10.234437
MA0072.10.579318
MA0073.10.596603
MA0074.10.281183
MA0076.10.122031
MA0077.12.35617
MA0078.10.354249
MA0081.10.163204
MA0083.10.665805
MA0084.11.22195
MA0087.10.625609
MA0088.10.216372
MA0089.10
MA0090.10.181323
MA0091.10.215731
MA0092.10.535473
MA0093.10.105788
MA0095.10
MA0098.10
MA0100.11.37158
MA0101.10.466845
MA0103.10.373479
MA0105.12.585
MA0106.10.360817
MA0107.10.363753
MA0108.21.10626
MA0109.10
MA0111.10.559312
MA0113.10.895012
MA0114.10.238352
MA0115.11.60586
MA0116.10.0949327
MA0117.10.639033
MA0119.11.46173
MA0122.10.657549
MA0124.10.851049
MA0125.10.780232
MA0130.10
MA0131.10.409473
MA0132.10
MA0133.10
MA0135.10.700734
MA0136.10.297196
MA0139.10.367034
MA0140.10.271883
MA0141.10.405018
MA0142.10.477975
MA0143.10.350815
MA0144.10.890316
MA0145.10.0402268
MA0146.10.0854498
MA0147.10.0750034
MA0148.10.218033
MA0149.10.476058
MA0062.20.0281188
MA0035.20.275617
MA0039.21.01082
MA0138.21.03931
MA0002.20.164166
MA0137.20.797731
MA0104.20.1822
MA0047.20.853678
MA0112.20.420656
MA0065.20.941441
MA0150.10.567944
MA0151.10
MA0152.10.853876
MA0153.10.716409
MA0154.10.0721234
MA0155.10.742144
MA0156.10.77202
MA0157.10.4495
MA0158.10
MA0159.10.976867
MA0160.10.220282
MA0161.10
MA0162.12.16067
MA0163.10.441382
MA0164.10.806095
MA0080.20.113741
MA0018.23.15148
MA0099.21.81477
MA0079.22.97298
MA0102.21.27355
MA0258.10.219649
MA0259.10.524511
MA0442.10
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