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MCL coexpression mm9:758: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=UBERON:0002384!1.82e-24!46;UBERON:0002390!5.68e-07!45;UBERON:0003061!5.68e-07!45
|tfbs_overrepresentation_for_novel_motifs=0.354643,0.0206456,0.330161,1.02163,1.20555,0.40827,0.495658,0.146465,0.154135,0.0330111,0.453212,0.484001,0.146657,0.507558,0.24249,0,0.696644,0.22065,0.829774,0.528436,0.296085,0.713323,0.50668,0.64218,0.337218,0.534339,0.801525,0.428336,0.268347,0.0963992,0.414842,0.796599,0.218674,0.364174,0.242923,0.00999634,0.210533,0.480503,0.191662,0.167387,1.19194,0.419787,0.663794,2.75085,0.0122159,0.383899,0.618203,0.443479,0.904531,0.745859,0.679429,0.560572,0.30602,0.937018,0.954342,0.514504,0.279148,0.471658,0.384731,0.512521,0.776777,0.569793,0.952934,0.668331,0.525334,0.708248,1.08987,3.17182,0.772155,1.29123,0.31262,0.151245,0.0512949,0.987652,0.116281,0.349958,0.364033,0.607043,0.759798,1.47357,0.152219,0.713779,0.568383,0.14134,0.873141,0.0176817,1.88733,0.0965007,0.623015,1.60001,1.15927,0.878077,0.809272,1.22553,0.188213,0.17334,0.14449,0.812053,0.618454,0.987389,1.13987,0.796322,0.919715,0.680015,0.678976,0.419366,1.74861,1.11973,0.30446,0.297733,0.348012,0.921485,0.301014,0.458194,1.16629,1.18588,0.0259088,0.398075,0.697928,0.207304,0.993019,0.647706,0.536114,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,1.91852,0.90286,1.00644,1.05894,1.30862,1.18781,0.705136,0.362565,0.421136,1.13883,1.96797,1.5682,1.09456,1.35119,0.806961,0.672593,1.07771,0.621266,1.92834,0.364791,0.229209,0.32395,0.161645,2.16083,0.178329,0.526881,1.01974,0.561556,2.01163,0.928824,0.362302,1.1483,0.872292,0.763895,0.914544,0.669337,0.519673,0.209556,2.10279,0.12239
|tfbs_overrepresentation_jaspar=MA0003.1;0.0343274,MA0004.1;0.394951,MA0006.1;0.670874,MA0007.1;0.38073,MA0009.1;0.82278,MA0014.1;0.0421798,MA0017.1;0.726051,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;0.311486,MA0043.1;0.918718,MA0046.1;0.858391,MA0048.1;0.281053,MA0050.1;1.10321,MA0051.1;0.542972,MA0052.1;0.84317,MA0055.1;0.221677,MA0056.1;0,MA0057.1;0.0745664,MA0058.1;0.305206,MA0059.1;0.316585,MA0060.1;0.169058,MA0061.1;0.56663,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;0.765781,MA0077.1;0.804033,MA0078.1;0.575205,MA0081.1;0.897217,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;0.362847,MA0093.1;0.2553,MA0095.1;0,MA0098.1;0,MA0100.1;0.477594,MA0101.1;0.867731,MA0103.1;0.272167,MA0105.1;0.720048,MA0106.1;0.582805,MA0107.1;0.266586,MA0108.2;0.665343,MA0109.1;0,MA0111.1;0.375908,MA0113.1;1.36684,MA0114.1;0.19245,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;2.19411,MA0136.1;0.508047,MA0139.1;0.441109,MA0140.1;0.477483,MA0141.1;0.29014,MA0142.1;0.714976,MA0143.1;0.571221,MA0144.1;1.07908,MA0145.1;0.200183,MA0146.1;0.0111657,MA0147.1;0.205697,MA0148.1;0.410398,MA0149.1;0.330018,MA0062.2;1.21132,MA0035.2;0.482026,MA0039.2;0.0946163,MA0138.2;0.630612,MA0002.2;1.41154,MA0137.2;0.783415,MA0104.2;0.157347,MA0047.2;0.533516,MA0112.2;0.200175,MA0065.2;0.773848,MA0150.1;0.991233,MA0151.1;0,MA0152.1;0.53362,MA0153.1;0.971406,MA0154.1;2.62783,MA0155.1;0.226288,MA0156.1;0.278949,MA0157.1;0.683365,MA0158.1;0,MA0159.1;0.214506,MA0160.1;0.413266,MA0161.1;0,MA0162.1;0.176565,MA0163.1;0.0124565,MA0164.1;1.26737,MA0080.2;0.737531,MA0018.2;0.51781,MA0099.2;0.624421,MA0079.2;0.00199657,MA0102.2;1.5442,MA0258.1;0.180934,MA0259.1;0.196451,MA0442.1;0
}}

Latest revision as of 15:50, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:13805833..13805851,+p@chr10:13805833..13805851
+
Mm9::chr11:54674517..54674528,+p@chr11:54674517..54674528
+
Mm9::chr15:72992459..72992477,-p@chr15:72992459..72992477
-
Mm9::chr4:133178624..133178661,+p@chr4:133178624..133178661
+
Mm9::chr4:138528720..138528749,-p@chr4:138528720..138528749
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Mm9::chr5:122669248..122669255,+p@chr5:122669248..122669255
+
Mm9::chr5:22893079..22893087,+p@chr5:22893079..22893087
+
Mm9::chr5:22893091..22893115,+p@chr5:22893091..22893115
+
Mm9::chr5:22893118..22893135,+p@chr5:22893118..22893135
+


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

no results for this coexpression

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
lymphoid lineage restricted progenitor cell1.07e-3812
lymphocyte1.39e-3513
common lymphoid progenitor1.39e-3513
mature alpha-beta T cell4.44e-359
alpha-beta T cell4.44e-359
immature T cell4.44e-359
mature T cell4.44e-359
immature alpha-beta T cell4.44e-359
T cell1.15e-3411
pro-T cell1.15e-3411
hematopoietic cell1.87e-3232
hematopoietic oligopotent progenitor cell1.87e-3232
hematopoietic stem cell1.87e-3232
angioblastic mesenchymal cell1.87e-3232
hematopoietic multipotent progenitor cell1.87e-3232
CD4-positive, alpha-beta T cell2.94e-318
hematopoietic lineage restricted progenitor cell1.30e-2825
nucleate cell1.43e-2816
leukocyte8.80e-2717
nongranular leukocyte8.80e-2717
connective tissue cell1.82e-2446
mesenchymal cell1.82e-2446
thymocyte2.59e-236
double negative thymocyte2.59e-236
naive T cell2.59e-236
double-positive, alpha-beta thymocyte2.59e-236
CD4-positive, alpha-beta thymocyte2.59e-236
naive thymus-derived CD4-positive, alpha-beta T cell2.59e-236
DN4 thymocyte2.59e-236
DN1 thymic pro-T cell2.59e-236
DN2 thymocyte2.59e-236
DN3 thymocyte2.59e-236
immature single positive thymocyte2.59e-236
early T lineage precursor2.59e-236
mature CD4 single-positive thymocyte2.59e-236
resting double-positive thymocyte2.59e-236
double-positive blast2.59e-236
CD69-positive double-positive thymocyte2.59e-236
CD69-positive, CD4-positive single-positive thymocyte2.59e-236
CD4-positive, CD8-intermediate double-positive thymocyte2.59e-236
CD24-positive, CD4 single-positive thymocyte2.59e-236
motile cell2.21e-2054
stem cell1.85e-1497
somatic stem cell8.47e-1191
multi fate stem cell8.47e-1191
animal cell7.29e-08115
eukaryotic cell7.29e-08115
somatic cell1.40e-07118

Uber Anatomy
Ontology termp-valuen
connective tissue1.82e-2446
hematopoietic system5.68e-0745
blood island5.68e-0745


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)
MA0003.10.0343274
MA0004.10.394951
MA0006.10.670874
MA0007.10.38073
MA0009.10.82278
MA0014.10.0421798
MA0017.10.726051
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
MA0042.10.311486
MA0043.10.918718
MA0046.10.858391
MA0048.10.281053
MA0050.11.10321
MA0051.10.542972
MA0052.10.84317
MA0055.10.221677
MA0056.10
MA0057.10.0745664
MA0058.10.305206
MA0059.10.316585
MA0060.10.169058
MA0061.10.56663
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
MA0076.10.765781
MA0077.10.804033
MA0078.10.575205
MA0081.10.897217
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.10.18495
MA0089.10
MA0090.10.362551
MA0091.10.407455
MA0092.10.362847
MA0093.10.2553
MA0095.10
MA0098.10
MA0100.10.477594
MA0101.10.867731
MA0103.10.272167
MA0105.10.720048
MA0106.10.582805
MA0107.10.266586
MA0108.20.665343
MA0109.10
MA0111.10.375908
MA0113.11.36684
MA0114.10.19245
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
MA0135.12.19411
MA0136.10.508047
MA0139.10.441109
MA0140.10.477483
MA0141.10.29014
MA0142.10.714976
MA0143.10.571221
MA0144.11.07908
MA0145.10.200183
MA0146.10.0111657
MA0147.10.205697
MA0148.10.410398
MA0149.10.330018
MA0062.21.21132
MA0035.20.482026
MA0039.20.0946163
MA0138.20.630612
MA0002.21.41154
MA0137.20.783415
MA0104.20.157347
MA0047.20.533516
MA0112.20.200175
MA0065.20.773848
MA0150.10.991233
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.12.62783
MA0155.10.226288
MA0156.10.278949
MA0157.10.683365
MA0158.10
MA0159.10.214506
MA0160.10.413266
MA0161.10
MA0162.10.176565
MA0163.10.0124565
MA0164.11.26737
MA0080.20.737531
MA0018.20.51781
MA0099.20.624421
MA0079.20.00199657
MA0102.21.5442
MA0258.10.180934
MA0259.10.196451
MA0442.10
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