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MCL coexpression mm9:576: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002384!1.63e-18!46;UBERON:0002193!7.35e-15!48;UBERON:0002405!7.35e-15!48;UBERON:0002390!5.35e-14!45;UBERON:0003061!5.35e-14!45;UBERON:0004177!3.41e-10!29;UBERON:0005057!3.41e-10!29;UBERON:0002370!7.56e-09!23;UBERON:0000974!7.56e-09!23;UBERON:0004807!7.56e-09!23;UBERON:0005058!7.56e-09!23;UBERON:0003351!7.56e-09!23;UBERON:0009113!7.56e-09!23;UBERON:0003295!7.56e-09!23;UBERON:0009722!7.56e-09!23;UBERON:0005562!7.56e-09!23;UBERON:0007690!7.56e-09!23;UBERON:0006562!2.03e-08!24;UBERON:0003408!2.03e-08!24;UBERON:0001557!2.03e-08!24;UBERON:0001042!2.03e-08!24;UBERON:0008814!2.03e-08!24;UBERON:0009145!2.03e-08!24;UBERON:0000077!4.23e-08!35;UBERON:0000072!2.55e-07!27
|ontology_enrichment_uberon=UBERON:0002384!1.63e-18!46;UBERON:0002193!7.35e-15!48;UBERON:0002405!7.35e-15!48;UBERON:0002390!5.35e-14!45;UBERON:0003061!5.35e-14!45;UBERON:0004177!3.41e-10!29;UBERON:0005057!3.41e-10!29;UBERON:0002370!7.56e-09!23;UBERON:0000974!7.56e-09!23;UBERON:0004807!7.56e-09!23;UBERON:0005058!7.56e-09!23;UBERON:0003351!7.56e-09!23;UBERON:0009113!7.56e-09!23;UBERON:0003295!7.56e-09!23;UBERON:0009722!7.56e-09!23;UBERON:0005562!7.56e-09!23;UBERON:0007690!7.56e-09!23;UBERON:0006562!2.03e-08!24;UBERON:0003408!2.03e-08!24;UBERON:0001557!2.03e-08!24;UBERON:0001042!2.03e-08!24;UBERON:0008814!2.03e-08!24;UBERON:0009145!2.03e-08!24;UBERON:0000077!4.23e-08!35;UBERON:0000072!2.55e-07!27
|tfbs_overrepresentation_for_novel_motifs=0.244604,0.341626,0.223558,0.279403,0.848472,0.792702,0.370193,0.566731,0.59395,0.282547,0.331725,0.35958,0.0780266,0.381063,0.898708,0,0.557619,0.824658,0.524522,0.119642,0.194751,0.197405,0.38026,0.427399,0.64994,0.405649,0.501183,0.309422,0.171781,0.384773,0.297405,0.653099,0.131928,0.0552712,0.151158,0.195932,0.125578,0.356403,0.725176,0.0929685,0.42301,0.301802,0.347242,0.152251,0.0508111,0.743728,0.48361,0.322976,0.742531,0.173974,0.541299,0.429887,0.366754,0.788877,0.805733,0.387424,0.18067,0.348382,0.218496,0.385607,0.634076,0.438439,0.090369,0.5308,0.397364,0.568642,0.938213,1.28193,0.629645,1.13654,0.208654,0.984639,0.0186364,0.838198,0.0571922,0.0517462,0.447182,0.473159,0.617814,1.09058,0.989763,0.573903,0.437131,0.932192,0.72691,0.00415894,1.1039,0.170021,0.488122,1.44275,1.0064,0.731688,0.665283,0.866261,0.108477,0.661488,0.264364,0.667958,0.483845,0.597503,0.125632,1.5718,0.772062,0.541854,0.54087,0.301427,0.596902,0.319507,0.201775,0.196131,0.238877,0.773781,0.19888,0.336214,1.01331,0.134943,0.00714903,1.41039,0.558838,0.123076,0.843435,1.27363,0.407285,0.472327,1.06644,0.621313,0.984184,0.658832,0.936732,0.145259,0.755703,0.273302,0.907893,0.399614,1.03449,0.193774,0.700863,0.303003,0.986296,1.80931,1.41113,2.16948,1.07314,0.66306,1.32358,0.302189,0.486482,1.76978,0.253405,0.140226,0.173337,0.0139939,0.790393,0.331601,1.03101,0.869538,0.430798,0.159498,0.242603,0.251242,0.995609,0.726089,0.621734,0.237049,0.531751,0.392164,0.39393,0.941787,0.00980506
|tfbs_overrepresentation_for_novel_motifs=0.244604,0.341626,0.223558,0.279403,0.848472,0.792702,0.370193,0.566731,0.59395,0.282547,0.331725,0.35958,0.0780266,0.381063,0.898708,0,0.557619,0.824658,0.524522,0.119642,0.194751,0.197405,0.38026,0.427399,0.64994,0.405649,0.501183,0.309422,0.171781,0.384773,0.297405,0.653099,0.131928,0.0552712,0.151158,0.195932,0.125578,0.356403,0.725176,0.0929685,0.42301,0.301802,0.347242,0.152251,0.0508111,0.743728,0.48361,0.322976,0.742531,0.173974,0.541299,0.429887,0.366754,0.788877,0.805733,0.387424,0.18067,0.348382,0.218496,0.385607,0.634076,0.438439,0.090369,0.5308,0.397364,0.568642,0.938213,1.28193,0.629645,1.13654,0.208654,0.984639,0.0186364,0.838198,0.0571922,0.0517462,0.447182,0.473159,0.617814,1.09058,0.989763,0.573903,0.437131,0.932192,0.72691,0.00415894,1.1039,0.170021,0.488122,1.44275,1.0064,0.731688,0.665283,0.866261,0.108477,0.661488,0.264364,0.667958,0.483845,0.597503,0.125632,1.5718,0.772062,0.541854,0.54087,0.301427,0.596902,0.319507,0.201775,0.196131,0.238877,0.773781,0.19888,0.336214,1.01331,0.134943,0.00714903,1.41039,0.558838,0.123076,0.843435,1.27363,0.407285,0.472327,1.06644,0.621313,0.984184,0.658832,0.936732,0.145259,0.755703,0.273302,0.907893,0.399614,1.03449,0.193774,0.700863,0.303003,0.986296,1.80931,1.41113,2.16948,1.07314,0.66306,1.32358,0.302189,0.486482,1.76978,0.253405,0.140226,0.173337,0.0139939,0.790393,0.331601,1.03101,0.869538,0.430798,0.159498,0.242603,0.251242,0.995609,0.726089,0.621734,0.237049,0.531751,0.392164,0.39393,0.941787,0.00980506
|tfbs_overrepresentation_jaspar=MA0003.1;0.0157697,MA0004.1;1.40032,MA0006.1;0.885417,MA0007.1;0.737361,MA0009.1;0.678286,MA0014.1;0.0332236,MA0017.1;0.166909,MA0019.1;0.506787,MA0024.1;0.636635,MA0025.1;0.9035,MA0027.1;2.3071,MA0028.1;0.155127,MA0029.1;0.616052,MA0030.1;0.622264,MA0031.1;0.588678,MA0038.1;0.405578,MA0040.1;0.690239,MA0041.1;0.218039,MA0042.1;0.207696,MA0043.1;0.771094,MA0046.1;0.712646,MA0048.1;0.142843,MA0050.1;0.312673,MA0051.1;0.413609,MA0052.1;0.697946,MA0055.1;0.0835619,MA0056.1;0,MA0057.1;0.0312525,MA0058.1;0.585652,MA0059.1;0.212009,MA0060.1;0.313143,MA0061.1;0.734828,MA0063.1;0,MA0066.1;0.395746,MA0067.1;1.01206,MA0068.1;0.132828,MA0069.1;0.698271,MA0070.1;0.688999,MA0071.1;0.311956,MA0072.1;0.680902,MA0073.1;0.0050008,MA0074.1;0.363923,MA0076.1;0.181159,MA0077.1;0.660245,MA0078.1;1.12807,MA0081.1;0.651709,MA0083.1;0.77033,MA0084.1;1.33532,MA0087.1;0.728855,MA0088.1;0.0799097,MA0089.1;0,MA0090.1;0.251458,MA0091.1;2.20385,MA0092.1;0.70143,MA0093.1;1.50408,MA0095.1;0,MA0098.1;0,MA0100.1;0.353762,MA0101.1;0.625174,MA0103.1;0.519343,MA0105.1;0.434904,MA0106.1;0.450539,MA0107.1;0.979629,MA0108.2;0.527977,MA0109.1;0,MA0111.1;0.263095,MA0113.1;0.424958,MA0114.1;0.111687,MA0115.1;0.773793,MA0116.1;0.147513,MA0117.1;0.742722,MA0119.1;0.219527,MA0122.1;0.761823,MA0124.1;0.959967,MA0125.1;0.887718,MA0130.1;0,MA0131.1;0.502588,MA0132.1;0,MA0133.1;0,MA0135.1;0.806261,MA0136.1;0.993181,MA0139.1;0.0756871,MA0140.1;0.353662,MA0141.1;0.555407,MA0142.1;0.575041,MA0143.1;0.439766,MA0144.1;0.1137,MA0145.1;0.0201868,MA0146.1;0.00215921,MA0147.1;0.386218,MA0148.1;0.796977,MA0149.1;0.223436,MA0062.2;0.0556611,MA0035.2;0.357786,MA0039.2;0.00145609,MA0138.2;0.495254,MA0002.2;1.96954,MA0137.2;0.187581,MA0104.2;0.289861,MA0047.2;1.04434,MA0112.2;0.0892873,MA0065.2;0.224871,MA0150.1;0.267221,MA0151.1;0,MA0152.1;1.04455,MA0153.1;0.822355,MA0154.1;0.139881,MA0155.1;0.258579,MA0156.1;0.532949,MA0157.1;0.545026,MA0158.1;0,MA0159.1;0.403827,MA0160.1;0.80274,MA0161.1;0,MA0162.1;0.0186388,MA0163.1;0.0157648,MA0164.1;0.381832,MA0080.2;1.56168,MA0018.2;0.390455,MA0099.2;0.489441,MA0079.2;1.85825e-08,MA0102.2;1.38728,MA0258.1;0.687966,MA0259.1;0.367748,MA0442.1;0
}}
}}

Revision as of 11:58, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr16:45225058..45225071,+p@chr16:45225058..45225071
+
Mm9::chr16:45225090..45225101,+p@chr16:45225090..45225101
+
Mm9::chr17:34115798..34115805,-p2@H2-K2
Mm9::chr17:88981299..88981314,+p@chr17:88981299..88981314
+
Mm9::chr1:54642295..54642307,-p@chr1:54642295..54642307
-
Mm9::chr2:58011604..58011622,-p@chr2:58011604..58011622
-
Mm9::chr2:58012598..58012610,+p@chr2:58012598..58012610
+
Mm9::chr2:58012625..58012639,+p@chr2:58012625..58012639
+
Mm9::chr2:58013483..58013521,-p3@Cytip
Mm9::chr5:112702785..112702808,-p@chr5:112702785..112702808
-
Mm9::chr5:139643031..139643037,+p4@Heatr2
Mm9::chr9:32423847..32423875,+p@chr9:32423847..32423875
+
Mm9::chr9:32562231..32562235,+p@chr9:32562231..32562235
+


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:0030155regulation of cell adhesion0.0193118939352435
GO:0005938cell cortex0.0193118939352435



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 cell6.49e-3012
hematopoietic lineage restricted progenitor cell1.42e-2925
hematopoietic cell2.61e-2832
hematopoietic oligopotent progenitor cell2.61e-2832
hematopoietic stem cell2.61e-2832
angioblastic mesenchymal cell2.61e-2832
hematopoietic multipotent progenitor cell2.61e-2832
lymphocyte1.90e-2713
common lymphoid progenitor1.90e-2713
T cell6.56e-2711
pro-T cell6.56e-2711
nucleate cell6.82e-2216
mature alpha-beta T cell1.58e-219
alpha-beta T cell1.58e-219
immature T cell1.58e-219
mature T cell1.58e-219
immature alpha-beta T cell1.58e-219
leukocyte1.78e-2017
nongranular leukocyte1.78e-2017
CD4-positive, alpha-beta T cell1.09e-188
connective tissue cell1.63e-1846
mesenchymal cell1.63e-1846
motile cell3.39e-1554
megakaryocyte progenitor cell1.23e-136
megakaryocyte1.23e-136
thymocyte7.43e-136
double negative thymocyte7.43e-136
naive T cell7.43e-136
double-positive, alpha-beta thymocyte7.43e-136
CD4-positive, alpha-beta thymocyte7.43e-136
naive thymus-derived CD4-positive, alpha-beta T cell7.43e-136
DN4 thymocyte7.43e-136
DN1 thymic pro-T cell7.43e-136
DN2 thymocyte7.43e-136
DN3 thymocyte7.43e-136
immature single positive thymocyte7.43e-136
early T lineage precursor7.43e-136
mature CD4 single-positive thymocyte7.43e-136
resting double-positive thymocyte7.43e-136
double-positive blast7.43e-136
CD69-positive double-positive thymocyte7.43e-136
CD69-positive, CD4-positive single-positive thymocyte7.43e-136
CD4-positive, CD8-intermediate double-positive thymocyte7.43e-136
CD24-positive, CD4 single-positive thymocyte7.43e-136
megakaryocyte-erythroid progenitor cell5.67e-099
stem cell9.27e-0997
somatic stem cell1.85e-0791
multi fate stem cell1.85e-0791
common myeloid progenitor3.08e-0719


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)
MA0003.10.0157697
MA0004.11.40032
MA0006.10.885417
MA0007.10.737361
MA0009.10.678286
MA0014.10.0332236
MA0017.10.166909
MA0019.10.506787
MA0024.10.636635
MA0025.10.9035
MA0027.12.3071
MA0028.10.155127
MA0029.10.616052
MA0030.10.622264
MA0031.10.588678
MA0038.10.405578
MA0040.10.690239
MA0041.10.218039
MA0042.10.207696
MA0043.10.771094
MA0046.10.712646
MA0048.10.142843
MA0050.10.312673
MA0051.10.413609
MA0052.10.697946
MA0055.10.0835619
MA0056.10
MA0057.10.0312525
MA0058.10.585652
MA0059.10.212009
MA0060.10.313143
MA0061.10.734828
MA0063.10
MA0066.10.395746
MA0067.11.01206
MA0068.10.132828
MA0069.10.698271
MA0070.10.688999
MA0071.10.311956
MA0072.10.680902
MA0073.10.0050008
MA0074.10.363923
MA0076.10.181159
MA0077.10.660245
MA0078.11.12807
MA0081.10.651709
MA0083.10.77033
MA0084.11.33532
MA0087.10.728855
MA0088.10.0799097
MA0089.10
MA0090.10.251458
MA0091.12.20385
MA0092.10.70143
MA0093.11.50408
MA0095.10
MA0098.10
MA0100.10.353762
MA0101.10.625174
MA0103.10.519343
MA0105.10.434904
MA0106.10.450539
MA0107.10.979629
MA0108.20.527977
MA0109.10
MA0111.10.263095
MA0113.10.424958
MA0114.10.111687
MA0115.10.773793
MA0116.10.147513
MA0117.10.742722
MA0119.10.219527
MA0122.10.761823
MA0124.10.959967
MA0125.10.887718
MA0130.10
MA0131.10.502588
MA0132.10
MA0133.10
MA0135.10.806261
MA0136.10.993181
MA0139.10.0756871
MA0140.10.353662
MA0141.10.555407
MA0142.10.575041
MA0143.10.439766
MA0144.10.1137
MA0145.10.0201868
MA0146.10.00215921
MA0147.10.386218
MA0148.10.796977
MA0149.10.223436
MA0062.20.0556611
MA0035.20.357786
MA0039.20.00145609
MA0138.20.495254
MA0002.21.96954
MA0137.20.187581
MA0104.20.289861
MA0047.21.04434
MA0112.20.0892873
MA0065.20.224871
MA0150.10.267221
MA0151.10
MA0152.11.04455
MA0153.10.822355
MA0154.10.139881
MA0155.10.258579
MA0156.10.532949
MA0157.10.545026
MA0158.10
MA0159.10.403827
MA0160.10.80274
MA0161.10
MA0162.10.0186388
MA0163.10.0157648
MA0164.10.381832
MA0080.21.56168
MA0018.20.390455
MA0099.20.489441
MA0079.21.85825e-08
MA0102.21.38728
MA0258.10.687966
MA0259.10.367748
MA0442.10
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