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MCL coexpression mm9:1129: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002384!7.19e-20!46;UBERON:0000344!2.61e-11!15;UBERON:0001242!7.57e-09!13;UBERON:0000060!7.57e-09!13;UBERON:0001262!7.57e-09!13;UBERON:0004786!7.57e-09!13;UBERON:0000485!4.94e-08!11
|ontology_enrichment_uberon=UBERON:0002384!7.19e-20!46;UBERON:0000344!2.61e-11!15;UBERON:0001242!7.57e-09!13;UBERON:0000060!7.57e-09!13;UBERON:0001262!7.57e-09!13;UBERON:0004786!7.57e-09!13;UBERON:0000485!4.94e-08!11
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.161863,0.411716,0.480627,0.299217,0.495263,0.587291,0.206208,0.215218,0.219671,0.542749,0.575086,0.206435,0.599731,0.315771,0,0.795315,0.291368,0.561256,0.361892,0.374752,0.08187,0.598814,0.29769,0.419327,0.62766,0.184473,0.516511,0.344372,0.145661,0.50223,0.897561,0.289148,0.498917,0.848378,0.468714,0.279977,0.57142,1.32199,0.230656,0.800988,0.507468,0.258106,0.317766,0.277561,0.469348,0.714592,0.532496,0.219744,0.347313,0.777641,0.654933,0.139618,1.04034,1.0579,0.606984,0.356236,0.56214,0.176152,0.604914,0.877332,0.664501,0.226529,0.766235,1.49952,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.21183,0.293368,1.09164,0.17012,0.159969,0.498755,0.703064,0.859987,0.378988,0.212973,0.812889,0.663039,0.580284,0.975495,0.0369809,0.164297,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.237542,0.589174,0.913319,0.71485,0.399703,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,0.430942,1.02459,0.380122,0.547992,1.27206,0.293461,0.418498,1.21618,0.796633,0.757997,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.829907,1.00568,0.473246,1.16374,0.620831,1.29374,0.0806013,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.147909,0.0736236,1.04192,0.243291,0.619892,1.12411,0.655955,0.327731,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.278874,0.573477,0.227149
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.161863,0.411716,0.480627,0.299217,0.495263,0.587291,0.206208,0.215218,0.219671,0.542749,0.575086,0.206435,0.599731,0.315771,0,0.795315,0.291368,0.561256,0.361892,0.374752,0.08187,0.598814,0.29769,0.419327,0.62766,0.184473,0.516511,0.344372,0.145661,0.50223,0.897561,0.289148,0.498917,0.848378,0.468714,0.279977,0.57142,1.32199,0.230656,0.800988,0.507468,0.258106,0.317766,0.277561,0.469348,0.714592,0.532496,0.219744,0.347313,0.777641,0.654933,0.139618,1.04034,1.0579,0.606984,0.356236,0.56214,0.176152,0.604914,0.877332,0.664501,0.226529,0.766235,1.49952,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.21183,0.293368,1.09164,0.17012,0.159969,0.498755,0.703064,0.859987,0.378988,0.212973,0.812889,0.663039,0.580284,0.975495,0.0369809,0.164297,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.237542,0.589174,0.913319,0.71485,0.399703,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,0.430942,1.02459,0.380122,0.547992,1.27206,0.293461,0.418498,1.21618,0.796633,0.757997,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.829907,1.00568,0.473246,1.16374,0.620831,1.29374,0.0806013,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.147909,0.0736236,1.04192,0.243291,0.619892,1.12411,0.655955,0.327731,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.278874,0.573477,0.227149
|tfbs_overrepresentation_jaspar=MA0003.1;0.0286946,MA0004.1;0.481116,MA0006.1;0.837454,MA0007.1;0.465969,MA0009.1;0.92425,MA0014.1;0.0200028,MA0017.1;0.337808,MA0019.1;1.753,MA0024.1;0.880057,MA0025.1;1.15921,MA0027.1;2.57545,MA0028.1;1.55156,MA0029.1;0.858105,MA0030.1;0.864739,MA0031.1;0.828781,MA0038.1;0.62758,MA0040.1;0.936879,MA0041.1;0.404721,MA0042.1;0.391504,MA0043.1;1.02178,MA0046.1;0.960497,MA0048.1;0.128106,MA0050.1;0.520357,MA0051.1;0.636645,MA0052.1;0.945011,MA0055.1;0.157978,MA0056.1;0,MA0057.1;0.117936,MA0058.1;0.384683,MA0059.1;0.397033,MA0060.1;0.232592,MA0061.1;0.261749,MA0063.1;0,MA0066.1;0.616444,MA0067.1;1.27078,MA0068.1;0.771749,MA0069.1;0.945354,MA0070.1;0.93557,MA0071.1;0.519509,MA0072.1;0.927016,MA0073.1;0.0004304,MA0074.1;0.580087,MA0076.1;1.67548,MA0077.1;0.905143,MA0078.1;0.670113,MA0081.1;0.420276,MA0083.1;1.02098,MA0084.1;1.59945,MA0087.1;0.977537,MA0088.1;0.0841779,MA0089.1;0,MA0090.1;0.446539,MA0091.1;0.494398,MA0092.1;0.446857,MA0093.1;0.329976,MA0095.1;0,MA0098.1;0,MA0100.1;0.568369,MA0101.1;0.406019,MA0103.1;0.348572,MA0105.1;0.162418,MA0106.1;0.677988,MA0107.1;0.342432,MA0108.2;0.763162,MA0109.1;0,MA0111.1;0.460823,MA0113.1;0.649407,MA0114.1;0.719313,MA0115.1;1.0246,MA0116.1;0.311187,MA0117.1;0.992087,MA0119.1;0.40661,MA0122.1;1.01209,MA0124.1;1.21735,MA0125.1;1.14291,MA0130.1;0,MA0131.1;0.735438,MA0132.1;0,MA0133.1;0,MA0135.1;1.05845,MA0136.1;0.600242,MA0139.1;0.202522,MA0140.1;0.568252,MA0141.1;0.368264,MA0142.1;0.814115,MA0143.1;0.665982,MA0144.1;1.33652,MA0145.1;0.0910975,MA0146.1;0.0256827,MA0147.1;0.274511,MA0148.1;0.49752,MA0149.1;0.411562,MA0062.2;0.967192,MA0035.2;0.573016,MA0039.2;0.113749,MA0138.2;0.727395,MA0002.2;0.205289,MA0137.2;0.957645,MA0104.2;0.218974,MA0047.2;0.626803,MA0112.2;0.0910939,MA0065.2;0.0914071,MA0150.1;0.465855,MA0151.1;0,MA0152.1;0.626912,MA0153.1;1.07519,MA0154.1;0.126143,MA0155.1;0.102995,MA0156.1;0.936991,MA0157.1;0.781683,MA0158.1;0,MA0159.1;0.284457,MA0160.1;0.50056,MA0161.1;0,MA0162.1;0.0312493,MA0163.1;0.116706,MA0164.1;0.600609,MA0080.2;0.343316,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;0.00878868,MA0102.2;1.65195,MA0258.1;0.246285,MA0259.1;0.26402,MA0442.1;0
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Revision as of 12:51, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr14:122230170..122230176,+p@chr14:122230170..122230176
+
Mm9::chr14:48189081..48189085,+p1@Gm6616
Mm9::chr18:75160143..75160153,+p4@Gm10294
p4@Rpl17
Mm9::chr19:37858699..37858749,+p@chr19:37858699..37858749
+
Mm9::chr1:39424719..39424730,+p3@Gm10191
p3@Gm13004
p3@Gm7689
p3@Gm8759
p3@LOC100505081
p3@LOC638399
p3@Rpl31
Mm9::chr7:58713316..58713326,+p1@ENSMUST00000077381
Mm9::chr9:57181873..57181884,+p1@Gm5121


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:0003735structural constituent of ribosome0.00114928015399592
GO:0005840ribosome0.00114928015399592
GO:0006412translation0.00426107607803767
GO:0030529ribonucleoprotein complex0.00426107607803767
GO:0009059macromolecule biosynthetic process0.00711973963157119
GO:0044249cellular biosynthetic process0.010248901411155
GO:0015934large ribosomal subunit0.0140788124567925
GO:0009058biosynthetic process0.0140788124567925
GO:0043228non-membrane-bound organelle0.0178799545036496
GO:0043232intracellular non-membrane-bound organelle0.0178799545036496
GO:0033279ribosomal subunit0.0178799545036496
GO:0032991macromolecular complex0.0279377444569467
GO:0044267cellular protein metabolic process0.0400583390841314
GO:0044260cellular macromolecule metabolic process0.0400583390841314
GO:0010467gene expression0.0400583390841314
GO:0019538protein metabolic process0.0400583390841314
GO:0044444cytoplasmic part0.0478671182542338



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 cell1.61e-2232
hematopoietic oligopotent progenitor cell1.61e-2232
hematopoietic stem cell1.61e-2232
angioblastic mesenchymal cell1.61e-2232
hematopoietic multipotent progenitor cell1.61e-2232
somatic cell2.54e-21118
motile cell3.14e-2054
connective tissue cell7.19e-2046
mesenchymal cell7.19e-2046
animal cell7.71e-20115
eukaryotic cell7.71e-20115
hematopoietic lineage restricted progenitor cell6.30e-1825
stem cell2.49e-1597
lymphoid lineage restricted progenitor cell3.18e-1312
leukocyte1.94e-1217
nongranular leukocyte1.94e-1217
mature alpha-beta T cell3.07e-129
alpha-beta T cell3.07e-129
immature T cell3.07e-129
mature T cell3.07e-129
immature alpha-beta T cell3.07e-129
T cell3.50e-1211
pro-T cell3.50e-1211
lymphocyte5.37e-1213
common lymphoid progenitor5.37e-1213
common myeloid progenitor1.13e-1119
nucleate cell3.07e-1116
CD4-positive, alpha-beta T cell3.37e-118
somatic stem cell1.10e-1091
multi fate stem cell1.10e-1091
epithelial cell2.73e-0925
thymocyte3.82e-096
double negative thymocyte3.82e-096
naive T cell3.82e-096
double-positive, alpha-beta thymocyte3.82e-096
CD4-positive, alpha-beta thymocyte3.82e-096
naive thymus-derived CD4-positive, alpha-beta T cell3.82e-096
DN4 thymocyte3.82e-096
DN1 thymic pro-T cell3.82e-096
DN2 thymocyte3.82e-096
DN3 thymocyte3.82e-096
immature single positive thymocyte3.82e-096
early T lineage precursor3.82e-096
mature CD4 single-positive thymocyte3.82e-096
resting double-positive thymocyte3.82e-096
double-positive blast3.82e-096
CD69-positive double-positive thymocyte3.82e-096
CD69-positive, CD4-positive single-positive thymocyte3.82e-096
CD4-positive, CD8-intermediate double-positive thymocyte3.82e-096
CD24-positive, CD4 single-positive thymocyte3.82e-096
myeloid cell3.08e-0816
endo-epithelial cell6.35e-0815

Uber Anatomy
Ontology termp-valuen
connective tissue7.19e-2046
mucosa2.61e-1115
intestinal mucosa7.57e-0913
anatomical wall7.57e-0913
wall of intestine7.57e-0913
gastrointestinal system mucosa7.57e-0913
simple columnar epithelium4.94e-0811


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)
MA0003.10.0286946
MA0004.10.481116
MA0006.10.837454
MA0007.10.465969
MA0009.10.92425
MA0014.10.0200028
MA0017.10.337808
MA0019.11.753
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.11.55156
MA0029.10.858105
MA0030.10.864739
MA0031.10.828781
MA0038.10.62758
MA0040.10.936879
MA0041.10.404721
MA0042.10.391504
MA0043.11.02178
MA0046.10.960497
MA0048.10.128106
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.157978
MA0056.10
MA0057.10.117936
MA0058.10.384683
MA0059.10.397033
MA0060.10.232592
MA0061.10.261749
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.771749
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.10.0004304
MA0074.10.580087
MA0076.11.67548
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.10.0841779
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.10.446857
MA0093.10.329976
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.10.348572
MA0105.10.162418
MA0106.10.677988
MA0107.10.342432
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.719313
MA0115.11.0246
MA0116.10.311187
MA0117.10.992087
MA0119.10.40661
MA0122.11.01209
MA0124.11.21735
MA0125.11.14291
MA0130.10
MA0131.10.735438
MA0132.10
MA0133.10
MA0135.11.05845
MA0136.10.600242
MA0139.10.202522
MA0140.10.568252
MA0141.10.368264
MA0142.10.814115
MA0143.10.665982
MA0144.11.33652
MA0145.10.0910975
MA0146.10.0256827
MA0147.10.274511
MA0148.10.49752
MA0149.10.411562
MA0062.20.967192
MA0035.20.573016
MA0039.20.113749
MA0138.20.727395
MA0002.20.205289
MA0137.20.957645
MA0104.20.218974
MA0047.20.626803
MA0112.20.0910939
MA0065.20.0914071
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.126143
MA0155.10.102995
MA0156.10.936991
MA0157.10.781683
MA0158.10
MA0159.10.284457
MA0160.10.50056
MA0161.10
MA0162.10.0312493
MA0163.10.116706
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.20.00878868
MA0102.21.65195
MA0258.10.246285
MA0259.10.26402
MA0442.10
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