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MCL coexpression mm9:504: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=
|ontology_enrichment_celltype=CL:0002371!3.74e-23!118;CL:0000548!9.85e-23!115;CL:0000255!9.85e-23!115;CL:0002031!9.22e-18!25;CL:0000988!2.83e-17!32;CL:0002032!2.83e-17!32;CL:0000037!2.83e-17!32;CL:0000566!2.83e-17!32;CL:0000837!2.83e-17!32;CL:0002320!8.52e-16!46;CL:0000134!8.52e-16!46;CL:0002076!8.65e-16!15;CL:0000066!8.96e-16!25;CL:0000219!5.38e-15!54;CL:0000838!1.45e-14!12;CL:0000034!4.02e-14!97;CL:0000738!6.15e-14!17;CL:0002087!6.15e-14!17;CL:0000542!3.19e-13!13;CL:0000051!3.19e-13!13;CL:0000791!4.70e-13!9;CL:0000789!4.70e-13!9;CL:0002420!4.70e-13!9;CL:0002419!4.70e-13!9;CL:0000790!4.70e-13!9;CL:0000084!5.11e-13!11;CL:0000827!5.11e-13!11;CL:0000223!6.11e-13!20;CL:0000624!1.24e-11!8;CL:0002242!3.26e-10!16;CL:0000723!4.90e-10!91;CL:0000048!4.90e-10!91;CL:0000893!5.61e-09!6;CL:0002489!5.61e-09!6;CL:0000898!5.61e-09!6;CL:0000809!5.61e-09!6;CL:0000810!5.61e-09!6;CL:0000895!5.61e-09!6;CL:0000808!5.61e-09!6;CL:0000894!5.61e-09!6;CL:0000806!5.61e-09!6;CL:0000807!5.61e-09!6;CL:0000805!5.61e-09!6;CL:0002425!5.61e-09!6;CL:0002436!5.61e-09!6;CL:0002427!5.61e-09!6;CL:0002428!5.61e-09!6;CL:0002429!5.61e-09!6;CL:0002433!5.61e-09!6;CL:0002431!5.61e-09!6;CL:0002432!5.61e-09!6;CL:0000553!3.24e-07!6;CL:0000556!3.24e-07!6;CL:0002563!5.45e-07!9;CL:0002251!5.45e-07!9
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002384!8.52e-16!46;UBERON:0000344!2.92e-11!15;UBERON:0001242!4.99e-09!13;UBERON:0000060!4.99e-09!13;UBERON:0001262!4.99e-09!13;UBERON:0004786!4.99e-09!13;UBERON:0000485!8.41e-09!11;UBERON:0002193!1.61e-08!48;UBERON:0002405!1.61e-08!48;UBERON:0000072!1.77e-07!27;UBERON:0002390!2.42e-07!45;UBERON:0003061!2.42e-07!45;UBERON:0003350!5.45e-07!9;UBERON:0004808!5.45e-07!9;UBERON:0001277!5.45e-07!9;UBERON:0000490!5.60e-07!66
|tfbs_overrepresentation_for_novel_motifs=0.224466,0.0679776,0.204219,0.25808,0.123731,0.269875,0.346405,0.0669598,0.0719629,0.0394224,0.308886,0.336042,0.511203,0.357027,0.419678,0,0.530547,0.377686,1.23738,0.24668,0.523517,0.0130128,0.356242,0.77745,0.210021,0.381085,0.203385,0.287195,0.469653,0.611262,0.275529,0.624931,0.117091,0.176308,0.420513,0.0766511,0.111136,0.885722,0.662669,0.0808072,0.77022,0.279796,0.0536251,0.423138,0.0109479,0.24907,1.15859,0.812613,0.415504,0.474834,0.514446,0.404841,0.321327,0.759566,0.776306,0.363247,0.490599,0.325117,0.0511827,0.36147,0.606104,0.413233,0.26973,0.504093,0.372973,0.541429,0.908031,1.25063,0.60172,1.10561,0.189925,0.246154,0.178539,0.808562,0.181606,0.166516,0.0464428,0.447339,2.45549,0.179738,0.247973,0.546623,0.411949,0.493111,0.69807,0.0177525,0.0223411,0.145915,0.462057,1.41118,0.975915,0.702809,0.636995,0.799202,1.08418,0.601346,0.0656861,0.639644,0.457849,0.119684,0.358446,0.624668,0.742871,0.514993,0.514023,0.279432,0.569344,0.296997,0.183341,0.177945,0.62491,0.744577,0.180573,0.841652,0.982794,0.381263,0.189757,0.26114,0.53175,0.108794,0.813766,0.484912,0.382687,0.446521,1.03573,0.593478,0.353461,0.630607,0.906557,0.129636,0.726634,0.702495,0.877862,0.375176,1.0039,0.162091,0.231086,0.280962,0.955897,1.77738,1.3796,0.91261,0.393303,0.634793,0.508066,0.280171,0.460443,1.73788,0.657796,0.394117,0.148959,0.0529032,0.761071,0.29706,0.374365,0.839715,0.405736,0.143092,0.222538,0.230865,0.96517,1.6643,0.593895,0.620756,0.50503,0.367885,0.110426,0.33468,0.238727
|tfbs_overrepresentation_jaspar=MA0003.1;0.000592671,MA0004.1;0.258473,MA0006.1;0.1319,MA0007.1;0.689082,MA0009.1;0.649874,MA0014.1;0.023905,MA0017.1;0.895796,MA0019.1;0.480432,MA0024.1;0.608636,MA0025.1;0.873493,MA0027.1;2.275,MA0028.1;0.138956,MA0029.1;0.588275,MA0030.1;0.594419,MA0031.1;0.561217,MA0038.1;0.381016,MA0040.1;0.661716,MA0041.1;0.577334,MA0042.1;0.553522,MA0043.1;0.74191,MA0046.1;0.683926,MA0048.1;0.534002,MA0050.1;0.290354,MA0051.1;0.388883,MA0052.1;0.669354,MA0055.1;0.276048,MA0056.1;0,MA0057.1;0.0252827,MA0058.1;0.183941,MA0059.1;0.19314,MA0060.1;0.0819399,MA0061.1;0.0995825,MA0063.1;0,MA0066.1;0.371389,MA0067.1;0.981551,MA0068.1;0.0266408,MA0069.1;0.669676,MA0070.1;0.660488,MA0071.1;0.289658,MA0072.1;0.652465,MA0073.1;7.73103e-07,MA0074.1;0.340281,MA0076.1;0.163664,MA0077.1;0.632005,MA0078.1;0.418168,MA0081.1;0.210747,MA0083.1;0.741151,MA0084.1;1.30392,MA0087.1;0.699999,MA0088.1;0.0136969,MA0089.1;0,MA0090.1;0.231074,MA0091.1;0.741628,MA0092.1;0.231323,MA0093.1;0.444403,MA0095.1;0,MA0098.1;0,MA0100.1;0.330364,MA0101.1;0.199903,MA0103.1;0.157724,MA0105.1;0.0444807,MA0106.1;0.425111,MA0107.1;0.153373,MA0108.2;0.50131,MA0109.1;0,MA0111.1;0.679612,MA0113.1;0.400008,MA0114.1;0.323836,MA0115.1;0.744589,MA0116.1;0.131762,MA0117.1;0.713754,MA0119.1;0.580747,MA0122.1;0.732707,MA0124.1;0.929684,MA0125.1;0.857794,MA0130.1;0,MA0131.1;0.476296,MA0132.1;0,MA0133.1;0,MA0135.1;1.82901,MA0136.1;0.940193,MA0139.1;0.0649474,MA0140.1;0.330266,MA0141.1;0.171891,MA0142.1;0.547747,MA0143.1;1.06535,MA0144.1;0.100037,MA0145.1;0.189432,MA0146.1;0.00972339,MA0147.1;0.349075,MA0148.1;0.747422,MA0149.1;0.204102,MA0062.2;0.046824,MA0035.2;0.888731,MA0039.2;0.00306976,MA0138.2;0.469076,MA0002.2;0.0664561,MA0137.2;0.169785,MA0104.2;0.257564,MA0047.2;0.380343,MA0112.2;0.189423,MA0065.2;0.190247,MA0150.1;0.246295,MA0151.1;0,MA0152.1;0.380437,MA0153.1;0.792819,MA0154.1;0.0285118,MA0155.1;0.0879017,MA0156.1;0.163042,MA0157.1;0.518122,MA0158.1;0,MA0159.1;0.114033,MA0160.1;0.274172,MA0161.1;0,MA0162.1;0.00209837,MA0163.1;0.00169705,MA0164.1;0.357779,MA0080.2;0.467794,MA0018.2;0.366212,MA0099.2;0.463355,MA0079.2;1.32368e-07,MA0102.2;1.35579,MA0258.1;0.0900907,MA0259.1;0.101001,MA0442.1;0
}}

Latest revision as of 15:25, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:114725078..114725089,-p@chr10:114725078..114725089
-
Mm9::chr11:52218757..52218764,+p1@ENSMUST00000122004
Mm9::chr13:111190894..111190898,+p@chr13:111190894..111190898
+
Mm9::chr15:27560399..27560469,-p1@Fam105b
Mm9::chr17:47547196..47547202,+p@chr17:47547196..47547202
+
Mm9::chr18:35955169..35955173,+p@chr18:35955169..35955173
+
Mm9::chr1:178709356..178709358,+p@chr1:178709356..178709358
+
Mm9::chr2:77129080..77129085,+p1@ENSMUST00000119086
Mm9::chr3:66789602..66789614,+p5@Rsrc1
Mm9::chr5:34142228..34142234,+p@chr5:34142228..34142234
+
Mm9::chr7:46843882..46843894,+p3@Gm2058
Mm9::chr8:49432892..49432894,+p@chr8:49432892..49432894
+
Mm9::chr9:3372522..3372525,+p@chr9:3372522..3372525
+
Mm9::chrX:59083372..59083385,+p2@ENSMUST00000117345


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
somatic cell3.74e-23118
animal cell9.85e-23115
eukaryotic cell9.85e-23115
hematopoietic lineage restricted progenitor cell9.22e-1825
hematopoietic cell2.83e-1732
hematopoietic oligopotent progenitor cell2.83e-1732
hematopoietic stem cell2.83e-1732
angioblastic mesenchymal cell2.83e-1732
hematopoietic multipotent progenitor cell2.83e-1732
connective tissue cell8.52e-1646
mesenchymal cell8.52e-1646
endo-epithelial cell8.65e-1615
epithelial cell8.96e-1625
motile cell5.38e-1554
lymphoid lineage restricted progenitor cell1.45e-1412
stem cell4.02e-1497
leukocyte6.15e-1417
nongranular leukocyte6.15e-1417
lymphocyte3.19e-1313
common lymphoid progenitor3.19e-1313
mature alpha-beta T cell4.70e-139
alpha-beta T cell4.70e-139
immature T cell4.70e-139
mature T cell4.70e-139
immature alpha-beta T cell4.70e-139
T cell5.11e-1311
pro-T cell5.11e-1311
endodermal cell6.11e-1320
CD4-positive, alpha-beta T cell1.24e-118
nucleate cell3.26e-1016
somatic stem cell4.90e-1091
multi fate stem cell4.90e-1091
thymocyte5.61e-096
double negative thymocyte5.61e-096
naive T cell5.61e-096
double-positive, alpha-beta thymocyte5.61e-096
CD4-positive, alpha-beta thymocyte5.61e-096
naive thymus-derived CD4-positive, alpha-beta T cell5.61e-096
DN4 thymocyte5.61e-096
DN1 thymic pro-T cell5.61e-096
DN2 thymocyte5.61e-096
DN3 thymocyte5.61e-096
immature single positive thymocyte5.61e-096
early T lineage precursor5.61e-096
mature CD4 single-positive thymocyte5.61e-096
resting double-positive thymocyte5.61e-096
double-positive blast5.61e-096
CD69-positive double-positive thymocyte5.61e-096
CD69-positive, CD4-positive single-positive thymocyte5.61e-096
CD4-positive, CD8-intermediate double-positive thymocyte5.61e-096
CD24-positive, CD4 single-positive thymocyte5.61e-096
megakaryocyte progenitor cell3.24e-076
megakaryocyte3.24e-076
intestinal epithelial cell5.45e-079
epithelial cell of alimentary canal5.45e-079


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)
MA0003.10.000592671
MA0004.10.258473
MA0006.10.1319
MA0007.10.689082
MA0009.10.649874
MA0014.10.023905
MA0017.10.895796
MA0019.10.480432
MA0024.10.608636
MA0025.10.873493
MA0027.12.275
MA0028.10.138956
MA0029.10.588275
MA0030.10.594419
MA0031.10.561217
MA0038.10.381016
MA0040.10.661716
MA0041.10.577334
MA0042.10.553522
MA0043.10.74191
MA0046.10.683926
MA0048.10.534002
MA0050.10.290354
MA0051.10.388883
MA0052.10.669354
MA0055.10.276048
MA0056.10
MA0057.10.0252827
MA0058.10.183941
MA0059.10.19314
MA0060.10.0819399
MA0061.10.0995825
MA0063.10
MA0066.10.371389
MA0067.10.981551
MA0068.10.0266408
MA0069.10.669676
MA0070.10.660488
MA0071.10.289658
MA0072.10.652465
MA0073.17.73103e-07
MA0074.10.340281
MA0076.10.163664
MA0077.10.632005
MA0078.10.418168
MA0081.10.210747
MA0083.10.741151
MA0084.11.30392
MA0087.10.699999
MA0088.10.0136969
MA0089.10
MA0090.10.231074
MA0091.10.741628
MA0092.10.231323
MA0093.10.444403
MA0095.10
MA0098.10
MA0100.10.330364
MA0101.10.199903
MA0103.10.157724
MA0105.10.0444807
MA0106.10.425111
MA0107.10.153373
MA0108.20.50131
MA0109.10
MA0111.10.679612
MA0113.10.400008
MA0114.10.323836
MA0115.10.744589
MA0116.10.131762
MA0117.10.713754
MA0119.10.580747
MA0122.10.732707
MA0124.10.929684
MA0125.10.857794
MA0130.10
MA0131.10.476296
MA0132.10
MA0133.10
MA0135.11.82901
MA0136.10.940193
MA0139.10.0649474
MA0140.10.330266
MA0141.10.171891
MA0142.10.547747
MA0143.11.06535
MA0144.10.100037
MA0145.10.189432
MA0146.10.00972339
MA0147.10.349075
MA0148.10.747422
MA0149.10.204102
MA0062.20.046824
MA0035.20.888731
MA0039.20.00306976
MA0138.20.469076
MA0002.20.0664561
MA0137.20.169785
MA0104.20.257564
MA0047.20.380343
MA0112.20.189423
MA0065.20.190247
MA0150.10.246295
MA0151.10
MA0152.10.380437
MA0153.10.792819
MA0154.10.0285118
MA0155.10.0879017
MA0156.10.163042
MA0157.10.518122
MA0158.10
MA0159.10.114033
MA0160.10.274172
MA0161.10
MA0162.10.00209837
MA0163.10.00169705
MA0164.10.357779
MA0080.20.467794
MA0018.20.366212
MA0099.20.463355
MA0079.21.32368e-07
MA0102.21.35579
MA0258.10.0900907
MA0259.10.101001
MA0442.10
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