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MCL coexpression mm9:532: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002193!1.17e-27!48;UBERON:0002405!1.17e-27!48;UBERON:0002390!1.08e-24!45;UBERON:0003061!1.08e-24!45;UBERON:0003081!6.91e-18!87;UBERON:0004177!1.15e-16!29;UBERON:0005057!1.15e-16!29;UBERON:0000077!2.60e-16!35;UBERON:0006562!6.37e-15!24;UBERON:0001557!6.37e-15!24;UBERON:0001042!6.37e-15!24;UBERON:0008814!6.37e-15!24;UBERON:0009145!6.37e-15!24;UBERON:0002370!2.28e-14!23;UBERON:0000974!2.28e-14!23;UBERON:0004807!2.28e-14!23;UBERON:0005058!2.28e-14!23;UBERON:0003351!2.28e-14!23;UBERON:0009113!2.28e-14!23;UBERON:0003295!2.28e-14!23;UBERON:0009722!2.28e-14!23;UBERON:0005562!2.28e-14!23;UBERON:0007690!2.28e-14!23;UBERON:0000065!9.38e-14!41;UBERON:0003408!1.67e-13!24;UBERON:0001004!3.23e-13!42;UBERON:0002384!6.41e-13!46;UBERON:0000072!1.57e-12!27;UBERON:0000926!5.94e-11!120;UBERON:0004120!5.94e-11!120;UBERON:0006603!5.94e-11!120;UBERON:0002371!1.35e-08!16;UBERON:0000063!3.00e-08!35;UBERON:0007811!7.41e-08!36;UBERON:0001041!1.96e-07!80;UBERON:0002204!2.96e-07!32
|ontology_enrichment_uberon=UBERON:0002193!1.17e-27!48;UBERON:0002405!1.17e-27!48;UBERON:0002390!1.08e-24!45;UBERON:0003061!1.08e-24!45;UBERON:0003081!6.91e-18!87;UBERON:0004177!1.15e-16!29;UBERON:0005057!1.15e-16!29;UBERON:0000077!2.60e-16!35;UBERON:0006562!6.37e-15!24;UBERON:0001557!6.37e-15!24;UBERON:0001042!6.37e-15!24;UBERON:0008814!6.37e-15!24;UBERON:0009145!6.37e-15!24;UBERON:0002370!2.28e-14!23;UBERON:0000974!2.28e-14!23;UBERON:0004807!2.28e-14!23;UBERON:0005058!2.28e-14!23;UBERON:0003351!2.28e-14!23;UBERON:0009113!2.28e-14!23;UBERON:0003295!2.28e-14!23;UBERON:0009722!2.28e-14!23;UBERON:0005562!2.28e-14!23;UBERON:0007690!2.28e-14!23;UBERON:0000065!9.38e-14!41;UBERON:0003408!1.67e-13!24;UBERON:0001004!3.23e-13!42;UBERON:0002384!6.41e-13!46;UBERON:0000072!1.57e-12!27;UBERON:0000926!5.94e-11!120;UBERON:0004120!5.94e-11!120;UBERON:0006603!5.94e-11!120;UBERON:0002371!1.35e-08!16;UBERON:0000063!3.00e-08!35;UBERON:0007811!7.41e-08!36;UBERON:0001041!1.96e-07!80;UBERON:0002204!2.96e-07!32
|tfbs_overrepresentation_for_novel_motifs=0.6379,0.954724,0.589984,1.32019,0.123731,0.269875,0.346405,0.51055,0.914437,0.112618,0.308886,0.336042,0.237599,0.357027,0.134875,0,0.530547,0.118546,0.215337,0.751449,0.176628,0.837419,0.356242,0.122718,0.603782,0.381085,1.19145,0.287195,0.154744,0.611262,0.275529,0.624931,0.373899,0.397142,0.135203,0.850523,0.111136,0.332941,0.097604,0.276416,0.384293,0.279796,0.295897,0.423138,0.314995,0.24907,0.457618,0.300372,0.237017,0.474834,0.514446,0.404841,0.584697,0.759566,0.776306,0.363247,0.163199,0.325117,0.424359,0.36147,1.47398,0.413233,0.569343,0.504093,0.372973,1.33757,0.908031,1.25063,0.60172,1.10561,0.555733,0.246154,0.178539,0.808562,0.181606,0.0433214,0.396955,0.447339,0.590017,0.531085,0.530081,0.546623,0.411949,0.0636668,0.69807,0.132803,0.00381013,1.84007,0.462057,1.41118,0.975915,0.702809,0.636995,0.127646,0.0951738,0.0848579,0.865338,0.639644,0.457849,0.286529,0.358446,0.624668,0.742871,0.514993,0.514023,0.279432,0.569344,0.296997,0.183341,0.177945,0.218949,0.744577,0.180573,0.313258,0.982794,0.119923,0.0869445,0.26114,0.53175,0.108794,0.813766,1.21719,0.382687,0.446521,1.03573,0.593478,0.931332,0.630607,0.906557,0.406303,0.726634,0.702495,0.877862,0.375176,1.0039,0.162091,0.65343,0.280962,0.955897,1.77738,1.3796,0.91261,0.393303,0.634793,0.508066,0.280171,0.460443,1.73788,0.232952,0.394117,0.0377782,0.0529032,0.761071,0.29706,0.977476,0.839715,0.405736,0.143092,0.222538,0.652913,0.96517,1.6643,0.593895,0.21719,0.50503,0.367885,0.356446,0.33468,0.00671205
|tfbs_overrepresentation_for_novel_motifs=0.6379,0.954724,0.589984,1.32019,0.123731,0.269875,0.346405,0.51055,0.914437,0.112618,0.308886,0.336042,0.237599,0.357027,0.134875,0,0.530547,0.118546,0.215337,0.751449,0.176628,0.837419,0.356242,0.122718,0.603782,0.381085,1.19145,0.287195,0.154744,0.611262,0.275529,0.624931,0.373899,0.397142,0.135203,0.850523,0.111136,0.332941,0.097604,0.276416,0.384293,0.279796,0.295897,0.423138,0.314995,0.24907,0.457618,0.300372,0.237017,0.474834,0.514446,0.404841,0.584697,0.759566,0.776306,0.363247,0.163199,0.325117,0.424359,0.36147,1.47398,0.413233,0.569343,0.504093,0.372973,1.33757,0.908031,1.25063,0.60172,1.10561,0.555733,0.246154,0.178539,0.808562,0.181606,0.0433214,0.396955,0.447339,0.590017,0.531085,0.530081,0.546623,0.411949,0.0636668,0.69807,0.132803,0.00381013,1.84007,0.462057,1.41118,0.975915,0.702809,0.636995,0.127646,0.0951738,0.0848579,0.865338,0.639644,0.457849,0.286529,0.358446,0.624668,0.742871,0.514993,0.514023,0.279432,0.569344,0.296997,0.183341,0.177945,0.218949,0.744577,0.180573,0.313258,0.982794,0.119923,0.0869445,0.26114,0.53175,0.108794,0.813766,1.21719,0.382687,0.446521,1.03573,0.593478,0.931332,0.630607,0.906557,0.406303,0.726634,0.702495,0.877862,0.375176,1.0039,0.162091,0.65343,0.280962,0.955897,1.77738,1.3796,0.91261,0.393303,0.634793,0.508066,0.280171,0.460443,1.73788,0.232952,0.394117,0.0377782,0.0529032,0.761071,0.29706,0.977476,0.839715,0.405736,0.143092,0.222538,0.652913,0.96517,1.6643,0.593895,0.21719,0.50503,0.367885,0.356446,0.33468,0.00671205
|tfbs_overrepresentation_jaspar=MA0003.1;0.934438,MA0004.1;0.258473,MA0006.1;0.817804,MA0007.1;0.689082,MA0009.1;0.649874,MA0014.1;0.37055,MA0017.1;1.43837,MA0019.1;0.480432,MA0024.1;0.608636,MA0025.1;0.873493,MA0027.1;2.275,MA0028.1;1.37032,MA0029.1;0.588275,MA0030.1;0.594419,MA0031.1;0.561217,MA0038.1;0.381016,MA0040.1;0.661716,MA0041.1;0.198922,MA0042.1;0.553522,MA0043.1;0.74191,MA0046.1;1.63659,MA0048.1;0.289404,MA0050.1;1.43876,MA0051.1;2.68041,MA0052.1;0.669354,MA0055.1;0.0206669,MA0056.1;0,MA0057.1;0.78569,MA0058.1;0.183941,MA0059.1;0.19314,MA0060.1;0.0819399,MA0061.1;1.64064,MA0063.1;0,MA0066.1;0.371389,MA0067.1;0.981551,MA0068.1;0.271058,MA0069.1;0.669676,MA0070.1;1.58777,MA0071.1;0.289658,MA0072.1;0.652465,MA0073.1;0.315764,MA0074.1;0.340281,MA0076.1;1.51892,MA0077.1;0.632005,MA0078.1;0.418168,MA0081.1;1.14043,MA0083.1;0.741151,MA0084.1;1.30392,MA0087.1;0.699999,MA0088.1;0.171343,MA0089.1;0,MA0090.1;0.653402,MA0091.1;0.741628,MA0092.1;0.653984,MA0093.1;0.144649,MA0095.1;0,MA0098.1;0,MA0100.1;0.330364,MA0101.1;0.57968,MA0103.1;0.477056,MA0105.1;2.55372,MA0106.1;1.08833,MA0107.1;1.45792,MA0108.2;0.50131,MA0109.1;0,MA0111.1;0.242308,MA0113.1;0.400008,MA0114.1;0.665298,MA0115.1;2.94907,MA0116.1;0.411741,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;0.77683,MA0136.1;0.357464,MA0139.1;0.499924,MA0140.1;0.330266,MA0141.1;0.511953,MA0142.1;0.547747,MA0143.1;0.414534,MA0144.1;0.674112,MA0145.1;0.614688,MA0146.1;0.170737,MA0147.1;0.107632,MA0148.1;1.37059,MA0149.1;0.204102,MA0062.2;1.53832,MA0035.2;0.33429,MA0039.2;0.0846004,MA0138.2;0.469076,MA0002.2;0.0664561,MA0137.2;0.169785,MA0104.2;0.0740839,MA0047.2;0.990617,MA0112.2;0.370361,MA0065.2;2.14144,MA0150.1;0.246295,MA0151.1;0,MA0152.1;0.380437,MA0153.1;0.792819,MA0154.1;0.837005,MA0155.1;0.423059,MA0156.1;0.490212,MA0157.1;0.518122,MA0158.1;0,MA0159.1;0.365914,MA0160.1;0.274172,MA0161.1;0,MA0162.1;0.108524,MA0163.1;1.24995,MA0164.1;0.357779,MA0080.2;0.467794,MA0018.2;0.366212,MA0099.2;0.463355,MA0079.2;1.60703,MA0102.2;1.35579,MA0258.1;0.301988,MA0259.1;0.331447,MA0442.1;0
}}
}}

Revision as of 11:54, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:69794834..69794871,+p5@Ctdnep1
Mm9::chr11:97857366..97857389,-p3@Arl5c
Mm9::chr1:74283176..74283202,+p2@Arpc2
Mm9::chr4:144836758..144836782,-p1@Tnfrsf1b
Mm9::chr5:106160848..106160866,+p13@Lrrc8d
Mm9::chr5:53981592..53981616,+p3@Rbpj
Mm9::chr6:129132950..129132968,+p@chr6:129132950..129132968
+
Mm9::chr6:129188176..129188217,+p@chr6:129188176..129188217
+
Mm9::chr7:109397876..109397888,-p@chr7:109397876..109397888
-
Mm9::chrX:104344399..104344411,+p9@A630033H20Rik
Mm9::chrX:98460079..98460088,-p@chrX:98460079..98460088
-
Mm9::chrX:98460133..98460154,-p@chrX:98460133..98460154
-
Mm9::chrX:98460249..98460271,-p@chrX:98460249..98460271
-
Mm9::chrX:98461002..98461015,-p@chrX:98461002..98461015
-


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:0050779RNA destabilization0.0498275096566748
GO:0043120tumor necrosis factor binding0.0498275096566748
GO:0005031tumor necrosis factor receptor activity0.0498275096566748
GO:0005035death receptor activity0.0498275096566748
GO:0048505regulation of timing of cell differentiation0.0498275096566748
GO:0040034regulation of development, heterochronic0.0498275096566748



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 cell4.10e-1532
hematopoietic oligopotent progenitor cell4.10e-1532
hematopoietic stem cell4.10e-1532
angioblastic mesenchymal cell4.10e-1532
hematopoietic multipotent progenitor cell4.10e-1532
leukocyte4.40e-1517
nongranular leukocyte4.40e-1517
hematopoietic lineage restricted progenitor cell1.13e-1425
lymphoid lineage restricted progenitor cell2.08e-1412
T cell2.64e-1311
pro-T cell2.64e-1311
lymphocyte5.59e-1313
common lymphoid progenitor5.59e-1313
connective tissue cell6.41e-1346
mesenchymal cell6.41e-1346
mature alpha-beta T cell5.93e-129
alpha-beta T cell5.93e-129
immature T cell5.93e-129
mature T cell5.93e-129
immature alpha-beta T cell5.93e-129
CD4-positive, alpha-beta T cell8.44e-118
motile cell1.94e-1054
nucleate cell8.64e-1016
thymocyte1.34e-086
double negative thymocyte1.34e-086
naive T cell1.34e-086
double-positive, alpha-beta thymocyte1.34e-086
CD4-positive, alpha-beta thymocyte1.34e-086
naive thymus-derived CD4-positive, alpha-beta T cell1.34e-086
DN4 thymocyte1.34e-086
DN1 thymic pro-T cell1.34e-086
DN2 thymocyte1.34e-086
DN3 thymocyte1.34e-086
immature single positive thymocyte1.34e-086
early T lineage precursor1.34e-086
mature CD4 single-positive thymocyte1.34e-086
resting double-positive thymocyte1.34e-086
double-positive blast1.34e-086
CD69-positive double-positive thymocyte1.34e-086
CD69-positive, CD4-positive single-positive thymocyte1.34e-086
CD4-positive, CD8-intermediate double-positive thymocyte1.34e-086
CD24-positive, CD4 single-positive thymocyte1.34e-086

Uber Anatomy
Ontology termp-valuen
hemolymphoid system1.17e-2748
immune system1.17e-2748
hematopoietic system1.08e-2445
blood island1.08e-2445
lateral plate mesoderm6.91e-1887
hemopoietic organ1.15e-1629
immune organ1.15e-1629
mixed endoderm/mesoderm-derived structure2.60e-1635
pharynx6.37e-1524
upper respiratory tract6.37e-1524
chordate pharynx6.37e-1524
pharyngeal arch system6.37e-1524
pharyngeal region of foregut6.37e-1524
thymus2.28e-1423
neck2.28e-1423
respiratory system epithelium2.28e-1423
hemolymphoid system gland2.28e-1423
pharyngeal epithelium2.28e-1423
thymic region2.28e-1423
pharyngeal gland2.28e-1423
entire pharyngeal arch endoderm2.28e-1423
thymus primordium2.28e-1423
early pharyngeal endoderm2.28e-1423
respiratory tract9.38e-1441
gland of gut1.67e-1324
respiratory system3.23e-1342
connective tissue6.41e-1346
segment of respiratory tract1.57e-1227
mesoderm5.94e-11120
mesoderm-derived structure5.94e-11120
presumptive mesoderm5.94e-11120
bone marrow1.35e-0816
organ segment3.00e-0835
craniocervical region7.41e-0836
foregut1.96e-0780
musculoskeletal system2.96e-0732


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)
MA0003.10.934438
MA0004.10.258473
MA0006.10.817804
MA0007.10.689082
MA0009.10.649874
MA0014.10.37055
MA0017.11.43837
MA0019.10.480432
MA0024.10.608636
MA0025.10.873493
MA0027.12.275
MA0028.11.37032
MA0029.10.588275
MA0030.10.594419
MA0031.10.561217
MA0038.10.381016
MA0040.10.661716
MA0041.10.198922
MA0042.10.553522
MA0043.10.74191
MA0046.11.63659
MA0048.10.289404
MA0050.11.43876
MA0051.12.68041
MA0052.10.669354
MA0055.10.0206669
MA0056.10
MA0057.10.78569
MA0058.10.183941
MA0059.10.19314
MA0060.10.0819399
MA0061.11.64064
MA0063.10
MA0066.10.371389
MA0067.10.981551
MA0068.10.271058
MA0069.10.669676
MA0070.11.58777
MA0071.10.289658
MA0072.10.652465
MA0073.10.315764
MA0074.10.340281
MA0076.11.51892
MA0077.10.632005
MA0078.10.418168
MA0081.11.14043
MA0083.10.741151
MA0084.11.30392
MA0087.10.699999
MA0088.10.171343
MA0089.10
MA0090.10.653402
MA0091.10.741628
MA0092.10.653984
MA0093.10.144649
MA0095.10
MA0098.10
MA0100.10.330364
MA0101.10.57968
MA0103.10.477056
MA0105.12.55372
MA0106.11.08833
MA0107.11.45792
MA0108.20.50131
MA0109.10
MA0111.10.242308
MA0113.10.400008
MA0114.10.665298
MA0115.12.94907
MA0116.10.411741
MA0117.10.713754
MA0119.10.580747
MA0122.10.732707
MA0124.10.929684
MA0125.10.857794
MA0130.10
MA0131.10.476296
MA0132.10
MA0133.10
MA0135.10.77683
MA0136.10.357464
MA0139.10.499924
MA0140.10.330266
MA0141.10.511953
MA0142.10.547747
MA0143.10.414534
MA0144.10.674112
MA0145.10.614688
MA0146.10.170737
MA0147.10.107632
MA0148.11.37059
MA0149.10.204102
MA0062.21.53832
MA0035.20.33429
MA0039.20.0846004
MA0138.20.469076
MA0002.20.0664561
MA0137.20.169785
MA0104.20.0740839
MA0047.20.990617
MA0112.20.370361
MA0065.22.14144
MA0150.10.246295
MA0151.10
MA0152.10.380437
MA0153.10.792819
MA0154.10.837005
MA0155.10.423059
MA0156.10.490212
MA0157.10.518122
MA0158.10
MA0159.10.365914
MA0160.10.274172
MA0161.10
MA0162.10.108524
MA0163.11.24995
MA0164.10.357779
MA0080.20.467794
MA0018.20.366212
MA0099.20.463355
MA0079.21.60703
MA0102.21.35579
MA0258.10.301988
MA0259.10.331447
MA0442.10
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