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MCL coexpression mm9:267: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=UBERON:0000065!1.44e-19!41;UBERON:0001004!6.22e-19!42;UBERON:0002370!2.06e-18!23;UBERON:0000974!2.06e-18!23;UBERON:0004807!2.06e-18!23;UBERON:0005058!2.06e-18!23;UBERON:0003351!2.06e-18!23;UBERON:0009113!2.06e-18!23;UBERON:0003295!2.06e-18!23;UBERON:0009722!2.06e-18!23;UBERON:0005562!2.06e-18!23;UBERON:0007690!2.06e-18!23;UBERON:0006562!1.94e-17!24;UBERON:0003408!1.94e-17!24;UBERON:0001557!1.94e-17!24;UBERON:0001042!1.94e-17!24;UBERON:0008814!1.94e-17!24;UBERON:0009145!1.94e-17!24;UBERON:0002193!4.97e-17!48;UBERON:0002405!4.97e-17!48;UBERON:0002390!5.22e-17!45;UBERON:0003061!5.22e-17!45;UBERON:0004177!1.10e-16!29;UBERON:0005057!1.10e-16!29;UBERON:0000072!5.87e-15!27;UBERON:0000077!1.58e-14!35;UBERON:0007811!3.92e-11!36;UBERON:0000063!1.86e-10!35;UBERON:0005911!7.80e-10!69;UBERON:0001041!9.47e-10!80;UBERON:0002384!1.02e-08!46;UBERON:0000153!1.52e-08!43;UBERON:0003081!1.50e-07!87;UBERON:0000490!1.72e-07!66
|tfbs_overrepresentation_for_novel_motifs=0.487079,1.63438,0.432388,0.0803981,0.0895641,0.293623,1.34037,0.577188,0.618787,1.65458,0.355895,0.400509,0.839352,0.857752,0.252098,0,0.740836,0.0186281,0.320534,0.318509,0.359144,1.00854,0.140634,0.0883885,1.19118,1.48234,0.29651,1.61783,0.302369,0.185929,0.627721,0.345924,0.402091,0.243363,0.103182,0.0777,0.933467,0.125378,0.546738,1.71548,0.684118,0.639618,0.511863,0.255497,0.58441,0.261432,0.6098,0.105003,0.100392,0.30772,0.711629,0.174075,0.294051,0.462148,0.477006,0.875514,0.324148,0.767045,0.271373,0.443095,0.330215,0.531848,0.119176,0.692928,0.462592,0.760654,0.596353,0.920398,0.871514,0.781435,1.07824,0.21646,0.844989,0.505848,0.626532,0.569165,0.0550687,0.204903,0.316915,0.0414786,0.218909,0.28165,0.179134,0.192046,0.408287,3.64643,0.758515,0.18626,1.81307,1.07627,0.659258,0.412394,0.356069,0.0215347,1.13529,0.133345,0.031133,0.358304,1.14813,0.139752,0.0164145,0.345703,0.44741,0.25656,0.710864,0.638602,0.299999,0.10296,0.165666,1.01049,0.817447,1.13982,0.0418408,1.75978,0.665677,0.0851703,1.91944,0.587754,0.743023,0.61238,1.2719,1.22681,0.158574,0.204297,0.715313,0.319766,0.138785,0.35069,0.594996,0.239081,0.433157,0.953835,1.3952,0.153414,0.685415,0.0991348,0.234265,0.311081,0.640623,1.43657,1.04548,0.600569,0.16595,0.354213,0.25114,0.0929729,0.214675,1.39749,0.237053,1.04011,1.59631,1.12209,0.46348,0.752137,0.464961,0.533955,0.174709,1.17873,0.0615652,2.38821,0.649247,0.407582,0.32011,1.23127,0.694619,0.148453,0.192381,0.126498,2.45114
|tfbs_overrepresentation_jaspar=MA0003.1;3.21441,MA0004.1;2.01092,MA0006.1;1.95094,MA0007.1;0.257336,MA0009.1;0.366963,MA0014.1;3.32274,MA0017.1;0.0294752,MA0019.1;0.650431,MA0024.1;0.332319,MA0025.1;1.38677,MA0027.1;1.93116,MA0028.1;0.490457,MA0029.1;0.315482,MA0030.1;0.320542,MA0031.1;0.293406,MA0038.1;0.157421,MA0040.1;0.377038,MA0041.1;0.0501054,MA0042.1;0.173505,MA0043.1;0.446565,MA0046.1;0.396073,MA0048.1;0.581576,MA0050.1;0.326024,MA0051.1;0.162867,MA0052.1;0.383564,MA0055.1;1.59112,MA0056.1;0,MA0057.1;0.954738,MA0058.1;3.76089,MA0059.1;2.05913,MA0060.1;0.0454236,MA0061.1;1.56656,MA0063.1;0,MA0066.1;0.898799,MA0067.1;0.664516,MA0068.1;0.060674,MA0069.1;0.383839,MA0070.1;0.37599,MA0071.1;0.667184,MA0072.1;0.369163,MA0073.1;0.00597862,MA0074.1;0.130125,MA0076.1;0.139184,MA0077.1;0.927798,MA0078.1;0.540438,MA0081.1;0.204366,MA0083.1;0.445897,MA0084.1;0.971934,MA0087.1;0.409958,MA0088.1;0.0549758,MA0089.1;0,MA0090.1;0.867207,MA0091.1;0.0866349,MA0092.1;0.234618,MA0093.1;3.79518,MA0095.1;0,MA0098.1;0,MA0100.1;0.391104,MA0101.1;2.11893,MA0103.1;0.566813,MA0105.1;6.25608,MA0106.1;0.552556,MA0107.1;3.31921,MA0108.2;0.245881,MA0109.1;0,MA0111.1;0.251142,MA0113.1;0.170658,MA0114.1;0.0614218,MA0115.1;0.448923,MA0116.1;0.24435,MA0117.1;0.42191,MA0119.1;1.6001,MA0122.1;1.11729,MA0124.1;0.616327,MA0125.1;0.55037,MA0130.1;0,MA0131.1;0.64304,MA0132.1;0,MA0133.1;0,MA0135.1;0.477472,MA0136.1;0.436338,MA0139.1;2.26552,MA0140.1;0.123662,MA0141.1;0.150112,MA0142.1;0.282551,MA0143.1;0.534111,MA0144.1;0.0633709,MA0145.1;0.340402,MA0146.1;0.68482,MA0147.1;4.29757,MA0148.1;0.617074,MA0149.1;0.0525422,MA0062.2;0.610483,MA0035.2;0.126246,MA0039.2;2.74137,MA0138.2;0.221177,MA0002.2;0.57298,MA0137.2;0.0372603,MA0104.2;3.46047,MA0047.2;0.475155,MA0112.2;1.41798,MA0065.2;0.129117,MA0150.1;0.257198,MA0151.1;0,MA0152.1;0.475315,MA0153.1;0.491737,MA0154.1;0.786364,MA0155.1;1.04221,MA0156.1;0.588508,MA0157.1;0.259017,MA0158.1;0,MA0159.1;0.0785092,MA0160.1;0.623941,MA0161.1;0,MA0162.1;2.59762,MA0163.1;1.58136,MA0164.1;0.141659,MA0080.2;0.874029,MA0018.2;1.42148,MA0099.2;0.619984,MA0079.2;1.09873,MA0102.2;1.0223,MA0258.1;0.50247,MA0259.1;1.19432,MA0442.1;0
}}

Latest revision as of 15:00, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:18724766..18724782,-p@chr10:18724766..18724782
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Mm9::chr10:18735010..18735015,-p6@Tnfaip3
Mm9::chr10:18735109..18735123,-p2@Tnfaip3
Mm9::chr10:18735153..18735185,-p1@Tnfaip3
Mm9::chr10:5958538..5958568,+p1@Zbtb2
Mm9::chr10:92628684..92628719,-p@chr10:92628684..92628719
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Mm9::chr11:120435018..120435029,-p7@P4hb
Mm9::chr12:114099097..114099178,-p1@Gpr132
Mm9::chr12:60320433..60320481,-p1@Fbxo33
Mm9::chr14:32149981..32149992,+p3@Capn7
Mm9::chr15:101084397..101084429,-p@chr15:101084397..101084429
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Mm9::chr16:78576894..78576911,-p1@D16Ertd472e
Mm9::chr16:78576927..78576941,-p3@D16Ertd472e
Mm9::chr17:71825231..71825243,-p@chr17:71825231..71825243
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Mm9::chr17:71948007..71948018,-p2@ENSMUST00000137830
Mm9::chr19:30105105..30105124,+p2@Uhrf2
Mm9::chr19:30105132..30105143,+p3@Uhrf2
Mm9::chr1:162836606..162836631,+p2@Rc3h1
Mm9::chr2:126501847..126501876,-p5@Gabpb1
Mm9::chr3:152059025..152059046,+p4@Gm8261
p4@Zzz3
Mm9::chr4:102242999..102243006,+p17@Pde4b
Mm9::chr4:48058102..48058110,+p5@Nr4a3
Mm9::chr4:8738493..8738504,+p@chr4:8738493..8738504
+
Mm9::chr4:8738510..8738524,+p@chr4:8738510..8738524
+
Mm9::chr5:52581099..52581110,+p@chr5:52581099..52581110
+
Mm9::chr7:148042601..148042621,-p2@Bet1l
Mm9::chr7:150812280..150812293,+p@chr7:150812280..150812293
+
Mm9::chr7:51053393..51053466,+p1@Klk8
Mm9::chr7:71083729..71083742,-p4@Klf13
Mm9::chr8:87501773..87501787,-p@chr8:87501773..87501787
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Mm9::chr9:45983558..45983575,-p@chr9:45983558..45983575
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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 cell6.15e-1512
mature alpha-beta T cell2.55e-149
alpha-beta T cell2.55e-149
immature T cell2.55e-149
mature T cell2.55e-149
immature alpha-beta T cell2.55e-149
lymphocyte1.41e-1313
common lymphoid progenitor1.41e-1313
T cell1.47e-1311
pro-T cell1.47e-1311
hematopoietic cell4.35e-1332
hematopoietic oligopotent progenitor cell4.35e-1332
hematopoietic stem cell4.35e-1332
angioblastic mesenchymal cell4.35e-1332
hematopoietic multipotent progenitor cell4.35e-1332
CD4-positive, alpha-beta T cell8.40e-138
thymocyte7.20e-106
double negative thymocyte7.20e-106
naive T cell7.20e-106
double-positive, alpha-beta thymocyte7.20e-106
CD4-positive, alpha-beta thymocyte7.20e-106
naive thymus-derived CD4-positive, alpha-beta T cell7.20e-106
DN4 thymocyte7.20e-106
DN1 thymic pro-T cell7.20e-106
DN2 thymocyte7.20e-106
DN3 thymocyte7.20e-106
immature single positive thymocyte7.20e-106
early T lineage precursor7.20e-106
mature CD4 single-positive thymocyte7.20e-106
resting double-positive thymocyte7.20e-106
double-positive blast7.20e-106
CD69-positive double-positive thymocyte7.20e-106
CD69-positive, CD4-positive single-positive thymocyte7.20e-106
CD4-positive, CD8-intermediate double-positive thymocyte7.20e-106
CD24-positive, CD4 single-positive thymocyte7.20e-106
leukocyte9.45e-1017
nongranular leukocyte9.45e-1017
connective tissue cell1.02e-0846
mesenchymal cell1.02e-0846
nucleate cell1.14e-0716
hematopoietic lineage restricted progenitor cell1.92e-0725

Uber Anatomy
Ontology termp-valuen
respiratory tract1.44e-1941
respiratory system6.22e-1942
thymus2.06e-1823
neck2.06e-1823
respiratory system epithelium2.06e-1823
hemolymphoid system gland2.06e-1823
pharyngeal epithelium2.06e-1823
thymic region2.06e-1823
pharyngeal gland2.06e-1823
entire pharyngeal arch endoderm2.06e-1823
thymus primordium2.06e-1823
early pharyngeal endoderm2.06e-1823
pharynx1.94e-1724
gland of gut1.94e-1724
upper respiratory tract1.94e-1724
chordate pharynx1.94e-1724
pharyngeal arch system1.94e-1724
pharyngeal region of foregut1.94e-1724
hemolymphoid system4.97e-1748
immune system4.97e-1748
hematopoietic system5.22e-1745
blood island5.22e-1745
hemopoietic organ1.10e-1629
immune organ1.10e-1629
segment of respiratory tract5.87e-1527
mixed endoderm/mesoderm-derived structure1.58e-1435
craniocervical region3.92e-1136
organ segment1.86e-1035
endo-epithelium7.80e-1069
foregut9.47e-1080
connective tissue1.02e-0846
anterior region of body1.52e-0843
lateral plate mesoderm1.50e-0787
unilaminar epithelium1.72e-0766


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)
MA0003.13.21441
MA0004.12.01092
MA0006.11.95094
MA0007.10.257336
MA0009.10.366963
MA0014.13.32274
MA0017.10.0294752
MA0019.10.650431
MA0024.10.332319
MA0025.11.38677
MA0027.11.93116
MA0028.10.490457
MA0029.10.315482
MA0030.10.320542
MA0031.10.293406
MA0038.10.157421
MA0040.10.377038
MA0041.10.0501054
MA0042.10.173505
MA0043.10.446565
MA0046.10.396073
MA0048.10.581576
MA0050.10.326024
MA0051.10.162867
MA0052.10.383564
MA0055.11.59112
MA0056.10
MA0057.10.954738
MA0058.13.76089
MA0059.12.05913
MA0060.10.0454236
MA0061.11.56656
MA0063.10
MA0066.10.898799
MA0067.10.664516
MA0068.10.060674
MA0069.10.383839
MA0070.10.37599
MA0071.10.667184
MA0072.10.369163
MA0073.10.00597862
MA0074.10.130125
MA0076.10.139184
MA0077.10.927798
MA0078.10.540438
MA0081.10.204366
MA0083.10.445897
MA0084.10.971934
MA0087.10.409958
MA0088.10.0549758
MA0089.10
MA0090.10.867207
MA0091.10.0866349
MA0092.10.234618
MA0093.13.79518
MA0095.10
MA0098.10
MA0100.10.391104
MA0101.12.11893
MA0103.10.566813
MA0105.16.25608
MA0106.10.552556
MA0107.13.31921
MA0108.20.245881
MA0109.10
MA0111.10.251142
MA0113.10.170658
MA0114.10.0614218
MA0115.10.448923
MA0116.10.24435
MA0117.10.42191
MA0119.11.6001
MA0122.11.11729
MA0124.10.616327
MA0125.10.55037
MA0130.10
MA0131.10.64304
MA0132.10
MA0133.10
MA0135.10.477472
MA0136.10.436338
MA0139.12.26552
MA0140.10.123662
MA0141.10.150112
MA0142.10.282551
MA0143.10.534111
MA0144.10.0633709
MA0145.10.340402
MA0146.10.68482
MA0147.14.29757
MA0148.10.617074
MA0149.10.0525422
MA0062.20.610483
MA0035.20.126246
MA0039.22.74137
MA0138.20.221177
MA0002.20.57298
MA0137.20.0372603
MA0104.23.46047
MA0047.20.475155
MA0112.21.41798
MA0065.20.129117
MA0150.10.257198
MA0151.10
MA0152.10.475315
MA0153.10.491737
MA0154.10.786364
MA0155.11.04221
MA0156.10.588508
MA0157.10.259017
MA0158.10
MA0159.10.0785092
MA0160.10.623941
MA0161.10
MA0162.12.59762
MA0163.11.58136
MA0164.10.141659
MA0080.20.874029
MA0018.21.42148
MA0099.20.619984
MA0079.21.09873
MA0102.21.0223
MA0258.10.50247
MA0259.11.19432
MA0442.10
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