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MCL coexpression mm9:284: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=
|ontology_enrichment_celltype=CL:0000791!1.87e-32!9;CL:0000789!1.87e-32!9;CL:0002420!1.87e-32!9;CL:0002419!1.87e-32!9;CL:0000790!1.87e-32!9;CL:0000084!1.48e-26!11;CL:0000827!1.48e-26!11;CL:0000624!1.74e-25!8;CL:0000838!2.42e-24!12;CL:0000542!1.82e-22!13;CL:0000051!1.82e-22!13;CL:0002031!2.66e-20!25;CL:0002242!3.04e-18!16;CL:0000738!3.65e-17!17;CL:0002087!3.65e-17!17;CL:0000988!9.12e-16!32;CL:0002032!9.12e-16!32;CL:0000037!9.12e-16!32;CL:0000566!9.12e-16!32;CL:0000837!9.12e-16!32;CL:0000893!5.78e-13!6;CL:0002489!5.78e-13!6;CL:0000898!5.78e-13!6;CL:0000809!5.78e-13!6;CL:0000810!5.78e-13!6;CL:0000895!5.78e-13!6;CL:0000808!5.78e-13!6;CL:0000894!5.78e-13!6;CL:0000806!5.78e-13!6;CL:0000807!5.78e-13!6;CL:0000805!5.78e-13!6;CL:0002425!5.78e-13!6;CL:0002436!5.78e-13!6;CL:0002427!5.78e-13!6;CL:0002428!5.78e-13!6;CL:0002429!5.78e-13!6;CL:0002433!5.78e-13!6;CL:0002431!5.78e-13!6;CL:0002432!5.78e-13!6;CL:0002320!8.15e-11!46;CL:0000134!8.15e-11!46;CL:0000625!1.19e-09!1;CL:0000815!3.65e-09!1;CL:0000792!3.65e-09!1;CL:0000219!3.96e-09!54
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002370!2.64e-12!23;UBERON:0000974!2.64e-12!23;UBERON:0004807!2.64e-12!23;UBERON:0005058!2.64e-12!23;UBERON:0003351!2.64e-12!23;UBERON:0009113!2.64e-12!23;UBERON:0003295!2.64e-12!23;UBERON:0009722!2.64e-12!23;UBERON:0005562!2.64e-12!23;UBERON:0007690!2.64e-12!23;UBERON:0006562!8.73e-12!24;UBERON:0003408!8.73e-12!24;UBERON:0001557!8.73e-12!24;UBERON:0001042!8.73e-12!24;UBERON:0008814!8.73e-12!24;UBERON:0009145!8.73e-12!24;UBERON:0002390!7.90e-11!45;UBERON:0003061!7.90e-11!45;UBERON:0002384!8.15e-11!46;UBERON:0000072!1.86e-10!27;UBERON:0002193!4.06e-10!48;UBERON:0002405!4.06e-10!48;UBERON:0004177!1.01e-09!29;UBERON:0005057!1.01e-09!29;UBERON:0000077!5.10e-08!35;UBERON:0000063!5.10e-08!35;UBERON:0007811!8.64e-08!36;UBERON:0000065!8.26e-07!41
|tfbs_overrepresentation_for_novel_motifs=0.0719497,0.0640434,0.220186,1.05672,0.778742,0.324459,0.148388,0.943591,0.263357,0.0042994,0.38953,0.435892,0.115878,0.155782,0.846378,0,0.288299,0.462025,0.00617798,0.241413,0.710633,0.0303668,0.155233,0.255788,0.495614,0.17289,0.348681,0.716363,0.0373647,0.0499757,0.101869,0.367297,0.0974128,0.0697721,0.0292504,0.0079125,0.0899817,0.139162,0.19064,0.0548666,1.52298,0.340818,0.191074,0.122302,0.0262293,0.0859418,0.230231,0.117576,0.133379,0.347605,0.27523,0.190239,0.107542,0.485586,0.500658,0.160159,1.44442,0.13388,0.176454,0.158905,0.351242,0.196469,0.758909,0.266898,0.167068,0.80545,0.621417,0.947606,0.347523,0.807939,0.0538018,0.255354,0.00298617,0.529888,0.073438,0.144287,0.069705,0.222296,0.337634,0.410777,0.258045,0.301475,1.701,0.905356,0.430864,1.34795e-05,0.548383,0.015138,0.233678,1.10402,0.684894,0.435043,0.377655,1.58849,0.01524,0.814454,0.236902,0.379937,0.23041,0.0871454,0.225558,0.367072,0.470627,0.275672,0.274889,0.10429,0.320303,1.22078,0.050559,0.047957,0.52086,0.472153,0.413098,0.125988,0.691366,0.248416,0.00234927,0.0930994,0.28928,0.420265,0.534627,1.29609,0.994733,0.631319,1.75578,0.340552,0.466031,0.372164,0.620047,0.11356,1.15543,0.615552,0.593454,0.503994,0.711262,0.0291867,0.555322,0.342749,0.6661,1.46501,1.07314,0.625675,1.0259,0.375761,0.743723,0.341439,0.656561,1.42588,0.0766814,0.0252905,0.121985,0.000196948,0.486938,0.167204,0.502569,0.558342,0.1909,0.895883,0.248498,0.0755084,0.674799,0.430147,0.903461,2.4239,0.738132,1.51762,0.0891063,0.140344,1.77152e-05
}}

Latest revision as of 15:02, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:118070499..118070503,-p@chr10:118070499..118070503
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Mm9::chr11:3005173..3005182,+p@chr11:3005173..3005182
+
Mm9::chr11:63788797..63788806,-p@chr11:63788797..63788806
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Mm9::chr11:63803193..63803202,+p@chr11:63803193..63803202
+
Mm9::chr11:63803209..63803231,+p@chr11:63803209..63803231
+
Mm9::chr11:63803242..63803245,+p@chr11:63803242..63803245
+
Mm9::chr11:63803269..63803274,+p@chr11:63803269..63803274
+
Mm9::chr11:63803295..63803303,+p@chr11:63803295..63803303
+
Mm9::chr11:63803376..63803385,+p@chr11:63803376..63803385
+
Mm9::chr12:114684617..114684621,+p@chr12:114684617..114684621
+
Mm9::chr17:35868798..35868840,-p@chr17:35868798..35868840
-
Mm9::chr17:5089896..5089901,+p@chr17:5089896..5089901
+
Mm9::chr17:75169401..75169411,+p@chr17:75169401..75169411
+
Mm9::chr18:80794300..80794313,-p@chr18:80794300..80794313
-
Mm9::chr19:11592983..11593024,+p1@Ms4a6b
Mm9::chr19:32261023..32261030,-p@chr19:32261023..32261030
-
Mm9::chr1:130509383..130509420,+p@chr1:130509383..130509420
+
Mm9::chr1:161977100..161977102,-p@chr1:161977100..161977102
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Mm9::chr1:78534537..78534547,+p@chr1:78534537..78534547
+
Mm9::chr2:122294867..122294874,-p@chr2:122294867..122294874
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Mm9::chr4:32335313..32335316,-p@chr4:32335313..32335316
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Mm9::chr4:45421980..45421983,+p@chr4:45421980..45421983
+
Mm9::chr5:107926893..107926904,+p@chr5:107926893..107926904
+
Mm9::chr6:22394429..22394437,-p@chr6:22394429..22394437
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Mm9::chr6:48504656..48504665,-p@chr6:48504656..48504665
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Mm9::chr7:90296900..90296911,+p2@uc009idk.1
Mm9::chr8:35209201..35209215,-p@chr8:35209201..35209215
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Mm9::chr9:110819395..110819404,-p1@Gm590
Mm9::chrX:45451921..45451922,-p@chrX:45451921..45451922
-


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
mature alpha-beta T cell1.87e-329
alpha-beta T cell1.87e-329
immature T cell1.87e-329
mature T cell1.87e-329
immature alpha-beta T cell1.87e-329
T cell1.48e-2611
pro-T cell1.48e-2611
CD4-positive, alpha-beta T cell1.74e-258
lymphoid lineage restricted progenitor cell2.42e-2412
lymphocyte1.82e-2213
common lymphoid progenitor1.82e-2213
hematopoietic lineage restricted progenitor cell2.66e-2025
nucleate cell3.04e-1816
leukocyte3.65e-1717
nongranular leukocyte3.65e-1717
hematopoietic cell9.12e-1632
hematopoietic oligopotent progenitor cell9.12e-1632
hematopoietic stem cell9.12e-1632
angioblastic mesenchymal cell9.12e-1632
hematopoietic multipotent progenitor cell9.12e-1632
thymocyte5.78e-136
double negative thymocyte5.78e-136
naive T cell5.78e-136
double-positive, alpha-beta thymocyte5.78e-136
CD4-positive, alpha-beta thymocyte5.78e-136
naive thymus-derived CD4-positive, alpha-beta T cell5.78e-136
DN4 thymocyte5.78e-136
DN1 thymic pro-T cell5.78e-136
DN2 thymocyte5.78e-136
DN3 thymocyte5.78e-136
immature single positive thymocyte5.78e-136
early T lineage precursor5.78e-136
mature CD4 single-positive thymocyte5.78e-136
resting double-positive thymocyte5.78e-136
double-positive blast5.78e-136
CD69-positive double-positive thymocyte5.78e-136
CD69-positive, CD4-positive single-positive thymocyte5.78e-136
CD4-positive, CD8-intermediate double-positive thymocyte5.78e-136
CD24-positive, CD4 single-positive thymocyte5.78e-136
connective tissue cell8.15e-1146
mesenchymal cell8.15e-1146
CD8-positive, alpha-beta T cell1.19e-091
regulatory T cell3.65e-091
CD4-positive, CD25-positive, alpha-beta regulatory T cell3.65e-091
motile cell3.96e-0954

Uber Anatomy
Ontology termp-valuen
thymus2.64e-1223
neck2.64e-1223
respiratory system epithelium2.64e-1223
hemolymphoid system gland2.64e-1223
pharyngeal epithelium2.64e-1223
thymic region2.64e-1223
pharyngeal gland2.64e-1223
entire pharyngeal arch endoderm2.64e-1223
thymus primordium2.64e-1223
early pharyngeal endoderm2.64e-1223
pharynx8.73e-1224
gland of gut8.73e-1224
upper respiratory tract8.73e-1224
chordate pharynx8.73e-1224
pharyngeal arch system8.73e-1224
pharyngeal region of foregut8.73e-1224
hematopoietic system7.90e-1145
blood island7.90e-1145
connective tissue8.15e-1146
segment of respiratory tract1.86e-1027
hemolymphoid system4.06e-1048
immune system4.06e-1048
hemopoietic organ1.01e-0929
immune organ1.01e-0929
mixed endoderm/mesoderm-derived structure5.10e-0835
organ segment5.10e-0835
craniocervical region8.64e-0836
respiratory tract8.26e-0741


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)
MA0003.15.38126e-06
MA0004.10.305832
MA0006.10.519243
MA0007.10.598973
MA0009.10.388771
MA0014.10.000515153
MA0017.10.0353746
MA0019.11.28283
MA0024.10.353393
MA0025.10.589418
MA0027.11.95996
MA0028.10.0307479
MA0029.10.336166
MA0030.10.341346
MA0031.10.313542
MA0038.10.17284
MA0040.10.399043
MA0041.11.22513
MA0042.10.197223
MA0043.11.18472
MA0046.11.07383
MA0048.10.176557
MA0050.10.111159
MA0051.10.178537
MA0052.10.405693
MA0055.10.0128114
MA0056.10
MA0057.14.80305
MA0058.10.422471
MA0059.10.203408
MA0060.10.056085
MA0061.10.0760325
MA0063.10
MA0066.10.165937
MA0067.10.690195
MA0068.10.0086894
MA0069.10.405974
MA0070.10.397975
MA0071.10.357212
MA0072.10.391015
MA0073.11.6966
MA0074.10.443199
MA0076.10.0413193
MA0077.10.373365
MA0078.10.580287
MA0081.10.0645216
MA0083.10.469091
MA0084.10.999346
MA0087.11.93543
MA0088.10.032575
MA0089.10
MA0090.10.261914
MA0091.10.0979655
MA0092.10.262306
MA0093.10.573856
MA0095.10
MA0098.10
MA0100.10.137416
MA0101.10.0588523
MA0103.10.151812
MA0105.10.0207906
MA0106.10.205373
MA0107.10.0367707
MA0108.20.264668
MA0109.10
MA0111.10.0820143
MA0113.10.186674
MA0114.10.0161534
MA0115.10.472164
MA0116.10.0279031
MA0117.10.44472
MA0119.10.214295
MA0122.10.461557
MA0124.11.5483
MA0125.10.574947
MA0130.10
MA0131.10.244817
MA0132.10
MA0133.10
MA0135.10.501131
MA0136.11.47414
MA0139.10.00733889
MA0140.10.425965
MA0141.10.17205
MA0142.13.13252
MA0143.15.9242
MA0144.11.72089
MA0145.10.000439128
MA0146.14.03018e-05
MA0147.10.0856832
MA0148.10.0995133
MA0149.10.061026
MA0062.20.0705122
MA0035.20.432878
MA0039.20.00733982
MA0138.20.67227
MA0002.20.420289
MA0137.20.383209
MA0104.20.132466
MA0047.20.172355
MA0112.20.000439063
MA0065.20.0399981
MA0150.10.286158
MA0151.10
MA0152.10.513252
MA0153.10.515592
MA0154.10.171274
MA0155.10.0199387
MA0156.12.46991
MA0157.10.762276
MA0158.10
MA0159.10.0935777
MA0160.10.678768
MA0161.10
MA0162.10.000504239
MA0163.14.44471e-06
MA0164.10.15631
MA0080.22.36784
MA0018.20.162257
MA0099.20.661855
MA0079.20.462981
MA0102.21.04989
MA0258.10.0137385
MA0259.10.07771
MA0442.10
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