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MCL coexpression mm9:806: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0000542!9.33e-09!13;CL:0000051!9.33e-09!13;CL:0000838!1.40e-08!12;CL:0000988!4.29e-08!32;CL:0002032!4.29e-08!32;CL:0000037!4.29e-08!32;CL:0000566!4.29e-08!32;CL:0000837!4.29e-08!32;CL:0000084!5.60e-08!11;CL:0000827!5.60e-08!11;CL:0000791!7.55e-07!9;CL:0000789!7.55e-07!9;CL:0002420!7.55e-07!9;CL:0002419!7.55e-07!9;CL:0000790!7.55e-07!9
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004177!4.78e-14!29;UBERON:0005057!4.78e-14!29;UBERON:0000077!2.66e-13!35;UBERON:0002193!1.42e-12!48;UBERON:0002405!1.42e-12!48;UBERON:0002390!2.14e-12!45;UBERON:0003061!2.14e-12!45;UBERON:0000072!3.88e-12!27;UBERON:0001004!4.46e-12!42;UBERON:0000065!7.84e-12!41;UBERON:0003408!8.97e-12!24;UBERON:0002370!1.40e-11!23;UBERON:0000974!1.40e-11!23;UBERON:0004807!1.40e-11!23;UBERON:0005058!1.40e-11!23;UBERON:0003351!1.40e-11!23;UBERON:0009113!1.40e-11!23;UBERON:0003295!1.40e-11!23;UBERON:0009722!1.40e-11!23;UBERON:0005562!1.40e-11!23;UBERON:0007690!1.40e-11!23;UBERON:0006562!7.89e-11!24;UBERON:0001557!7.89e-11!24;UBERON:0001042!7.89e-11!24;UBERON:0008814!7.89e-11!24;UBERON:0009145!7.89e-11!24;UBERON:0001041!8.46e-11!80;UBERON:0000926!1.00e-09!120;UBERON:0004120!1.00e-09!120;UBERON:0006603!1.00e-09!120;UBERON:0000153!4.23e-09!43;UBERON:0003081!6.44e-09!87;UBERON:0000475!9.03e-09!150;UBERON:0001048!9.47e-08!134;UBERON:0007811!1.63e-07!36
|tfbs_overrepresentation_for_novel_motifs=0.354643,0.433653,0.330161,0.394491,0.645379,0.40827,0.495658,0.146465,0.468136,0.314043,0.453212,0.484001,0.146657,0.507558,0.24249,0,0.696644,0.22065,0.419123,0.902262,0.296085,0.047629,0.50668,0.226287,0.895255,0.534339,0.402559,0.428336,0.268347,0.656973,0.414842,0.796599,0.624261,0.364174,0.681042,1.0491,0.210533,1.20775,1.06548,0.500908,0.224094,0.419787,0.163087,0.244285,0.812975,0.383899,0.618203,0.443479,0.573356,0.271021,0.679429,0.560572,0.633942,0.937018,0.954342,0.514504,0.279148,2.06677,0.12126,1.27615,0.776777,1.39755,0.163832,0.668331,1.30341,0.708248,1.08987,1.43807,0.772155,1.29123,0.31262,0.151245,0.0512949,0.987652,0.371787,0.349958,0.735293,1.47595,0.759798,0.299972,0.152219,1.6986,0.568383,0.14134,0.873141,0.395495,0.092683,0.657454,0.623015,1.60001,1.15927,0.878077,0.809272,0.232894,0.551605,0.17334,0.444003,0.812053,0.618454,0.0816605,1.13987,0.796322,0.919715,0.680015,0.678976,0.419366,0.737915,0.439611,0.30446,0.806647,0.348012,0.921485,0.301014,2.02173,1.16629,0.633313,0.265919,1.02946,0.697928,0.597328,0.993019,0.647706,0.536114,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,0.235546,0.90286,1.00644,1.05894,0.527782,1.18781,0.398576,0.362565,0.421136,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,0.672593,0.420221,0.621266,1.92834,0.364791,0.229209,0.32395,1.02444,0.938577,1.01208,0.526881,1.01974,0.561556,1.30227,0.352329,0.950885,1.1483,0.872292,0.763895,0.345891,0.669337,1.29138,0.602679,0.482466,0.442118
|tfbs_overrepresentation_jaspar=MA0003.1;0.458525,MA0004.1;0.394951,MA0006.1;0.670874,MA0007.1;0.38073,MA0009.1;0.82278,MA0014.1;0.67203,MA0017.1;0.26239,MA0019.1;1.551,MA0024.1;0.779446,MA0025.1;1.05446,MA0027.1;2.46647,MA0028.1;4.57359,MA0029.1;0.757957,MA0030.1;0.764448,MA0031.1;0.729293,MA0038.1;0.534262,MA0040.1;0.835181,MA0041.1;0.323687,MA0042.1;0.311486,MA0043.1;0.918718,MA0046.1;0.858391,MA0048.1;0.589612,MA0050.1;0.431976,MA0051.1;0.542972,MA0052.1;0.84317,MA0055.1;0.0882028,MA0056.1;0,MA0057.1;0.258928,MA0058.1;0.305206,MA0059.1;0.316585,MA0060.1;0.9744,MA0061.1;0.194456,MA0063.1;0,MA0066.1;0.523573,MA0067.1;1.16502,MA0068.1;0.077274,MA0069.1;0.843506,MA0070.1;0.833895,MA0071.1;0.431174,MA0072.1;0.825495,MA0073.1;0.0431817,MA0074.1;0.488775,MA0076.1;2.9863,MA0077.1;0.804033,MA0078.1;0.575205,MA0081.1;0.897217,MA0083.1;0.917931,MA0084.1;1.49188,MA0087.1;0.87515,MA0088.1;0.18495,MA0089.1;0,MA0090.1;0.951436,MA0091.1;0.407455,MA0092.1;0.362847,MA0093.1;0.2553,MA0095.1;0,MA0098.1;0,MA0100.1;1.20151,MA0101.1;0.867731,MA0103.1;0.272167,MA0105.1;0.720048,MA0106.1;0.582805,MA0107.1;0.73569,MA0108.2;0.665343,MA0109.1;0,MA0111.1;0.375908,MA0113.1;0.555251,MA0114.1;0.561811,MA0115.1;0.921497,MA0116.1;0.238371,MA0117.1;0.88947,MA0119.1;0.325434,MA0122.1;0.909168,MA0124.1;1.11203,MA0125.1;1.03833,MA0130.1;0,MA0131.1;0.638414,MA0132.1;0,MA0133.1;0,MA0135.1;0.954884,MA0136.1;0.508047,MA0139.1;0.143341,MA0140.1;0.477483,MA0141.1;0.29014,MA0142.1;0.714976,MA0143.1;0.571221,MA0144.1;0.195095,MA0145.1;1.17902,MA0146.1;0.30073,MA0147.1;0.593505,MA0148.1;0.410398,MA0149.1;0.330018,MA0062.2;3.09014,MA0035.2;0.482026,MA0039.2;1.08337,MA0138.2;0.630612,MA0002.2;0.447007,MA0137.2;0.287486,MA0104.2;0.476119,MA0047.2;0.533516,MA0112.2;0.0543294,MA0065.2;0.0545595,MA0150.1;0.380623,MA0151.1;0,MA0152.1;0.53362,MA0153.1;0.971406,MA0154.1;0.276788,MA0155.1;0.490492,MA0156.1;0.763978,MA0157.1;0.683365,MA0158.1;0,MA0159.1;0.214506,MA0160.1;0.413266,MA0161.1;0,MA0162.1;0.582797,MA0163.1;1.15194,MA0164.1;0.508398,MA0080.2;0.737531,MA0018.2;0.51781,MA0099.2;0.624421,MA0079.2;0.253208,MA0102.2;1.5442,MA0258.1;0.180934,MA0259.1;0.196451,MA0442.1;0
}}

Latest revision as of 15:55, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:4824467..4824478,+p2@0610009D07Rik
Mm9::chr13:38129104..38129179,+p1@Riok1
Mm9::chr1:135028028..135028050,+p4@Ppp1r15b
Mm9::chr2:3630751..3630772,+p1@Fam107b
Mm9::chr2:3697194..3697210,+p@chr2:3697194..3697210
+
Mm9::chr6:83276065..83276079,+p2@Mob1a
Mm9::chr8:107694628..107694659,+p1@Cbfb
Mm9::chrX:48194566..48194598,+p1@2610018G03Rik
Mm9::chrX:48194611..48194626,+p2@2610018G03Rik


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:0000164protein phosphatase type 1 complex0.0405412808853339



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>

Uber Anatomy
Ontology termp-valuen
hemopoietic organ4.78e-1429
immune organ4.78e-1429
mixed endoderm/mesoderm-derived structure2.66e-1335
hemolymphoid system1.42e-1248
immune system1.42e-1248
hematopoietic system2.14e-1245
blood island2.14e-1245
segment of respiratory tract3.88e-1227
respiratory system4.46e-1242
respiratory tract7.84e-1241
gland of gut8.97e-1224
thymus1.40e-1123
neck1.40e-1123
respiratory system epithelium1.40e-1123
hemolymphoid system gland1.40e-1123
pharyngeal epithelium1.40e-1123
thymic region1.40e-1123
pharyngeal gland1.40e-1123
entire pharyngeal arch endoderm1.40e-1123
thymus primordium1.40e-1123
early pharyngeal endoderm1.40e-1123
pharynx7.89e-1124
upper respiratory tract7.89e-1124
chordate pharynx7.89e-1124
pharyngeal arch system7.89e-1124
pharyngeal region of foregut7.89e-1124
foregut8.46e-1180
mesoderm1.00e-09120
mesoderm-derived structure1.00e-09120
presumptive mesoderm1.00e-09120
anterior region of body4.23e-0943
lateral plate mesoderm6.44e-0987
organism subdivision9.03e-09150
primordium9.47e-08134
craniocervical region1.63e-0736


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)
MA0003.10.458525
MA0004.10.394951
MA0006.10.670874
MA0007.10.38073
MA0009.10.82278
MA0014.10.67203
MA0017.10.26239
MA0019.11.551
MA0024.10.779446
MA0025.11.05446
MA0027.12.46647
MA0028.14.57359
MA0029.10.757957
MA0030.10.764448
MA0031.10.729293
MA0038.10.534262
MA0040.10.835181
MA0041.10.323687
MA0042.10.311486
MA0043.10.918718
MA0046.10.858391
MA0048.10.589612
MA0050.10.431976
MA0051.10.542972
MA0052.10.84317
MA0055.10.0882028
MA0056.10
MA0057.10.258928
MA0058.10.305206
MA0059.10.316585
MA0060.10.9744
MA0061.10.194456
MA0063.10
MA0066.10.523573
MA0067.11.16502
MA0068.10.077274
MA0069.10.843506
MA0070.10.833895
MA0071.10.431174
MA0072.10.825495
MA0073.10.0431817
MA0074.10.488775
MA0076.12.9863
MA0077.10.804033
MA0078.10.575205
MA0081.10.897217
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.10.18495
MA0089.10
MA0090.10.951436
MA0091.10.407455
MA0092.10.362847
MA0093.10.2553
MA0095.10
MA0098.10
MA0100.11.20151
MA0101.10.867731
MA0103.10.272167
MA0105.10.720048
MA0106.10.582805
MA0107.10.73569
MA0108.20.665343
MA0109.10
MA0111.10.375908
MA0113.10.555251
MA0114.10.561811
MA0115.10.921497
MA0116.10.238371
MA0117.10.88947
MA0119.10.325434
MA0122.10.909168
MA0124.11.11203
MA0125.11.03833
MA0130.10
MA0131.10.638414
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.10.508047
MA0139.10.143341
MA0140.10.477483
MA0141.10.29014
MA0142.10.714976
MA0143.10.571221
MA0144.10.195095
MA0145.11.17902
MA0146.10.30073
MA0147.10.593505
MA0148.10.410398
MA0149.10.330018
MA0062.23.09014
MA0035.20.482026
MA0039.21.08337
MA0138.20.630612
MA0002.20.447007
MA0137.20.287486
MA0104.20.476119
MA0047.20.533516
MA0112.20.0543294
MA0065.20.0545595
MA0150.10.380623
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.276788
MA0155.10.490492
MA0156.10.763978
MA0157.10.683365
MA0158.10
MA0159.10.214506
MA0160.10.413266
MA0161.10
MA0162.10.582797
MA0163.11.15194
MA0164.10.508398
MA0080.20.737531
MA0018.20.51781
MA0099.20.624421
MA0079.20.253208
MA0102.21.5442
MA0258.10.180934
MA0259.10.196451
MA0442.10
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