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MCL coexpression mm9:1862: Difference between revisions

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{{MCL_coexpression_mm9
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DNA specific endodeoxyribonuclease activity;0.0129841669862488;227525!GO:0008409;5'-3' exonuclease activity;0.0324533040229507;227525!GO:0004520;endodeoxyribonuclease activity;0.0340461036786531;227525!GO:0032200;telomere organization and biogenesis;0.0340461036786531;227525!GO:0000723;telomere maintenance;0.0340461036786531;227525!GO:0004536;deoxyribonuclease activity;0.0340461036786531;227525!GO:0006302;double-strand break repair;0.0340461036786531;227525!GO:0010212;response to ionizing 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|gostat_on_MCL_coexpression=GO:0000014;single-stranded DNA specific endodeoxyribonuclease activity;0.0129841669862488;227525!GO:0008409;5'-3' exonuclease activity;0.0324533040229507;227525!GO:0004520;endodeoxyribonuclease activity;0.0340461036786531;227525!GO:0032200;telomere organization and biogenesis;0.0340461036786531;227525!GO:0000723;telomere maintenance;0.0340461036786531;227525!GO:0004536;deoxyribonuclease activity;0.0340461036786531;227525!GO:0006302;double-strand break repair;0.0340461036786531;227525!GO:0010212;response to ionizing radiation;0.0340461036786531;227525!
|ontology_enrichment_celltype=CL:0000988!2.69e-09!32;CL:0002032!2.69e-09!32;CL:0000037!2.69e-09!32;CL:0000566!2.69e-09!32;CL:0000837!2.69e-09!32;CL:0002031!5.90e-08!25;CL:0000738!7.13e-08!17;CL:0002087!7.13e-08!17;CL:0000838!2.86e-07!12;CL:0002320!3.38e-07!46;CL:0000134!3.38e-07!46;CL:0000791!8.39e-07!9;CL:0000789!8.39e-07!9;CL:0002420!8.39e-07!9;CL:0002419!8.39e-07!9;CL:0000790!8.39e-07!9;CL:0000542!9.18e-07!13;CL:0000051!9.18e-07!13
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!2.96e-17!48;UBERON:0002405!2.96e-17!48;UBERON:0002390!1.85e-16!45;UBERON:0003061!1.85e-16!45;UBERON:0003081!5.54e-11!87;UBERON:0000077!5.17e-10!35;UBERON:0004177!5.70e-10!29;UBERON:0005057!5.70e-10!29;UBERON:0001041!1.14e-09!80;UBERON:0005911!1.77e-08!69;UBERON:0003929!5.19e-08!55;UBERON:0000926!8.27e-08!120;UBERON:0004120!8.27e-08!120;UBERON:0006603!8.27e-08!120;UBERON:0003408!8.66e-08!24;UBERON:0001474!1.17e-07!22;UBERON:0004765!1.17e-07!22;UBERON:0001434!1.17e-07!22;UBERON:0002370!1.42e-07!23;UBERON:0000974!1.42e-07!23;UBERON:0004807!1.42e-07!23;UBERON:0005058!1.42e-07!23;UBERON:0003351!1.42e-07!23;UBERON:0009113!1.42e-07!23;UBERON:0003295!1.42e-07!23;UBERON:0009722!1.42e-07!23;UBERON:0005562!1.42e-07!23;UBERON:0007690!1.42e-07!23;UBERON:0000490!1.59e-07!66;UBERON:0006562!1.71e-07!24;UBERON:0001557!1.71e-07!24;UBERON:0001042!1.71e-07!24;UBERON:0008814!1.71e-07!24;UBERON:0009145!1.71e-07!24;UBERON:0002371!2.00e-07!16;UBERON:0002530!2.48e-07!65;UBERON:0002204!3.23e-07!32;UBERON:0002384!3.38e-07!46
|tfbs_overrepresentation_for_novel_motifs=0.641384,0.801438,0.612053,0.688265,1.21364,0.704257,0.803568,0.370124,0.381467,0.162942,0.755749,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,0.352304,0.24402,0.570433,0.197567,0.815872,0.481455,0.620553,0.846564,0.342316,0.727368,0.535752,0.290745,0.711848,1.12823,0.471365,0.318879,1.2563,0.089443,0.460474,0.786577,0.434783,0.40068,0.478558,0.717547,0.185353,0.504971,0.0986756,0.675898,0.938241,0.744678,0.162985,0.539131,1.0041,0.875451,0.282443,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,0.205546,1.32691,0.323563,0.310084,0.318792,0.926147,1.08947,0.575233,0.986898,1.04072,0.884013,0.362446,1.20828,0.377699,0.40635,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.961641,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,1.4032,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,0.143825,0.692434,1.02384,0.456123,1.33244,2.22508,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,1.56752,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.293812,0.184289,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,0.280875
|tfbs_overrepresentation_jaspar=MA0003.1;0.142214,MA0004.1;0.6888,MA0006.1;0.497533,MA0007.1;1.61215,MA0009.1;1.15569,MA0014.1;0.276754,MA0017.1;0.528196,MA0019.1;0.964875,MA0024.1;1.11019,MA0025.1;1.39562,MA0027.1;2.81824,MA0028.1;1.26991,MA0029.1;1.08753,MA0030.1;1.09438,MA0031.1;1.05719,MA0038.1;0.846479,MA0040.1;1.16866,MA0041.1;0.604221,MA0042.1;0.589368,MA0043.1;1.25564,MA0046.1;1.1929,MA0048.1;1.35097,MA0050.1;0.731539,MA0051.1;0.856094,MA0052.1;1.17701,MA0055.1;1.86956,MA0056.1;0,MA0057.1;0.251896,MA0058.1;0.581673,MA0059.1;0.59559,MA0060.1;1.04037,MA0061.1;0.438628,MA0063.1;0,MA0066.1;0.834648,MA0067.1;1.50873,MA0068.1;0.256913,MA0069.1;1.17737,MA0070.1;1.16732,MA0071.1;0.73062,MA0072.1;1.15853,MA0073.1;0.00221226,MA0074.1;0.795862,MA0076.1;1.35592,MA0077.1;1.13603,MA0078.1;0.891476,MA0081.1;0.621611,MA0083.1;1.25482,MA0084.1;1.84013,MA0087.1;1.21037,MA0088.1;0.201215,MA0089.1;0,MA0090.1;0.650768,MA0091.1;0.703314,MA0092.1;1.56822,MA0093.1;1.29026,MA0095.1;0,MA0098.1;0,MA0100.1;0.783305,MA0101.1;0.605676,MA0103.1;0.540576,MA0105.1;0.313353,MA0106.1;0.899777,MA0107.1;0.533522,MA0108.2;0.989014,MA0109.1;0,MA0111.1;0.666525,MA0113.1;0.869608,MA0114.1;0.43587,MA0115.1;1.25852,MA0116.1;0.497293,MA0117.1;1.22527,MA0119.1;1.47447,MA0122.1;1.24573,MA0124.1;1.45461,MA0125.1;1.37907,MA0130.1;0,MA0131.1;0.960068,MA0132.1;0,MA0133.1;0,MA0135.1;1.29308,MA0136.1;0.817395,MA0139.1;0.365453,MA0140.1;0.78318,MA0141.1;0.563066,MA0142.1;1.04199,MA0143.1;0.887119,MA0144.1;1.95888,MA0145.1;0.608454,MA0146.1;0.313734,MA0147.1;0.453952,MA0148.1;0.706718,MA0149.1;0.611881,MA0062.2;0.856416,MA0035.2;0.788288,MA0039.2;0.731226,MA0138.2;0.951653,MA0002.2;0.368961,MA0137.2;0.559766,MA0104.2;0.386166,MA0047.2;0.845655,MA0112.2;0.211985,MA0065.2;0.212467,MA0150.1;0.67206,MA0151.1;0,MA0152.1;0.84577,MA0153.1;1.31015,MA0154.1;0.263609,MA0155.1;0.650923,MA0156.1;1.35382,MA0157.1;1.0083,MA0158.1;0,MA0159.1;0.465802,MA0160.1;0.71003,MA0161.1;0,MA0162.1;0.10667,MA0163.1;0.0996272,MA0164.1;0.817786,MA0080.2;1.32296,MA0018.2;0.828253,MA0099.2;0.944966,MA0079.2;0.190089,MA0102.2;1.8929,MA0258.1;0.419871,MA0259.1;0.441366,MA0442.1;0
}}

Latest revision as of 17:37, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:110601850..110601867,+p1@Osbpl8
Mm9::chr1:173770688..173770701,+p4@Cd84
Mm9::chr1:173770738..173770772,+p1@Cd84
Mm9::chr2:3341395..3341479,+p1@Dclre1c


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:0000014single-stranded DNA specific endodeoxyribonuclease activity0.0129841669862488
GO:00084095'-3' exonuclease activity0.0324533040229507
GO:0004520endodeoxyribonuclease activity0.0340461036786531
GO:0032200telomere organization and biogenesis0.0340461036786531
GO:0000723telomere maintenance0.0340461036786531
GO:0004536deoxyribonuclease activity0.0340461036786531
GO:0006302double-strand break repair0.0340461036786531
GO:0010212response to ionizing radiation0.0340461036786531



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
hemolymphoid system2.96e-1748
immune system2.96e-1748
hematopoietic system1.85e-1645
blood island1.85e-1645
lateral plate mesoderm5.54e-1187
mixed endoderm/mesoderm-derived structure5.17e-1035
hemopoietic organ5.70e-1029
immune organ5.70e-1029
foregut1.14e-0980
endo-epithelium1.77e-0869
gut epithelium5.19e-0855
mesoderm8.27e-08120
mesoderm-derived structure8.27e-08120
presumptive mesoderm8.27e-08120
gland of gut8.66e-0824
bone element1.17e-0722
skeletal element1.17e-0722
skeletal system1.17e-0722
thymus1.42e-0723
neck1.42e-0723
respiratory system epithelium1.42e-0723
hemolymphoid system gland1.42e-0723
pharyngeal epithelium1.42e-0723
thymic region1.42e-0723
pharyngeal gland1.42e-0723
entire pharyngeal arch endoderm1.42e-0723
thymus primordium1.42e-0723
early pharyngeal endoderm1.42e-0723
unilaminar epithelium1.59e-0766
pharynx1.71e-0724
upper respiratory tract1.71e-0724
chordate pharynx1.71e-0724
pharyngeal arch system1.71e-0724
pharyngeal region of foregut1.71e-0724
bone marrow2.00e-0716
gland2.48e-0765
musculoskeletal system3.23e-0732
connective tissue3.38e-0746


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)
MA0003.10.142214
MA0004.10.6888
MA0006.10.497533
MA0007.11.61215
MA0009.11.15569
MA0014.10.276754
MA0017.10.528196
MA0019.10.964875
MA0024.11.11019
MA0025.11.39562
MA0027.12.81824
MA0028.11.26991
MA0029.11.08753
MA0030.11.09438
MA0031.11.05719
MA0038.10.846479
MA0040.11.16866
MA0041.10.604221
MA0042.10.589368
MA0043.11.25564
MA0046.11.1929
MA0048.11.35097
MA0050.10.731539
MA0051.10.856094
MA0052.11.17701
MA0055.11.86956
MA0056.10
MA0057.10.251896
MA0058.10.581673
MA0059.10.59559
MA0060.11.04037
MA0061.10.438628
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.10.256913
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.10.00221226
MA0074.10.795862
MA0076.11.35592
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.10.201215
MA0089.10
MA0090.10.650768
MA0091.10.703314
MA0092.11.56822
MA0093.11.29026
MA0095.10
MA0098.10
MA0100.10.783305
MA0101.10.605676
MA0103.10.540576
MA0105.10.313353
MA0106.10.899777
MA0107.10.533522
MA0108.20.989014
MA0109.10
MA0111.10.666525
MA0113.10.869608
MA0114.10.43587
MA0115.11.25852
MA0116.10.497293
MA0117.11.22527
MA0119.11.47447
MA0122.11.24573
MA0124.11.45461
MA0125.11.37907
MA0130.10
MA0131.10.960068
MA0132.10
MA0133.10
MA0135.11.29308
MA0136.10.817395
MA0139.10.365453
MA0140.10.78318
MA0141.10.563066
MA0142.11.04199
MA0143.10.887119
MA0144.11.95888
MA0145.10.608454
MA0146.10.313734
MA0147.10.453952
MA0148.10.706718
MA0149.10.611881
MA0062.20.856416
MA0035.20.788288
MA0039.20.731226
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.20.386166
MA0047.20.845655
MA0112.20.211985
MA0065.20.212467
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.10.263609
MA0155.10.650923
MA0156.11.35382
MA0157.11.0083
MA0158.10
MA0159.10.465802
MA0160.10.71003
MA0161.10
MA0162.10.10667
MA0163.10.0996272
MA0164.10.817786
MA0080.21.32296
MA0018.20.828253
MA0099.20.944966
MA0079.20.190089
MA0102.21.8929
MA0258.10.419871
MA0259.10.441366
MA0442.10
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