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MCL coexpression mm9:288: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0008067;metabotropic glutamate, GABA-B-like receptor activity;0.0174155064064894;54393,108071!GO:0030054;cell junction;0.0174155064064894;54524,19894,14402,54393!GO:0016917;GABA receptor activity;0.0174155064064894;14402,54393!GO:0008066;glutamate receptor activity;0.0324413044456912;54393,108071!GO:0008021;synaptic vesicle;0.0376436272770898;54524,19894!
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|ontology_enrichment_uberon=UBERON:0000073!8.13e-33!54;UBERON:0001049!8.66e-33!52;UBERON:0005068!8.66e-33!52;UBERON:0006241!8.66e-33!52;UBERON:0007135!8.66e-33!52;UBERON:0002020!5.43e-32!34;UBERON:0002346!4.02e-30!64;UBERON:0003075!4.02e-30!64;UBERON:0007284!4.02e-30!64;UBERON:0000955!5.56e-28!47;UBERON:0006238!5.56e-28!47;UBERON:0001017!1.89e-27!73;UBERON:0003528!6.96e-27!29;UBERON:0002791!6.96e-27!29;UBERON:0001893!6.96e-27!29;UBERON:0002616!8.23e-27!46;UBERON:0001016!2.80e-26!75;UBERON:0003080!9.85e-25!40;UBERON:0010371!1.88e-24!73;UBERON:0003056!3.12e-24!49;UBERON:0002780!1.09e-23!39;UBERON:0001890!1.09e-23!39;UBERON:0006240!1.09e-23!39;UBERON:0004121!6.14e-22!95;UBERON:0000924!6.14e-22!95;UBERON:0006601!6.14e-22!95;UBERON:0000956!5.63e-19!21;UBERON:0001869!5.63e-19!21;UBERON:0000203!5.63e-19!21;UBERON:0010314!3.06e-16!92;UBERON:0002619!2.23e-15!17;UBERON:0002021!7.09e-13!10;UBERON:0000411!7.09e-13!10;UBERON:0001950!7.09e-13!10;UBERON:0002420!5.99e-09!8;UBERON:0007245!5.99e-09!8;UBERON:0010009!5.99e-09!8;UBERON:0010011!5.99e-09!8;UBERON:0000454!5.99e-09!8;UBERON:0003076!2.70e-08!12;UBERON:0003057!2.70e-08!12;UBERON:0000025!1.43e-07!114;UBERON:0002240!6.14e-07!6;UBERON:0005174!6.14e-07!6;UBERON:0001137!6.14e-07!6
|tfbs_overrepresentation_for_novel_motifs=0.251516,1.60606,0.220186,0.305194,0.0248591,0.324459,0.148388,0.242259,0.127399,0.641284,0.779211,0.141272,0.115878,0.155782,0.0291208,0,0.288299,0.0992523,0.210715,0.383901,0.17894,0.226539,0.155233,0.0244851,0.495614,0.990032,0.348681,0.353106,0.341908,0.377483,0.101869,0.367297,0.0974128,0.697346,0.289024,0.350945,0.225428,0.849202,0.19064,0.512008,0.102492,0.340818,0.442687,0.291794,0.089721,0.290621,0.651428,0.754508,0.64161,0.347605,0.27523,0.190239,0.351522,0.485586,0.500658,0.937751,0.159565,0.13388,0.755872,0.158905,0.351242,0.196469,0.142906,0.736407,0.500124,0.297204,0.621417,0.947606,0.347523,0.807939,0.439167,0.0437316,0.984329,0.529888,0.301544,0.269451,0.069705,0.632797,0.337634,0.723913,0.447591,0.301475,0.195512,0.0374831,0.430864,0.783003,3.25623,3.47092,0.233678,1.10402,0.684894,0.435043,0.377655,0.110957,0.901851,0.158698,0.646914,0.379937,0.23041,0.299156,0.0203943,0.367072,0.470627,0.275672,0.274889,0.340215,0.320303,0.115402,1.13437,0.716259,0.242899,0.472153,0.727478,0.396939,0.691366,0.467924,0.360282,0.641269,0.787491,0.0871017,0.534627,0.701195,0.174046,0.221668,0.741383,0.340552,0.153289,0.972632,0.620047,0.509539,0.456151,0.615552,0.593454,0.972702,0.711262,15.6176,0.261933,0.105244,0.6661,1.46501,1.07314,0.625675,0.535988,0.375761,0.270089,0.696071,0.232424,1.42588,0.950341,0.489217,0.232803,0.297344,0.486938,2.9848,0.502569,0.558342,0.558081,0.0324329,0.0708891,1.4089,1.61759,0.430147,0.340904,0.240163,0.26765,0.163443,0.427254,0.140344,0.526867
|tfbs_overrepresentation_jaspar=MA0003.1;0.518656,MA0004.1;0.0915017,MA0006.1;0.280185,MA0007.1;0.598973,MA0009.1;0.388771,MA0014.1;0.049151,MA0017.1;0.141194,MA0019.1;0.692998,MA0024.1;0.931181,MA0025.1;0.589418,MA0027.1;1.95996,MA0028.1;0.12595,MA0029.1;0.336166,MA0030.1;0.341346,MA0031.1;0.313542,MA0038.1;0.17284,MA0040.1;0.399043,MA0041.1;0.0583487,MA0042.1;0.0533455,MA0043.1;0.469769,MA0046.1;0.418434,MA0048.1;0.470706,MA0050.1;1.19283,MA0051.1;0.178537,MA0052.1;0.405693,MA0055.1;0.516648,MA0056.1;0,MA0057.1;4.28974,MA0058.1;0.189695,MA0059.1;0.203408,MA0060.1;0.0114726,MA0061.1;1.7151,MA0063.1;0,MA0066.1;0.165937,MA0067.1;0.690195,MA0068.1;0.0786082,MA0069.1;0.405974,MA0070.1;0.397975,MA0071.1;0.110717,MA0072.1;0.391015,MA0073.1;4.27687,MA0074.1;0.144171,MA0076.1;0.160227,MA0077.1;0.373365,MA0078.1;0.200156,MA0081.1;0.230196,MA0083.1;0.469091,MA0084.1;0.999346,MA0087.1;0.432564,MA0088.1;1.2039,MA0089.1;0,MA0090.1;0.0756256,MA0091.1;0.32331,MA0092.1;0.0757649,MA0093.1;0.133673,MA0095.1;0,MA0098.1;0,MA0100.1;0.137416,MA0101.1;0.809895,MA0103.1;0.350053,MA0105.1;2.82746,MA0106.1;0.205373,MA0107.1;0.957408,MA0108.2;0.731286,MA0109.1;0,MA0111.1;2.02836,MA0113.1;0.186674,MA0114.1;0.0743624,MA0115.1;0.472164,MA0116.1;0.279815,MA0117.1;0.44472,MA0119.1;0.059082,MA0122.1;0.461557,MA0124.1;0.641584,MA0125.1;0.574947,MA0130.1;0,MA0131.1;0.244817,MA0132.1;0,MA0133.1;0,MA0135.1;0.501131,MA0136.1;0.156089,MA0139.1;0.233798,MA0140.1;1.96532,MA0141.1;0.17205,MA0142.1;0.817195,MA0143.1;0.573785,MA0144.1;0.942473,MA0145.1;0.797964,MA0146.1;0.19688,MA0147.1;0.216343,MA0148.1;0.0995133,MA0149.1;0.478932,MA0062.2;0.0226466,MA0035.2;1.37725,MA0039.2;0.678975,MA0138.2;0.239154,MA0002.2;0.420289,MA0137.2;0.383209,MA0104.2;0.132466,MA0047.2;0.172355,MA0112.2;0.0875465,MA0065.2;1.316,MA0150.1;0.286158,MA0151.1;0,MA0152.1;0.172422,MA0153.1;0.515592,MA0154.1;0.663509,MA0155.1;0.928842,MA0156.1;0.159341,MA0157.1;0.278203,MA0158.1;0,MA0159.1;0.0935777,MA0160.1;0.101031,MA0161.1;0,MA0162.1;1.02067,MA0163.1;2.74457,MA0164.1;0.473545,MA0080.2;0.146586,MA0018.2;0.488272,MA0099.2;0.234689,MA0079.2;9.76852,MA0102.2;1.04989,MA0258.1;0.171703,MA0259.1;0.07771,MA0442.1;0
}}

Latest revision as of 15:02, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:6505664..6505673,-p@chr11:6505664..6505673
-
Mm9::chr11:72020498..72020513,-p@chr11:72020498..72020513
-
Mm9::chr12:30220046..30220070,+p6@Myt1l
Mm9::chr12:30220074..30220102,+p3@Myt1l
Mm9::chr15:78541224..78541236,-p@chr15:78541224..78541236
-
Mm9::chr17:37187549..37187560,+p7@Gabbr1
Mm9::chr18:64424264..64424293,+p@chr18:64424264..64424293
+
Mm9::chr18:64424505..64424516,+p@chr18:64424505..64424516
+
Mm9::chr18:67293367..67293388,+p5@Gnal
Mm9::chr18:86564164..86564174,+p4@Neto1
Mm9::chr18:86564576..86564625,+p3@Neto1
Mm9::chr18:86564667..86564677,+p8@Neto1
Mm9::chr1:89407123..89407159,-p5@Ngef
Mm9::chr2:115891770..115891799,-p25@Meis2
Mm9::chr2:151907604..151907629,+p4@Scrt2
Mm9::chr2:156137489..156137502,+p@chr2:156137489..156137502
+
Mm9::chr3:103379161..103379178,+p3@Syt6
Mm9::chr4:129662027..129662032,+p6@Bai2
Mm9::chr4:129662053..129662065,+p3@Bai2
Mm9::chr4:24357985..24358002,-p@chr4:24357985..24358002
-
Mm9::chr5:121460094..121460135,-p5@Rph3a
Mm9::chr5:130924685..130924700,+p3@Caln1
Mm9::chr7:64845896..64845923,+p2@Gabrb3
Mm9::chr7:64845935..64845942,+p8@Gabrb3
Mm9::chr7:94732650..94732683,+p3@Grm5
Mm9::chr9:44290614..44290635,+p@chr9:44290614..44290635
+
Mm9::chr9:62385142..62385161,-p9@Coro2b
Mm9::chr9:62385178..62385187,-p17@Coro2b
Mm9::chr9:79708145..79708172,-p@chr9:79708145..79708172
-


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:0008067metabotropic glutamate, GABA-B-like receptor activity0.0174155064064894
GO:0030054cell junction0.0174155064064894
GO:0016917GABA receptor activity0.0174155064064894
GO:0008066glutamate receptor activity0.0324413044456912
GO:0008021synaptic vesicle0.0376436272770898



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
regional part of nervous system8.13e-3354
neural tube8.66e-3352
neural rod8.66e-3352
future spinal cord8.66e-3352
neural keel8.66e-3352
gray matter5.43e-3234
neurectoderm4.02e-3064
neural plate4.02e-3064
presumptive neural plate4.02e-3064
brain5.56e-2847
future brain5.56e-2847
central nervous system1.89e-2773
brain grey matter6.96e-2729
regional part of telencephalon6.96e-2729
telencephalon6.96e-2729
regional part of brain8.23e-2746
nervous system2.80e-2675
anterior neural tube9.85e-2540
ecto-epithelium1.88e-2473
pre-chordal neural plate3.12e-2449
regional part of forebrain1.09e-2339
forebrain1.09e-2339
future forebrain1.09e-2339
ectoderm-derived structure6.14e-2295
ectoderm6.14e-2295
presumptive ectoderm6.14e-2295
cerebral cortex5.63e-1921
cerebral hemisphere5.63e-1921
pallium5.63e-1921
structure with developmental contribution from neural crest3.06e-1692
regional part of cerebral cortex2.23e-1517
occipital lobe7.09e-1310
visual cortex7.09e-1310
neocortex7.09e-1310
basal ganglion5.99e-098
nuclear complex of neuraxis5.99e-098
aggregate regional part of brain5.99e-098
collection of basal ganglia5.99e-098
cerebral subcortex5.99e-098
posterior neural tube2.70e-0812
chordal neural plate2.70e-0812
tube1.43e-07114
spinal cord6.14e-076
dorsal region element6.14e-076
dorsum6.14e-076


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)
MA0003.10.518656
MA0004.10.0915017
MA0006.10.280185
MA0007.10.598973
MA0009.10.388771
MA0014.10.049151
MA0017.10.141194
MA0019.10.692998
MA0024.10.931181
MA0025.10.589418
MA0027.11.95996
MA0028.10.12595
MA0029.10.336166
MA0030.10.341346
MA0031.10.313542
MA0038.10.17284
MA0040.10.399043
MA0041.10.0583487
MA0042.10.0533455
MA0043.10.469769
MA0046.10.418434
MA0048.10.470706
MA0050.11.19283
MA0051.10.178537
MA0052.10.405693
MA0055.10.516648
MA0056.10
MA0057.14.28974
MA0058.10.189695
MA0059.10.203408
MA0060.10.0114726
MA0061.11.7151
MA0063.10
MA0066.10.165937
MA0067.10.690195
MA0068.10.0786082
MA0069.10.405974
MA0070.10.397975
MA0071.10.110717
MA0072.10.391015
MA0073.14.27687
MA0074.10.144171
MA0076.10.160227
MA0077.10.373365
MA0078.10.200156
MA0081.10.230196
MA0083.10.469091
MA0084.10.999346
MA0087.10.432564
MA0088.11.2039
MA0089.10
MA0090.10.0756256
MA0091.10.32331
MA0092.10.0757649
MA0093.10.133673
MA0095.10
MA0098.10
MA0100.10.137416
MA0101.10.809895
MA0103.10.350053
MA0105.12.82746
MA0106.10.205373
MA0107.10.957408
MA0108.20.731286
MA0109.10
MA0111.12.02836
MA0113.10.186674
MA0114.10.0743624
MA0115.10.472164
MA0116.10.279815
MA0117.10.44472
MA0119.10.059082
MA0122.10.461557
MA0124.10.641584
MA0125.10.574947
MA0130.10
MA0131.10.244817
MA0132.10
MA0133.10
MA0135.10.501131
MA0136.10.156089
MA0139.10.233798
MA0140.11.96532
MA0141.10.17205
MA0142.10.817195
MA0143.10.573785
MA0144.10.942473
MA0145.10.797964
MA0146.10.19688
MA0147.10.216343
MA0148.10.0995133
MA0149.10.478932
MA0062.20.0226466
MA0035.21.37725
MA0039.20.678975
MA0138.20.239154
MA0002.20.420289
MA0137.20.383209
MA0104.20.132466
MA0047.20.172355
MA0112.20.0875465
MA0065.21.316
MA0150.10.286158
MA0151.10
MA0152.10.172422
MA0153.10.515592
MA0154.10.663509
MA0155.10.928842
MA0156.10.159341
MA0157.10.278203
MA0158.10
MA0159.10.0935777
MA0160.10.101031
MA0161.10
MA0162.11.02067
MA0163.12.74457
MA0164.10.473545
MA0080.20.146586
MA0018.20.488272
MA0099.20.234689
MA0079.29.76852
MA0102.21.04989
MA0258.10.171703
MA0259.10.07771
MA0442.10
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