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MCL coexpression mm9:1982: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000073!4.30e-20!54;UBERON:0001049!7.38e-19!52;UBERON:0005068!7.38e-19!52;UBERON:0006241!7.38e-19!52;UBERON:0007135!7.38e-19!52;UBERON:0002346!1.12e-18!64;UBERON:0003075!1.12e-18!64;UBERON:0007284!1.12e-18!64;UBERON:0010371!6.06e-18!73;UBERON:0010314!2.18e-16!92;UBERON:0003056!3.54e-16!49;UBERON:0000955!4.37e-16!47;UBERON:0006238!4.37e-16!47;UBERON:0002616!1.15e-15!46;UBERON:0004121!2.51e-15!95;UBERON:0000924!2.51e-15!95;UBERON:0006601!2.51e-15!95;UBERON:0002020!3.87e-15!34;UBERON:0003080!7.63e-15!40;UBERON:0002780!2.90e-14!39;UBERON:0001890!2.90e-14!39;UBERON:0006240!2.90e-14!39;UBERON:0001017!3.14e-14!73;UBERON:0001016!9.30e-14!75;UBERON:0003528!1.10e-12!29;UBERON:0002791!1.10e-12!29;UBERON:0001893!1.10e-12!29;UBERON:0000956!9.88e-09!21;UBERON:0001869!9.88e-09!21;UBERON:0000203!9.88e-09!21;UBERON:0002021!1.03e-07!10;UBERON:0000411!1.03e-07!10;UBERON:0001950!1.03e-07!10;UBERON:0002619!3.73e-07!17
|ontology_enrichment_uberon=UBERON:0000073!4.30e-20!54;UBERON:0001049!7.38e-19!52;UBERON:0005068!7.38e-19!52;UBERON:0006241!7.38e-19!52;UBERON:0007135!7.38e-19!52;UBERON:0002346!1.12e-18!64;UBERON:0003075!1.12e-18!64;UBERON:0007284!1.12e-18!64;UBERON:0010371!6.06e-18!73;UBERON:0010314!2.18e-16!92;UBERON:0003056!3.54e-16!49;UBERON:0000955!4.37e-16!47;UBERON:0006238!4.37e-16!47;UBERON:0002616!1.15e-15!46;UBERON:0004121!2.51e-15!95;UBERON:0000924!2.51e-15!95;UBERON:0006601!2.51e-15!95;UBERON:0002020!3.87e-15!34;UBERON:0003080!7.63e-15!40;UBERON:0002780!2.90e-14!39;UBERON:0001890!2.90e-14!39;UBERON:0006240!2.90e-14!39;UBERON:0001017!3.14e-14!73;UBERON:0001016!9.30e-14!75;UBERON:0003528!1.10e-12!29;UBERON:0002791!1.10e-12!29;UBERON:0001893!1.10e-12!29;UBERON:0000956!9.88e-09!21;UBERON:0001869!9.88e-09!21;UBERON:0000203!9.88e-09!21;UBERON:0002021!1.03e-07!10;UBERON:0000411!1.03e-07!10;UBERON:0001950!1.03e-07!10;UBERON:0002619!3.73e-07!17
|tfbs_overrepresentation_for_novel_motifs=0.641384,0.128156,1.48646,0.688265,0.483253,0.704257,0.803568,0.370124,0.381467,0.489964,0.755749,0.790506,0.96877,0.81685,0.502646,0,1.02248,0.473993,0.352304,0.24402,0.570433,0.197567,0.815872,0.481455,0.620553,0.846564,0.342316,0.727368,1.32554,0.290745,0.711848,1.12823,0.471365,0.318879,0.503207,0.30022,0.460474,0.786577,0.434783,0.40068,0.478558,0.717547,0.544696,0.504971,0.325217,0.675898,0.938241,0.744678,0.162985,0.539131,1.0041,0.875451,0.771943,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,0.593145,1.32691,0.864765,0.310084,0.318792,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,1.24129,0.129654,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,1.05366,0.367176,1.14445,0.938512,0.731844,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,2.42089,0.740267,0.580757,0.57247,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,0.869142,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,1.4513,1.03606,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,0.589293
|tfbs_overrepresentation_for_novel_motifs=0.641384,0.128156,1.48646,0.688265,0.483253,0.704257,0.803568,0.370124,0.381467,0.489964,0.755749,0.790506,0.96877,0.81685,0.502646,0,1.02248,0.473993,0.352304,0.24402,0.570433,0.197567,0.815872,0.481455,0.620553,0.846564,0.342316,0.727368,1.32554,0.290745,0.711848,1.12823,0.471365,0.318879,0.503207,0.30022,0.460474,0.786577,0.434783,0.40068,0.478558,0.717547,0.544696,0.504971,0.325217,0.675898,0.938241,0.744678,0.162985,0.539131,1.0041,0.875451,0.771943,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,0.593145,1.32691,0.864765,0.310084,0.318792,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,1.24129,0.129654,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,1.05366,0.367176,1.14445,0.938512,0.731844,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,2.42089,0.740267,0.580757,0.57247,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,0.869142,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,1.4513,1.03606,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,0.589293
|tfbs_overrepresentation_jaspar=MA0003.1;1.81465,MA0004.1;0.6888,MA0006.1;1.24418,MA0007.1;0.672186,MA0009.1;1.15569,MA0014.1;4.76991,MA0017.1;0.528196,MA0019.1;0.964875,MA0024.1;1.11019,MA0025.1;1.39562,MA0027.1;2.81824,MA0028.1;0.509589,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;0.266382,MA0050.1;0.731539,MA0051.1;0.856094,MA0052.1;1.17701,MA0055.1;0.125758,MA0056.1;0,MA0057.1;0.251896,MA0058.1;0.581673,MA0059.1;0.59559,MA0060.1;0.403071,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;0.0140887,MA0074.1;0.795862,MA0076.1;0.550092,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;1.1032,MA0089.1;0,MA0090.1;0.650768,MA0091.1;0.703314,MA0092.1;0.651119,MA0093.1;1.29026,MA0095.1;0,MA0098.1;0,MA0100.1;1.84237,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;2.15201,MA0117.1;1.22527,MA0119.1;0.606338,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;1.11951,MA0145.1;1.79187,MA0146.1;1.07887,MA0147.1;0.453952,MA0148.1;0.706718,MA0149.1;0.611881,MA0062.2;0.319836,MA0035.2;0.788288,MA0039.2;1.47117,MA0138.2;0.951653,MA0002.2;0.368961,MA0137.2;0.559766,MA0104.2;0.386166,MA0047.2;0.845655,MA0112.2;0.608441,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;1.21457,MA0156.1;0.549102,MA0157.1;1.0083,MA0158.1;0,MA0159.1;0.465802,MA0160.1;0.71003,MA0161.1;0,MA0162.1;0.704935,MA0163.1;1.11502,MA0164.1;0.817786,MA0080.2;0.534538,MA0018.2;1.93488,MA0099.2;0.944966,MA0079.2;2.24437,MA0102.2;1.8929,MA0258.1;0.419871,MA0259.1;0.441366,MA0442.1;0
}}
}}

Revision as of 14:10, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:68666621..68666642,-p2@Ndel1
Mm9::chr11:97141940..97141964,-p3@Npepps
Mm9::chr2:132403980..132403991,-p3@Gpcpd1
Mm9::chr5:130505255..130505266,+p3@Crcp


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:0001635calcitonin gene-related polypeptide receptor activity0.0251163494431265
GO:0008090retrograde axon cargo transport0.0251163494431265
GO:0047496vesicle transport along microtubule0.0251163494431265
GO:0001833inner cell mass cell proliferation0.0251163494431265
GO:0060053neurofilament cytoskeleton0.0251163494431265
GO:0021955central nervous system neuron axonogenesis0.0251163494431265
GO:0060052neurofilament cytoskeleton organization and biogenesis0.0251163494431265
GO:0008088axon cargo transport0.0251163494431265
GO:0004179membrane alanyl aminopeptidase activity0.0251163494431265
GO:0016284alanine aminopeptidase activity0.0251163494431265
GO:0001832blastocyst growth0.026981550297944
GO:0045104intermediate filament cytoskeleton organization and biogenesis0.0316028594612309
GO:0001633secretin-like receptor activity0.0316028594612309
GO:0045103intermediate filament-based process0.0319487487684913
GO:0021954central nervous system neuron development0.0319487487684913
GO:0001669acrosome0.0322119285064847
GO:0021953central nervous system neuron differentiation0.0322119285064847
GO:0001824blastocyst development0.0392804948935897
GO:0003899DNA-directed RNA polymerase activity0.0408076563027618
GO:0004177aminopeptidase activity0.0421809771009908
GO:0005813centrosome0.0455885569561132
GO:0008017microtubule binding0.0463997002075004
GO:0048589developmental growth0.0463997002075004
GO:0005815microtubule organizing center0.0463997002075004
GO:0015631tubulin binding0.0463997002075004
GO:0001764neuron migration0.0463997002075004
GO:0008235metalloexopeptidase activity0.0463997002075004



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
CNS neuron (sensu Vertebrata)7.59e-1023
neuroblast (sensu Vertebrata)7.59e-1023

Uber Anatomy
Ontology termp-valuen
regional part of nervous system4.30e-2054
neural tube7.38e-1952
neural rod7.38e-1952
future spinal cord7.38e-1952
neural keel7.38e-1952
neurectoderm1.12e-1864
neural plate1.12e-1864
presumptive neural plate1.12e-1864
ecto-epithelium6.06e-1873
structure with developmental contribution from neural crest2.18e-1692
pre-chordal neural plate3.54e-1649
brain4.37e-1647
future brain4.37e-1647
regional part of brain1.15e-1546
ectoderm-derived structure2.51e-1595
ectoderm2.51e-1595
presumptive ectoderm2.51e-1595
gray matter3.87e-1534
anterior neural tube7.63e-1540
regional part of forebrain2.90e-1439
forebrain2.90e-1439
future forebrain2.90e-1439
central nervous system3.14e-1473
nervous system9.30e-1475
brain grey matter1.10e-1229
regional part of telencephalon1.10e-1229
telencephalon1.10e-1229
cerebral cortex9.88e-0921
cerebral hemisphere9.88e-0921
pallium9.88e-0921
occipital lobe1.03e-0710
visual cortex1.03e-0710
neocortex1.03e-0710
regional part of cerebral cortex3.73e-0717


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)
MA0003.11.81465
MA0004.10.6888
MA0006.11.24418
MA0007.10.672186
MA0009.11.15569
MA0014.14.76991
MA0017.10.528196
MA0019.10.964875
MA0024.11.11019
MA0025.11.39562
MA0027.12.81824
MA0028.10.509589
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
MA0048.10.266382
MA0050.10.731539
MA0051.10.856094
MA0052.11.17701
MA0055.10.125758
MA0056.10
MA0057.10.251896
MA0058.10.581673
MA0059.10.59559
MA0060.10.403071
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
MA0073.10.0140887
MA0074.10.795862
MA0076.10.550092
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.11.1032
MA0089.10
MA0090.10.650768
MA0091.10.703314
MA0092.10.651119
MA0093.11.29026
MA0095.10
MA0098.10
MA0100.11.84237
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
MA0116.12.15201
MA0117.11.22527
MA0119.10.606338
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
MA0144.11.11951
MA0145.11.79187
MA0146.11.07887
MA0147.10.453952
MA0148.10.706718
MA0149.10.611881
MA0062.20.319836
MA0035.20.788288
MA0039.21.47117
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.20.386166
MA0047.20.845655
MA0112.20.608441
MA0065.20.212467
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.10.263609
MA0155.11.21457
MA0156.10.549102
MA0157.11.0083
MA0158.10
MA0159.10.465802
MA0160.10.71003
MA0161.10
MA0162.10.704935
MA0163.11.11502
MA0164.10.817786
MA0080.20.534538
MA0018.21.93488
MA0099.20.944966
MA0079.22.24437
MA0102.21.8929
MA0258.10.419871
MA0259.10.441366
MA0442.10
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