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MCL coexpression mm9:1873: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001017!1.41e-18!73;UBERON:0001016!1.58e-17!75;UBERON:0000073!1.95e-16!54;UBERON:0001049!3.18e-15!52;UBERON:0005068!3.18e-15!52;UBERON:0006241!3.18e-15!52;UBERON:0007135!3.18e-15!52;UBERON:0004121!1.31e-14!95;UBERON:0000924!1.31e-14!95;UBERON:0006601!1.31e-14!95;UBERON:0000955!3.78e-14!47;UBERON:0006238!3.78e-14!47;UBERON:0002616!1.31e-13!46;UBERON:0010314!6.33e-13!92;UBERON:0002346!1.06e-12!64;UBERON:0003075!1.06e-12!64;UBERON:0007284!1.06e-12!64;UBERON:0010371!3.36e-12!73;UBERON:0003080!4.70e-12!40;UBERON:0002780!1.49e-11!39;UBERON:0001890!1.49e-11!39;UBERON:0006240!1.49e-11!39;UBERON:0002020!4.12e-11!34;UBERON:0000025!2.13e-10!114;UBERON:0003528!3.86e-10!29;UBERON:0002791!3.86e-10!29;UBERON:0001893!3.86e-10!29;UBERON:0003056!4.10e-10!49;UBERON:0004111!9.16e-10!122;UBERON:0000468!4.68e-08!333;UBERON:0000956!4.78e-08!21;UBERON:0001869!4.78e-08!21;UBERON:0000203!4.78e-08!21;UBERON:0002021!1.45e-07!10;UBERON:0000411!1.45e-07!10;UBERON:0001950!1.45e-07!10;UBERON:0002619!3.04e-07!17
|ontology_enrichment_uberon=UBERON:0001017!1.41e-18!73;UBERON:0001016!1.58e-17!75;UBERON:0000073!1.95e-16!54;UBERON:0001049!3.18e-15!52;UBERON:0005068!3.18e-15!52;UBERON:0006241!3.18e-15!52;UBERON:0007135!3.18e-15!52;UBERON:0004121!1.31e-14!95;UBERON:0000924!1.31e-14!95;UBERON:0006601!1.31e-14!95;UBERON:0000955!3.78e-14!47;UBERON:0006238!3.78e-14!47;UBERON:0002616!1.31e-13!46;UBERON:0010314!6.33e-13!92;UBERON:0002346!1.06e-12!64;UBERON:0003075!1.06e-12!64;UBERON:0007284!1.06e-12!64;UBERON:0010371!3.36e-12!73;UBERON:0003080!4.70e-12!40;UBERON:0002780!1.49e-11!39;UBERON:0001890!1.49e-11!39;UBERON:0006240!1.49e-11!39;UBERON:0002020!4.12e-11!34;UBERON:0000025!2.13e-10!114;UBERON:0003528!3.86e-10!29;UBERON:0002791!3.86e-10!29;UBERON:0001893!3.86e-10!29;UBERON:0003056!4.10e-10!49;UBERON:0004111!9.16e-10!122;UBERON:0000468!4.68e-08!333;UBERON:0000956!4.78e-08!21;UBERON:0001869!4.78e-08!21;UBERON:0000203!4.78e-08!21;UBERON:0002021!1.45e-07!10;UBERON:0000411!1.45e-07!10;UBERON:0001950!1.45e-07!10;UBERON:0002619!3.04e-07!17
|tfbs_overrepresentation_for_novel_motifs=0.641384,0.402508,0.612053,0.688265,0.483253,0.704257,0.803568,0.96814,0.381467,0.949265,0.755749,0.790506,0.37041,0.81685,1.2551,0,1.02248,0.473993,0.352304,0.683591,0.570433,0.57409,0.815872,0.481455,0.620553,0.846564,0.342316,0.727368,0.535752,0.790816,0.711848,1.12823,0.471365,0.318879,0.503207,0.623685,0.460474,0.786577,0.434783,0.40068,0.478558,0.717547,0.185353,0.504971,0.325217,0.675898,0.938241,0.744678,0.162985,0.539131,1.0041,0.875451,0.771943,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.98374,0.205546,1.32691,1.55806,0.310084,0.318792,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,2.70843,0.758875,0.40635,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,1.05366,0.367176,1.14445,0.938512,0.731844,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,1.40021,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.79777,0.542121,1.27621,1.87995,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,1.16191,0.788782,1.47798
|tfbs_overrepresentation_for_novel_motifs=0.641384,0.402508,0.612053,0.688265,0.483253,0.704257,0.803568,0.96814,0.381467,0.949265,0.755749,0.790506,0.37041,0.81685,1.2551,0,1.02248,0.473993,0.352304,0.683591,0.570433,0.57409,0.815872,0.481455,0.620553,0.846564,0.342316,0.727368,0.535752,0.790816,0.711848,1.12823,0.471365,0.318879,0.503207,0.623685,0.460474,0.786577,0.434783,0.40068,0.478558,0.717547,0.185353,0.504971,0.325217,0.675898,0.938241,0.744678,0.162985,0.539131,1.0041,0.875451,0.771943,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.98374,0.205546,1.32691,1.55806,0.310084,0.318792,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,2.70843,0.758875,0.40635,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,1.05366,0.367176,1.14445,0.938512,0.731844,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,1.40021,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.79777,0.542121,1.27621,1.87995,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,1.16191,0.788782,1.47798
|tfbs_overrepresentation_jaspar=MA0003.1;1.81465,MA0004.1;0.6888,MA0006.1;0.497533,MA0007.1;0.672186,MA0009.1;1.15569,MA0014.1;4.01037,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;0.396346,MA0056.1;0,MA0057.1;0.701847,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;0.713436,MA0069.1;1.17737,MA0070.1;1.16732,MA0071.1;0.73062,MA0072.1;1.15853,MA0073.1;3.89236,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;0.582815,MA0089.1;0,MA0090.1;0.650768,MA0091.1;0.703314,MA0092.1;0.651119,MA0093.1;0.519148,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;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;0.957842,MA0140.1;0.78318,MA0141.1;0.563066,MA0142.1;1.04199,MA0143.1;0.887119,MA0144.1;0.439506,MA0145.1;0.608454,MA0146.1;3.52627,MA0147.1;0.453952,MA0148.1;0.706718,MA0149.1;0.611881,MA0062.2;0.856416,MA0035.2;0.788288,MA0039.2;4.7835,MA0138.2;0.951653,MA0002.2;0.368961,MA0137.2;0.559766,MA0104.2;1.0034,MA0047.2;0.845655,MA0112.2;0.211985,MA0065.2;0.609584,MA0150.1;0.67206,MA0151.1;0,MA0152.1;0.84577,MA0153.1;1.31015,MA0154.1;2.06517,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;2.23835,MA0164.1;0.817786,MA0080.2;0.534538,MA0018.2;0.828253,MA0099.2;0.944966,MA0079.2;9.69117,MA0102.2;1.8929,MA0258.1;0.419871,MA0259.1;0.441366,MA0442.1;0
}}
}}

Revision as of 13:59, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:126625832..126625862,-p@chr10:126625832..126625862
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Mm9::chr10:69903391..69903420,+p3@Fam13c
Mm9::chr10:69903424..69903468,+p1@Fam13c
Mm9::chr4:151460939..151461002,+p1@Plekhg5


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:0043542endothelial cell migration0.0118884566920506
GO:0005089Rho guanyl-nucleotide exchange factor activity0.0250506766011067
GO:0035023regulation of Rho protein signal transduction0.0250506766011067
GO:0005088Ras guanyl-nucleotide exchange factor activity0.0250506766011067
GO:0007266Rho protein signal transduction0.0256450994357092
GO:0046578regulation of Ras protein signal transduction0.0256450994357092
GO:0005085guanyl-nucleotide exchange factor activity0.0256450994357092
GO:0051056regulation of small GTPase mediated signal transduction0.0256450994357092
GO:0007265Ras protein signal transduction0.0256450994357092
GO:0005083small GTPase regulator activity0.0256450994357092
GO:0016477cell migration0.0357715170109023
GO:0030695GTPase regulator activity0.0357715170109023
GO:0051674localization of cell0.0357715170109023
GO:0006928cell motility0.0357715170109023
GO:0009966regulation of signal transduction0.0357715170109023
GO:0007264small GTPase mediated signal transduction0.0357715170109023



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
electrically responsive cell2.68e-0939
electrically active cell2.68e-0939
non-terminally differentiated cell5.11e-0849

Uber Anatomy
Ontology termp-valuen
central nervous system1.41e-1873
nervous system1.58e-1775
regional part of nervous system1.95e-1654
neural tube3.18e-1552
neural rod3.18e-1552
future spinal cord3.18e-1552
neural keel3.18e-1552
ectoderm-derived structure1.31e-1495
ectoderm1.31e-1495
presumptive ectoderm1.31e-1495
brain3.78e-1447
future brain3.78e-1447
regional part of brain1.31e-1346
structure with developmental contribution from neural crest6.33e-1392
neurectoderm1.06e-1264
neural plate1.06e-1264
presumptive neural plate1.06e-1264
ecto-epithelium3.36e-1273
anterior neural tube4.70e-1240
regional part of forebrain1.49e-1139
forebrain1.49e-1139
future forebrain1.49e-1139
gray matter4.12e-1134
tube2.13e-10114
brain grey matter3.86e-1029
regional part of telencephalon3.86e-1029
telencephalon3.86e-1029
pre-chordal neural plate4.10e-1049
anatomical conduit9.16e-10122
multi-cellular organism4.68e-08333
cerebral cortex4.78e-0821
cerebral hemisphere4.78e-0821
pallium4.78e-0821
occipital lobe1.45e-0710
visual cortex1.45e-0710
neocortex1.45e-0710
regional part of cerebral cortex3.04e-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
MA0006.10.497533
MA0007.10.672186
MA0009.11.15569
MA0014.14.01037
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
MA0055.10.396346
MA0056.10
MA0057.10.701847
MA0058.10.581673
MA0059.10.59559
MA0060.10.403071
MA0061.10.438628
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.10.713436
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.13.89236
MA0074.10.795862
MA0076.10.550092
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.10.582815
MA0089.10
MA0090.10.650768
MA0091.10.703314
MA0092.10.651119
MA0093.10.519148
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
MA0116.12.15201
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
MA0139.10.957842
MA0140.10.78318
MA0141.10.563066
MA0142.11.04199
MA0143.10.887119
MA0144.10.439506
MA0145.10.608454
MA0146.13.52627
MA0147.10.453952
MA0148.10.706718
MA0149.10.611881
MA0062.20.856416
MA0035.20.788288
MA0039.24.7835
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.21.0034
MA0047.20.845655
MA0112.20.211985
MA0065.20.609584
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.12.06517
MA0155.11.21457
MA0156.10.549102
MA0157.11.0083
MA0158.10
MA0159.10.465802
MA0160.10.71003
MA0161.10
MA0162.10.704935
MA0163.12.23835
MA0164.10.817786
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.29.69117
MA0102.21.8929
MA0258.10.419871
MA0259.10.441366
MA0442.10
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