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MCL coexpression mm9:2356: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002346!5.73e-21!64;UBERON:0003075!5.73e-21!64;UBERON:0007284!5.73e-21!64;UBERON:0001017!1.34e-20!73;UBERON:0001016!3.92e-20!75;UBERON:0000073!1.80e-19!54;UBERON:0001049!4.61e-18!52;UBERON:0005068!4.61e-18!52;UBERON:0006241!4.61e-18!52;UBERON:0007135!4.61e-18!52;UBERON:0004121!4.71e-18!95;UBERON:0000924!4.71e-18!95;UBERON:0006601!4.71e-18!95;UBERON:0010371!5.91e-17!73;UBERON:0010314!2.18e-16!92;UBERON:0000955!3.12e-16!47;UBERON:0006238!3.12e-16!47;UBERON:0003056!5.00e-16!49;UBERON:0002616!1.55e-15!46;UBERON:0002020!5.87e-14!34;UBERON:0003080!7.25e-14!40;UBERON:0002780!3.12e-13!39;UBERON:0001890!3.12e-13!39;UBERON:0006240!3.12e-13!39;UBERON:0003528!4.95e-12!29;UBERON:0002791!4.95e-12!29;UBERON:0001893!4.95e-12!29;UBERON:0000468!2.19e-08!333;UBERON:0000956!5.31e-08!21;UBERON:0001869!5.31e-08!21;UBERON:0000203!5.31e-08!21;UBERON:0002619!2.41e-07!17;UBERON:0005156!8.14e-07!26;UBERON:0000990!8.14e-07!26
|ontology_enrichment_uberon=UBERON:0002346!5.73e-21!64;UBERON:0003075!5.73e-21!64;UBERON:0007284!5.73e-21!64;UBERON:0001017!1.34e-20!73;UBERON:0001016!3.92e-20!75;UBERON:0000073!1.80e-19!54;UBERON:0001049!4.61e-18!52;UBERON:0005068!4.61e-18!52;UBERON:0006241!4.61e-18!52;UBERON:0007135!4.61e-18!52;UBERON:0004121!4.71e-18!95;UBERON:0000924!4.71e-18!95;UBERON:0006601!4.71e-18!95;UBERON:0010371!5.91e-17!73;UBERON:0010314!2.18e-16!92;UBERON:0000955!3.12e-16!47;UBERON:0006238!3.12e-16!47;UBERON:0003056!5.00e-16!49;UBERON:0002616!1.55e-15!46;UBERON:0002020!5.87e-14!34;UBERON:0003080!7.25e-14!40;UBERON:0002780!3.12e-13!39;UBERON:0001890!3.12e-13!39;UBERON:0006240!3.12e-13!39;UBERON:0003528!4.95e-12!29;UBERON:0002791!4.95e-12!29;UBERON:0001893!4.95e-12!29;UBERON:0000468!2.19e-08!333;UBERON:0000956!5.31e-08!21;UBERON:0001869!5.31e-08!21;UBERON:0000203!5.31e-08!21;UBERON:0002619!2.41e-07!17;UBERON:0005156!8.14e-07!26;UBERON:0000990!8.14e-07!26
|tfbs_overrepresentation_for_novel_motifs=0.641384,1.30284,0.612053,0.688265,0.483253,0.704257,0.803568,0.370124,0.381467,0.489964,0.755749,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,0.352304,0.683591,0.570433,0.197567,0.815872,0.481455,0.620553,0.846564,0.342316,0.727368,1.32554,0.290745,0.711848,1.12823,2.06579,0.854272,0.503207,1.54603,0.460474,0.786577,0.434783,0.40068,0.478558,0.717547,0.185353,0.504971,0.325217,0.675898,0.938241,0.744678,0.162985,0.539131,1.0041,0.875451,0.771943,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,3.59454,0.377213,1.12016,1.32691,1.55806,0.310084,0.854076,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,1.24129,12.8657,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,3.46168,0.692434,1.02384,1.15537,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,1.21803,0.293812,1.03606,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,1.16191,0.788782,4.04063
|tfbs_overrepresentation_for_novel_motifs=0.641384,1.30284,0.612053,0.688265,0.483253,0.704257,0.803568,0.370124,0.381467,0.489964,0.755749,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,0.352304,0.683591,0.570433,0.197567,0.815872,0.481455,0.620553,0.846564,0.342316,0.727368,1.32554,0.290745,0.711848,1.12823,2.06579,0.854272,0.503207,1.54603,0.460474,0.786577,0.434783,0.40068,0.478558,0.717547,0.185353,0.504971,0.325217,0.675898,0.938241,0.744678,0.162985,0.539131,1.0041,0.875451,0.771943,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,3.59454,0.377213,1.12016,1.32691,1.55806,0.310084,0.854076,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,1.24129,12.8657,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,3.46168,0.692434,1.02384,1.15537,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,1.21803,0.293812,1.03606,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,1.16191,0.788782,4.04063
|tfbs_overrepresentation_jaspar=MA0003.1;2.89651,MA0004.1;0.6888,MA0006.1;2.1528,MA0007.1;0.672186,MA0009.1;1.15569,MA0014.1;7.27597,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;1.29714,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;23.0266,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;0.201215,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;1.24367,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;2.56916,MA0140.1;0.78318,MA0141.1;1.38335,MA0142.1;1.04199,MA0143.1;0.887119,MA0144.1;0.439506,MA0145.1;0.21199,MA0146.1;1.5929,MA0147.1;0.453952,MA0148.1;0.706718,MA0149.1;0.611881,MA0062.2;0.319836,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;4.21304,MA0065.2;0.212467,MA0150.1;1.61189,MA0151.1;0,MA0152.1;0.84577,MA0153.1;1.31015,MA0154.1;0.728853,MA0155.1;4.39658,MA0156.1;0.549102,MA0157.1;1.0083,MA0158.1;0,MA0159.1;0.465802,MA0160.1;0.71003,MA0161.1;0,MA0162.1;4.50355,MA0163.1;0.672192,MA0164.1;0.817786,MA0080.2;0.534538,MA0018.2;0.828253,MA0099.2;0.944966,MA0079.2;6.24625,MA0102.2;1.8929,MA0258.1;1.89239,MA0259.1;1.96515,MA0442.1;0
}}
}}

Revision as of 14:44, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr3:105254767..105254855,+p1@Kcnd3
Mm9::chr3:105255022..105255063,+p2@Kcnd3
Mm9::chr3:105255067..105255095,+p4@Kcnd3
Mm9::chr3:105255244..105255283,+p3@Kcnd3


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

no results for this coexpression

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)4.23e-1023
neuroblast (sensu Vertebrata)4.23e-1023
neural cell2.38e-0843
ectodermal cell3.61e-0844
neurectodermal cell3.61e-0844
neuron1.20e-0733
neuronal stem cell1.20e-0733
neuroblast1.20e-0733
electrically signaling cell1.20e-0733

Uber Anatomy
Ontology termp-valuen
neurectoderm5.73e-2164
neural plate5.73e-2164
presumptive neural plate5.73e-2164
central nervous system1.34e-2073
nervous system3.92e-2075
regional part of nervous system1.80e-1954
neural tube4.61e-1852
neural rod4.61e-1852
future spinal cord4.61e-1852
neural keel4.61e-1852
ectoderm-derived structure4.71e-1895
ectoderm4.71e-1895
presumptive ectoderm4.71e-1895
ecto-epithelium5.91e-1773
structure with developmental contribution from neural crest2.18e-1692
brain3.12e-1647
future brain3.12e-1647
pre-chordal neural plate5.00e-1649
regional part of brain1.55e-1546
gray matter5.87e-1434
anterior neural tube7.25e-1440
regional part of forebrain3.12e-1339
forebrain3.12e-1339
future forebrain3.12e-1339
brain grey matter4.95e-1229
regional part of telencephalon4.95e-1229
telencephalon4.95e-1229
multi-cellular organism2.19e-08333
cerebral cortex5.31e-0821
cerebral hemisphere5.31e-0821
pallium5.31e-0821
regional part of cerebral cortex2.41e-0717
reproductive structure8.14e-0726
reproductive system8.14e-0726


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)
MA0003.12.89651
MA0004.10.6888
MA0006.12.1528
MA0007.10.672186
MA0009.11.15569
MA0014.17.27597
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
MA0057.11.29714
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
MA0073.123.0266
MA0074.10.795862
MA0076.10.550092
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.10.201215
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
MA0116.11.24367
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
MA0139.12.56916
MA0140.10.78318
MA0141.11.38335
MA0142.11.04199
MA0143.10.887119
MA0144.10.439506
MA0145.10.21199
MA0146.11.5929
MA0147.10.453952
MA0148.10.706718
MA0149.10.611881
MA0062.20.319836
MA0035.20.788288
MA0039.20.731226
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.20.386166
MA0047.20.845655
MA0112.24.21304
MA0065.20.212467
MA0150.11.61189
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.10.728853
MA0155.14.39658
MA0156.10.549102
MA0157.11.0083
MA0158.10
MA0159.10.465802
MA0160.10.71003
MA0161.10
MA0162.14.50355
MA0163.10.672192
MA0164.10.817786
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.26.24625
MA0102.21.8929
MA0258.11.89239
MA0259.11.96515
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:2356&oldid=2575751"