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MCL coexpression mm9:1538: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=UBERON:0002020!3.73e-26!34;UBERON:0000073!2.10e-21!54;UBERON:0001049!1.38e-19!52;UBERON:0005068!1.38e-19!52;UBERON:0006241!1.38e-19!52;UBERON:0007135!1.38e-19!52;UBERON:0003528!1.41e-19!29;UBERON:0002791!1.41e-19!29;UBERON:0001893!1.41e-19!29;UBERON:0001017!1.43e-18!73;UBERON:0002346!2.16e-18!64;UBERON:0003075!2.16e-18!64;UBERON:0007284!2.16e-18!64;UBERON:0001016!9.03e-18!75;UBERON:0003080!9.28e-17!40;UBERON:0003056!9.30e-17!49;UBERON:0000955!8.41e-16!47;UBERON:0006238!8.41e-16!47;UBERON:0002780!8.72e-16!39;UBERON:0001890!8.72e-16!39;UBERON:0006240!8.72e-16!39;UBERON:0004121!5.20e-15!95;UBERON:0000924!5.20e-15!95;UBERON:0006601!5.20e-15!95;UBERON:0010371!7.94e-15!73;UBERON:0002616!1.08e-14!46;UBERON:0000956!1.28e-14!21;UBERON:0001869!1.28e-14!21;UBERON:0000203!1.28e-14!21;UBERON:0002619!1.96e-10!17;UBERON:0010314!1.08e-09!92;UBERON:0001948!2.85e-08!5;UBERON:0002315!2.85e-08!5;UBERON:0000369!5.66e-08!5;UBERON:0002435!5.66e-08!5;UBERON:0000204!5.66e-08!5;UBERON:0010082!5.66e-08!5;UBERON:0002240!9.34e-07!6;UBERON:0005174!9.34e-07!6;UBERON:0001137!9.34e-07!6
|tfbs_overrepresentation_for_novel_motifs=0.557864,1.02681,0.529553,0.603273,0.406364,0.618805,0.715644,0.812379,0.310789,0.115752,0.668936,0.702872,0.812978,0.728641,1.90904,0,0.930881,0.397593,1.41491,0.185796,1.22707,0.874994,0.727684,1.04384,0.537749,0.757752,1.38127,0.641282,0.456327,0.227599,0.626183,1.03545,1.02297,0.704734,0.425309,2.82585,0.384813,0.699032,0.360612,1.57622,0.401916,0.631725,0.419293,0.426986,0.227872,0.591277,0.847828,0.658142,0.746467,0.459555,0.912738,0.786094,0.627649,1.18062,1.19842,0.73621,0.469329,0.689304,0.26467,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.827208,0.152094,1.23259,0.257421,0.245132,0.70455,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.796301,2.51921,0.0793594,0.0882907,1.87702,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.3366,0.806207,1.05152,0.848095,1.75016,0.384901,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,0.491483,2.3261,1.16464,0.495367,1.61686,1.41481,0.399936,0.0998646,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.143464,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,1.5287,0.851091,2.18247,0.569503,0.408309,0.230371,0.133815,1.18223,0.343194,1.77291,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,0.425122
|tfbs_overrepresentation_jaspar=MA0003.1;0.211284,MA0004.1;0.603793,MA0006.1;0.419915,MA0007.1;0.587678,MA0009.1;1.06266,MA0014.1;0.187732,MA0017.1;1.99124,MA0019.1;0.874061,MA0024.1;2.32185,MA0025.1;1.30092,MA0027.1;2.72141,MA0028.1;0.43138,MA0029.1;0.995171,MA0030.1;1.00195,MA0031.1;0.965177,MA0038.1;0.757669,MA0040.1;1.07552,MA0041.1;0.522007,MA0042.1;0.507715,MA0043.1;1.1618,MA0046.1;1.09955,MA0048.1;0.205696,MA0050.1;0.645342,MA0051.1;0.767098,MA0052.1;1.08379,MA0055.1;0.0851423,MA0056.1;0,MA0057.1;0.562607,MA0058.1;1.25013,MA0059.1;0.513699,MA0060.1;0.330907,MA0061.1;0.364227,MA0063.1;0,MA0066.1;0.746072,MA0067.1;1.41352,MA0068.1;0.197245,MA0069.1;1.08414,MA0070.1;1.07418,MA0071.1;0.644448,MA0072.1;1.06547,MA0073.1;6.2889,MA0074.1;0.708108,MA0076.1;0.470037,MA0077.1;1.04318,MA0078.1;0.801834,MA0081.1;0.53877,MA0083.1;1.16099,MA0084.1;1.74401,MA0087.1;1.11687,MA0088.1;1.42769,MA0089.1;0,MA0090.1;0.566938,MA0091.1;4.97552,MA0092.1;0.567278,MA0093.1;0.440484,MA0095.1;0,MA0098.1;0,MA0100.1;0.695835,MA0101.1;0.523409,MA0103.1;0.460936,MA0105.1;1.98468,MA0106.1;0.809991,MA0107.1;0.454197,MA0108.2;0.897859,MA0109.1;0,MA0111.1;0.582193,MA0113.1;0.780358,MA0114.1;1.69206,MA0115.1;2.6202,MA0116.1;0.419688,MA0117.1;1.13165,MA0119.1;0.524046,MA0122.1;1.15196,MA0124.1;1.35963,MA0125.1;1.28445,MA0130.1;0,MA0131.1;0.869325,MA0132.1;0,MA0133.1;0,MA0135.1;1.19898,MA0136.1;0.729175,MA0139.1;2.22941,MA0140.1;0.695713,MA0141.1;0.482463,MA0142.1;0.950155,MA0143.1;0.797553,MA0144.1;0.365053,MA0145.1;0.927481,MA0146.1;0.0604336,MA0147.1;0.378658,MA0148.1;0.621195,MA0149.1;0.529387,MA0062.2;0.254018,MA0035.2;0.700704,MA0039.2;1.42062,MA0138.2;0.861035,MA0002.2;0.299191,MA0137.2;0.479301,MA0104.2;0.315156,MA0047.2;0.75686,MA0112.2;0.47695,MA0065.2;2.84751,MA0150.1;0.587557,MA0151.1;0,MA0152.1;0.756973,MA0153.1;1.21594,MA0154.1;0.203217,MA0155.1;0.173445,MA0156.1;0.469089,MA0157.1;0.91689,MA0158.1;0,MA0159.1;0.389847,MA0160.1;0.624415,MA0161.1;0,MA0162.1;0.898893,MA0163.1;4.36666,MA0164.1;1.7313,MA0080.2;0.455167,MA0018.2;0.739807,MA0099.2;0.854449,MA0079.2;4.18591,MA0102.2;1.79669,MA0258.1;0.91616,MA0259.1;0.366802,MA0442.1;0
}}

Latest revision as of 17:05, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:80935604..80935613,-p5@Celf5
Mm9::chr2:180625380..180625391,+p@chr2:180625380..180625391
+
Mm9::chr2:180625392..180625403,+p@chr2:180625392..180625403
+
Mm9::chr2:180625404..180625417,+p@chr2:180625404..180625417
+
Mm9::chr2:70399341..70399364,+p@chr2:70399341..70399364
+


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>

Uber Anatomy
Ontology termp-valuen
gray matter3.73e-2634
regional part of nervous system2.10e-2154
neural tube1.38e-1952
neural rod1.38e-1952
future spinal cord1.38e-1952
neural keel1.38e-1952
brain grey matter1.41e-1929
regional part of telencephalon1.41e-1929
telencephalon1.41e-1929
central nervous system1.43e-1873
neurectoderm2.16e-1864
neural plate2.16e-1864
presumptive neural plate2.16e-1864
nervous system9.03e-1875
anterior neural tube9.28e-1740
pre-chordal neural plate9.30e-1749
brain8.41e-1647
future brain8.41e-1647
regional part of forebrain8.72e-1639
forebrain8.72e-1639
future forebrain8.72e-1639
ectoderm-derived structure5.20e-1595
ectoderm5.20e-1595
presumptive ectoderm5.20e-1595
ecto-epithelium7.94e-1573
regional part of brain1.08e-1446
cerebral cortex1.28e-1421
cerebral hemisphere1.28e-1421
pallium1.28e-1421
regional part of cerebral cortex1.96e-1017
structure with developmental contribution from neural crest1.08e-0992
regional part of spinal cord2.85e-085
gray matter of spinal cord2.85e-085
corpus striatum5.66e-085
striatum5.66e-085
ventral part of telencephalon5.66e-085
future corpus striatum5.66e-085
spinal cord9.34e-076
dorsal region element9.34e-076
dorsum9.34e-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)
MA0003.10.211284
MA0004.10.603793
MA0006.10.419915
MA0007.10.587678
MA0009.11.06266
MA0014.10.187732
MA0017.11.99124
MA0019.10.874061
MA0024.12.32185
MA0025.11.30092
MA0027.12.72141
MA0028.10.43138
MA0029.10.995171
MA0030.11.00195
MA0031.10.965177
MA0038.10.757669
MA0040.11.07552
MA0041.10.522007
MA0042.10.507715
MA0043.11.1618
MA0046.11.09955
MA0048.10.205696
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.10.0851423
MA0056.10
MA0057.10.562607
MA0058.11.25013
MA0059.10.513699
MA0060.10.330907
MA0061.10.364227
MA0063.10
MA0066.10.746072
MA0067.11.41352
MA0068.10.197245
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.16.2889
MA0074.10.708108
MA0076.10.470037
MA0077.11.04318
MA0078.10.801834
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.11.42769
MA0089.10
MA0090.10.566938
MA0091.14.97552
MA0092.10.567278
MA0093.10.440484
MA0095.10
MA0098.10
MA0100.10.695835
MA0101.10.523409
MA0103.10.460936
MA0105.11.98468
MA0106.10.809991
MA0107.10.454197
MA0108.20.897859
MA0109.10
MA0111.10.582193
MA0113.10.780358
MA0114.11.69206
MA0115.12.6202
MA0116.10.419688
MA0117.11.13165
MA0119.10.524046
MA0122.11.15196
MA0124.11.35963
MA0125.11.28445
MA0130.10
MA0131.10.869325
MA0132.10
MA0133.10
MA0135.11.19898
MA0136.10.729175
MA0139.12.22941
MA0140.10.695713
MA0141.10.482463
MA0142.10.950155
MA0143.10.797553
MA0144.10.365053
MA0145.10.927481
MA0146.10.0604336
MA0147.10.378658
MA0148.10.621195
MA0149.10.529387
MA0062.20.254018
MA0035.20.700704
MA0039.21.42062
MA0138.20.861035
MA0002.20.299191
MA0137.20.479301
MA0104.20.315156
MA0047.20.75686
MA0112.20.47695
MA0065.22.84751
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.10.203217
MA0155.10.173445
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.10.898893
MA0163.14.36666
MA0164.11.7313
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.24.18591
MA0102.21.79669
MA0258.10.91616
MA0259.10.366802
MA0442.10
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