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MCL coexpression mm9:1589: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000073!1.07e-13!54;UBERON:0010314!1.09e-13!92;UBERON:0001017!6.10e-13!73;UBERON:0000025!9.25e-13!114;UBERON:0004111!1.17e-12!122;UBERON:0001049!1.56e-12!52;UBERON:0005068!1.56e-12!52;UBERON:0006241!1.56e-12!52;UBERON:0007135!1.56e-12!52;UBERON:0001016!1.66e-12!75;UBERON:0002346!5.48e-11!64;UBERON:0003075!5.48e-11!64;UBERON:0007284!5.48e-11!64;UBERON:0000955!1.78e-10!47;UBERON:0006238!1.78e-10!47;UBERON:0002616!4.87e-10!46;UBERON:0004121!6.19e-10!95;UBERON:0000924!6.19e-10!95;UBERON:0006601!6.19e-10!95;UBERON:0010371!1.50e-09!73;UBERON:0000468!1.59e-09!333;UBERON:0002048!7.31e-09!14;UBERON:0000117!7.31e-09!14;UBERON:0000171!7.31e-09!14;UBERON:0000170!7.31e-09!14;UBERON:0005597!7.31e-09!14;UBERON:0000118!7.31e-09!14;UBERON:0005153!5.53e-08!17;UBERON:0003080!8.92e-08!40;UBERON:0002780!2.66e-07!39;UBERON:0001890!2.66e-07!39;UBERON:0006240!2.66e-07!39;UBERON:0005157!5.30e-07!20;UBERON:0003056!5.83e-07!49
|ontology_enrichment_uberon=UBERON:0000073!1.07e-13!54;UBERON:0010314!1.09e-13!92;UBERON:0001017!6.10e-13!73;UBERON:0000025!9.25e-13!114;UBERON:0004111!1.17e-12!122;UBERON:0001049!1.56e-12!52;UBERON:0005068!1.56e-12!52;UBERON:0006241!1.56e-12!52;UBERON:0007135!1.56e-12!52;UBERON:0001016!1.66e-12!75;UBERON:0002346!5.48e-11!64;UBERON:0003075!5.48e-11!64;UBERON:0007284!5.48e-11!64;UBERON:0000955!1.78e-10!47;UBERON:0006238!1.78e-10!47;UBERON:0002616!4.87e-10!46;UBERON:0004121!6.19e-10!95;UBERON:0000924!6.19e-10!95;UBERON:0006601!6.19e-10!95;UBERON:0010371!1.50e-09!73;UBERON:0000468!1.59e-09!333;UBERON:0002048!7.31e-09!14;UBERON:0000117!7.31e-09!14;UBERON:0000171!7.31e-09!14;UBERON:0000170!7.31e-09!14;UBERON:0005597!7.31e-09!14;UBERON:0000118!7.31e-09!14;UBERON:0005153!5.53e-08!17;UBERON:0003080!8.92e-08!40;UBERON:0002780!2.66e-07!39;UBERON:0001890!2.66e-07!39;UBERON:0006240!2.66e-07!39;UBERON:0005157!5.30e-07!20;UBERON:0003056!5.83e-07!49
|tfbs_overrepresentation_for_novel_motifs=0.557864,0.612204,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.310789,1.78433,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,0.397593,0.775038,0.185796,0.489529,2.72171,0.727684,1.04384,0.537749,1.78963,1.38127,1.54767,1.15581,0.645258,0.626183,1.03545,0.395107,0.704734,1.91085,0.0566307,1.00043,0.699032,0.360612,0.328675,0.401916,0.631725,0.419293,0.426986,1.28479,0.591277,0.847828,0.658142,0.370501,1.16276,0.912738,0.786094,0.627649,1.18062,1.19842,0.73621,0.469329,0.689304,1.34464,0.734051,1.01481,0.796017,0.865544,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.30684,0.46305,1.23259,1.31774,1.27178,0.253065,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.293164,2.51921,1.44773,0.618102,0.227755,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.3366,0.297538,1.05152,0.848095,0.20438,0.384901,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,0.491483,0.550229,1.16464,0.495367,0.674448,1.41481,0.399936,4.37906,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.867604,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,3.4958,0.416978,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,2.13308
|tfbs_overrepresentation_for_novel_motifs=0.557864,0.612204,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.310789,1.78433,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,0.397593,0.775038,0.185796,0.489529,2.72171,0.727684,1.04384,0.537749,1.78963,1.38127,1.54767,1.15581,0.645258,0.626183,1.03545,0.395107,0.704734,1.91085,0.0566307,1.00043,0.699032,0.360612,0.328675,0.401916,0.631725,0.419293,0.426986,1.28479,0.591277,0.847828,0.658142,0.370501,1.16276,0.912738,0.786094,0.627649,1.18062,1.19842,0.73621,0.469329,0.689304,1.34464,0.734051,1.01481,0.796017,0.865544,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.30684,0.46305,1.23259,1.31774,1.27178,0.253065,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.293164,2.51921,1.44773,0.618102,0.227755,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.3366,0.297538,1.05152,0.848095,0.20438,0.384901,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,0.491483,0.550229,1.16464,0.495367,0.674448,1.41481,0.399936,4.37906,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.867604,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,3.4958,0.416978,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,2.13308
|tfbs_overrepresentation_jaspar=MA0003.1;2.26461,MA0004.1;0.603793,MA0006.1;1.07705,MA0007.1;0.587678,MA0009.1;1.06266,MA0014.1;1.59137,MA0017.1;0.449113,MA0019.1;3.35456,MA0024.1;1.01759,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;0.192781,MA0058.1;0.50032,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;2.46751,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;0.888325,MA0089.1;0,MA0090.1;0.566938,MA0091.1;0.617887,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;0.361633,MA0115.1;1.16466,MA0116.1;1.07655,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;0.295945,MA0140.1;0.695713,MA0141.1;2.10278,MA0142.1;0.950155,MA0143.1;0.797553,MA0144.1;0.365053,MA0145.1;2.12682,MA0146.1;4.26043,MA0147.1;0.986917,MA0148.1;0.621195,MA0149.1;0.529387,MA0062.2;0.706751,MA0035.2;0.700704,MA0039.2;2.75243,MA0138.2;0.861035,MA0002.2;0.809945,MA0137.2;0.479301,MA0104.2;1.52809,MA0047.2;0.75686,MA0112.2;0.157681,MA0065.2;0.158101,MA0150.1;0.587557,MA0151.1;0,MA0152.1;0.756973,MA0153.1;1.21594,MA0154.1;0.587595,MA0155.1;0.99229,MA0156.1;0.469089,MA0157.1;0.91689,MA0158.1;0,MA0159.1;0.389847,MA0160.1;0.624415,MA0161.1;0,MA0162.1;3.09272,MA0163.1;3.65448,MA0164.1;0.729558,MA0080.2;0.455167,MA0018.2;0.739807,MA0099.2;0.854449,MA0079.2;0.765158,MA0102.2;1.79669,MA0258.1;0.91616,MA0259.1;0.366802,MA0442.1;0
}}
}}

Revision as of 13:34, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:87391886..87391972,+p1@Sept4
Mm9::chr14:70930626..70930654,+p2@Lgi3
Mm9::chr14:70930656..70930686,+p1@Lgi3
Mm9::chr14:70930803..70930810,+p4@Lgi3
Mm9::chr3:102538826..102538875,+p2@Tspan2


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:0030382sperm mitochondrion organization and biogenesis0.0167616121174166
GO:0048240sperm capacitation0.0167616121174166



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.07e-1354
structure with developmental contribution from neural crest1.09e-1392
central nervous system6.10e-1373
tube9.25e-13114
anatomical conduit1.17e-12122
neural tube1.56e-1252
neural rod1.56e-1252
future spinal cord1.56e-1252
neural keel1.56e-1252
nervous system1.66e-1275
neurectoderm5.48e-1164
neural plate5.48e-1164
presumptive neural plate5.48e-1164
brain1.78e-1047
future brain1.78e-1047
regional part of brain4.87e-1046
ectoderm-derived structure6.19e-1095
ectoderm6.19e-1095
presumptive ectoderm6.19e-1095
ecto-epithelium1.50e-0973
multi-cellular organism1.59e-09333
lung7.31e-0914
respiratory tube7.31e-0914
respiration organ7.31e-0914
pair of lungs7.31e-0914
lung primordium7.31e-0914
lung bud7.31e-0914
epithelial bud5.53e-0817
anterior neural tube8.92e-0840
regional part of forebrain2.66e-0739
forebrain2.66e-0739
future forebrain2.66e-0739
epithelial fold5.30e-0720
pre-chordal neural plate5.83e-0749


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)
MA0003.12.26461
MA0004.10.603793
MA0006.11.07705
MA0007.10.587678
MA0009.11.06266
MA0014.11.59137
MA0017.10.449113
MA0019.13.35456
MA0024.11.01759
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
MA0057.10.192781
MA0058.10.50032
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
MA0073.12.46751
MA0074.10.708108
MA0076.10.470037
MA0077.11.04318
MA0078.10.801834
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.10.888325
MA0089.10
MA0090.10.566938
MA0091.10.617887
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
MA0114.10.361633
MA0115.11.16466
MA0116.11.07655
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
MA0139.10.295945
MA0140.10.695713
MA0141.12.10278
MA0142.10.950155
MA0143.10.797553
MA0144.10.365053
MA0145.12.12682
MA0146.14.26043
MA0147.10.986917
MA0148.10.621195
MA0149.10.529387
MA0062.20.706751
MA0035.20.700704
MA0039.22.75243
MA0138.20.861035
MA0002.20.809945
MA0137.20.479301
MA0104.21.52809
MA0047.20.75686
MA0112.20.157681
MA0065.20.158101
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.10.587595
MA0155.10.99229
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.13.09272
MA0163.13.65448
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.20.765158
MA0102.21.79669
MA0258.10.91616
MA0259.10.366802
MA0442.10
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