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MCL coexpression mm9:1664: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0005153!9.14e-08!17;UBERON:0007100!1.11e-07!18;UBERON:0000948!1.11e-07!18;UBERON:0005498!1.11e-07!18;UBERON:0004140!1.11e-07!18;UBERON:0009881!1.11e-07!18;UBERON:0004141!1.11e-07!18;UBERON:0003084!1.11e-07!18;UBERON:0007005!1.11e-07!18;UBERON:0004139!1.11e-07!18;UBERON:0004291!1.11e-07!18;UBERON:0004872!1.28e-07!33;UBERON:0002048!1.40e-07!14;UBERON:0000117!1.40e-07!14;UBERON:0000171!1.40e-07!14;UBERON:0000170!1.40e-07!14;UBERON:0005597!1.40e-07!14;UBERON:0000118!1.40e-07!14
|ontology_enrichment_uberon=UBERON:0005153!9.14e-08!17;UBERON:0007100!1.11e-07!18;UBERON:0000948!1.11e-07!18;UBERON:0005498!1.11e-07!18;UBERON:0004140!1.11e-07!18;UBERON:0009881!1.11e-07!18;UBERON:0004141!1.11e-07!18;UBERON:0003084!1.11e-07!18;UBERON:0007005!1.11e-07!18;UBERON:0004139!1.11e-07!18;UBERON:0004291!1.11e-07!18;UBERON:0004872!1.28e-07!33;UBERON:0002048!1.40e-07!14;UBERON:0000117!1.40e-07!14;UBERON:0000171!1.40e-07!14;UBERON:0000170!1.40e-07!14;UBERON:0005597!1.40e-07!14;UBERON:0000118!1.40e-07!14
|tfbs_overrepresentation_for_novel_motifs=0.557864,0.612204,1.31238,0.603273,1.04755,0.618805,1.70247,0.300268,0.310789,0.370407,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,0.397593,0.283802,0.185796,0.489529,1.4086,0.727684,0.404661,2.28527,0.757752,0.274609,0.641282,0.456327,0.645258,0.626183,1.03545,0.395107,0.253145,1.08876,0.454919,0.384813,0.699032,0.360612,0.328675,1.03785,0.631725,0.419293,1.91654,0.0637209,0.591277,0.847828,0.658142,0.370501,1.16276,0.912738,0.786094,0.220111,1.18062,1.19842,0.73621,1.18377,1.64777,0.26467,0.734051,1.01481,1.86856,0.865544,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.30684,1.45025,1.23259,2.03319,0.245132,0.253065,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.293164,1.1148,2.60379,0.0882907,0.645625,0.852952,1.85284,1.40768,1.11989,2.38494,0.412897,0.937248,0.89388,0.297538,1.05152,3.27368,0.20438,1.7727,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,1.5739,0.499439,0.491483,0.550229,1.16464,1.23956,0.674448,1.41481,1.82437,2.90094,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.143464,0.566955,5.05969,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,1.21592,2.6072,1.18223,0.343194,0.749664,1.26545,0.787153,1.11626,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,0.191104
|tfbs_overrepresentation_for_novel_motifs=0.557864,0.612204,1.31238,0.603273,1.04755,0.618805,1.70247,0.300268,0.310789,0.370407,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,0.397593,0.283802,0.185796,0.489529,1.4086,0.727684,0.404661,2.28527,0.757752,0.274609,0.641282,0.456327,0.645258,0.626183,1.03545,0.395107,0.253145,1.08876,0.454919,0.384813,0.699032,0.360612,0.328675,1.03785,0.631725,0.419293,1.91654,0.0637209,0.591277,0.847828,0.658142,0.370501,1.16276,0.912738,0.786094,0.220111,1.18062,1.19842,0.73621,1.18377,1.64777,0.26467,0.734051,1.01481,1.86856,0.865544,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.30684,1.45025,1.23259,2.03319,0.245132,0.253065,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.293164,1.1148,2.60379,0.0882907,0.645625,0.852952,1.85284,1.40768,1.11989,2.38494,0.412897,0.937248,0.89388,0.297538,1.05152,3.27368,0.20438,1.7727,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,1.5739,0.499439,0.491483,0.550229,1.16464,1.23956,0.674448,1.41481,1.82437,2.90094,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.143464,0.566955,5.05969,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,1.21592,2.6072,1.18223,0.343194,0.749664,1.26545,0.787153,1.11626,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,0.191104
|tfbs_overrepresentation_jaspar=MA0003.1;1.36559,MA0004.1;0.603793,MA0006.1;1.07705,MA0007.1;0.587678,MA0009.1;2.41343,MA0014.1;4.67725,MA0017.1;0.449113,MA0019.1;0.874061,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;1.12075,MA0050.1;0.645342,MA0051.1;0.767098,MA0052.1;1.08379,MA0055.1;0.28842,MA0056.1;0,MA0057.1;1.06992,MA0058.1;0.50032,MA0059.1;0.513699,MA0060.1;0.330907,MA0061.1;0.955135,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;1.55428,MA0072.1;1.06547,MA0073.1;0.65603,MA0074.1;2.83367,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;3.51516,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;2.77668,MA0106.1;0.809991,MA0107.1;1.15122,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;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;2.10278,MA0142.1;0.950155,MA0143.1;0.797553,MA0144.1;0.365053,MA0145.1;0.157686,MA0146.1;0.822925,MA0147.1;0.378658,MA0148.1;0.621195,MA0149.1;0.529387,MA0062.2;0.254018,MA0035.2;0.700704,MA0039.2;1.8247,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;0.158101,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;0.245828,MA0163.1;0.497328,MA0164.1;0.729558,MA0080.2;0.455167,MA0018.2;0.739807,MA0099.2;0.854449,MA0079.2;3.77735,MA0102.2;1.79669,MA0258.1;0.346619,MA0259.1;0.366802,MA0442.1;0
}}
}}

Revision as of 13:40, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr14:46149805..46149857,-p4@Fermt2
Mm9::chr17:44325552..44325567,+p2@Clic5
Mm9::chr17:44325602..44325613,+p4@Clic5
Mm9::chr17:44325614..44325625,+p5@Clic5
Mm9::chr17:44325638..44325651,+p3@Clic5


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:0060088auditory receptor cell stereocilium organization and biogenesis0.00584378823572381
GO:0002093auditory receptor cell morphogenesis0.00584378823572381
GO:0060122inner ear receptor stereocilium organization and biogenesis0.00584378823572381
GO:0032420stereocilium0.00584378823572381
GO:0060119inner ear receptor cell development0.00584378823572381
GO:0060117auditory receptor cell development0.00584378823572381
GO:0032421stereocilium bundle0.00626120168113265
GO:0005247voltage-gated chloride channel activity0.00730473529465476
GO:0022844voltage-gated anion channel activity0.00730473529465476
GO:0005902microvillus0.00745083000054786
GO:0042491auditory receptor cell differentiation0.00916412246056688
GO:0060113inner ear receptor cell differentiation0.00986139264778393
GO:0050885neuromuscular process controlling balance0.0103309827738689
GO:0042490mechanoreceptor differentiation0.0103309827738689
GO:0050905neuromuscular process0.0119532032094351
GO:0043168anion binding0.0119532032094351
GO:0042472inner ear morphogenesis0.0119532032094351
GO:0031404chloride ion binding0.0119532032094351
GO:0005254chloride channel activity0.0119532032094351
GO:0006821chloride transport0.0119532032094351
GO:0042471ear morphogenesis0.0119532032094351
GO:0005253anion channel activity0.0119532032094351
GO:0048839inner ear development0.013339081842413
GO:0043583ear development0.013878997059844
GO:0007605sensory perception of sound0.0161288555305977
GO:0050954sensory perception of mechanical stimulus0.0163513690057272
GO:0008509anion transmembrane transporter activity0.0181806745111407
GO:0015698inorganic anion transport0.0219142058839643
GO:0006820anion transport0.0236107895653035
GO:0022832voltage-gated channel activity0.0236107895653035
GO:0005244voltage-gated ion channel activity0.0236107895653035
GO:0007423sensory organ development0.0254752643401085
GO:0048598embryonic morphogenesis0.0266954871677383
GO:0022836gated channel activity0.0316275295730728
GO:0032990cell part morphogenesis0.0316275295730728
GO:0030030cell projection organization and biogenesis0.0316275295730728
GO:0048858cell projection morphogenesis0.0316275295730728
GO:0005216ion channel activity0.0389238037843747
GO:0022838substrate specific channel activity0.0389238037843747
GO:0042995cell projection0.0389238037843747
GO:0022803passive transmembrane transporter activity0.0389238037843747
GO:0015267channel activity0.0389238037843747
GO:0009790embryonic development0.0448023764738825
GO:0000902cell morphogenesis0.0448023764738825
GO:0032989cellular structure morphogenesis0.0448023764738825
GO:0009887organ morphogenesis0.0474490196965835



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
epithelial bud9.14e-0817
primary circulatory organ1.11e-0718
heart1.11e-0718
primitive heart tube1.11e-0718
primary heart field1.11e-0718
anterior lateral plate mesoderm1.11e-0718
heart tube1.11e-0718
heart primordium1.11e-0718
cardiac mesoderm1.11e-0718
cardiogenic plate1.11e-0718
heart rudiment1.11e-0718
splanchnic layer of lateral plate mesoderm1.28e-0733
lung1.40e-0714
respiratory tube1.40e-0714
respiration organ1.40e-0714
pair of lungs1.40e-0714
lung primordium1.40e-0714
lung bud1.40e-0714


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)
MA0003.11.36559
MA0004.10.603793
MA0006.11.07705
MA0007.10.587678
MA0009.12.41343
MA0014.14.67725
MA0017.10.449113
MA0019.10.874061
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
MA0048.11.12075
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.10.28842
MA0056.10
MA0057.11.06992
MA0058.10.50032
MA0059.10.513699
MA0060.10.330907
MA0061.10.955135
MA0063.10
MA0066.10.746072
MA0067.11.41352
MA0068.10.197245
MA0069.11.08414
MA0070.11.07418
MA0071.11.55428
MA0072.11.06547
MA0073.10.65603
MA0074.12.83367
MA0076.10.470037
MA0077.11.04318
MA0078.10.801834
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.13.51516
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
MA0105.12.77668
MA0106.10.809991
MA0107.11.15122
MA0108.20.897859
MA0109.10
MA0111.10.582193
MA0113.10.780358
MA0114.10.361633
MA0115.11.16466
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
MA0141.12.10278
MA0142.10.950155
MA0143.10.797553
MA0144.10.365053
MA0145.10.157686
MA0146.10.822925
MA0147.10.378658
MA0148.10.621195
MA0149.10.529387
MA0062.20.254018
MA0035.20.700704
MA0039.21.8247
MA0138.20.861035
MA0002.20.299191
MA0137.20.479301
MA0104.20.315156
MA0047.20.75686
MA0112.20.47695
MA0065.20.158101
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
MA0162.10.245828
MA0163.10.497328
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.23.77735
MA0102.21.79669
MA0258.10.346619
MA0259.10.366802
MA0442.10
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