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MCL coexpression mm9:1805: Difference between revisions

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{{MCL_coexpression_mm9
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cytoskeleton organization and biogenesis;0.00300527903998777;11641,50768!GO:0030029;actin filament-based process;0.00300527903998777;11641,50768!GO:0048041;focal adhesion formation;0.0110705550622698;50768!GO:0007010;cytoskeleton organization and biogenesis;0.0110705550622698;11641,50768!GO:0051018;protein kinase A binding;0.0129707221430816;11641!GO:0005100;Rho GTPase activator activity;0.0185255414448508;50768!GO:0021575;hindbrain morphogenesis;0.0185255414448508;50768!GO:0006996;organelle organization and biogenesis;0.0230730798064303;11641,50768!GO:0003007;heart morphogenesis;0.0230730798064303;50768!GO:0007015;actin filament organization;0.0230730798064303;11641!GO:0030902;hindbrain development;0.0230730798064303;50768!GO:0001843;neural tube closure;0.0230730798064303;50768!GO:0014020;primary neural tube formation;0.0230730798064303;50768!GO:0005099;Ras GTPase activator activity;0.0230730798064303;50768!GO:0019901;protein kinase binding;0.0230730798064303;11641!GO:0019900;kinase binding;0.0230730798064303;11641!GO:0001841;neural tube formation;0.0230730798064303;50768!GO:0001839;neural plate morphogenesis;0.0230730798064303;50768!GO:0001840;neural plate development;0.0230730798064303;50768!GO:0001838;embryonic epithelial tube formation;0.0230730798064303;50768!GO:0007160;cell-matrix adhesion;0.0235769978571226;50768!GO:0021915;neural tube development;0.0235769978571226;50768!GO:0031589;cell-substrate adhesion;0.0235769978571226;50768!GO:0016331;morphogenesis of embryonic epithelium;0.0246139683323876;50768!GO:0007178;transmembrane receptor protein serine/threonine kinase signaling pathway;0.0248944883805912;11641!GO:0007266;Rho protein signal transduction;0.0248944883805912;50768!GO:0030900;forebrain development;0.0299491345571582;50768!GO:0002009;morphogenesis of an epithelium;0.0354993707898815;50768!GO:0019899;enzyme binding;0.0358622256579649;11641!GO:0016043;cellular component organization and biogenesis;0.0358622256579649;11641,50768!GO:0035239;tube morphogenesis;0.0358622256579649;50768!GO:0007265;Ras protein signal transduction;0.0358622256579649;50768!GO:0005083;small GTPase regulator activity;0.0358622256579649;50768!GO:0005096;GTPase activator activity;0.0358622256579649;50768!GO:0007507;heart development;0.0392006300624062;50768!GO:0007420;brain development;0.0412344423135765;50768!GO:0048598;embryonic morphogenesis;0.0417653652618351;50768!GO:0035295;tube development;0.0417653652618351;50768!GO:0008047;enzyme activator activity;0.0417653652618351;50768!GO:0016337;cell-cell adhesion;0.041923842515526;50768!GO:0043009;chordate embryonic development;0.0429798586251968;50768!GO:0009792;embryonic development ending in birth or egg hatching;0.0429798586251968;50768!GO:0007417;central nervous system development;0.043283859516484;50768!GO:0007167;enzyme linked receptor protein signaling 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|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004535!6.40e-11!23;UBERON:0001009!6.40e-11!23;UBERON:0004872!7.47e-11!33;UBERON:0007100!1.23e-10!18;UBERON:0000948!1.23e-10!18;UBERON:0005498!1.23e-10!18;UBERON:0004140!1.23e-10!18;UBERON:0009881!1.23e-10!18;UBERON:0004141!1.23e-10!18;UBERON:0003084!1.23e-10!18;UBERON:0007005!1.23e-10!18;UBERON:0004139!1.23e-10!18;UBERON:0004291!1.23e-10!18;UBERON:0003103!9.73e-08!43;UBERON:0002048!1.57e-07!14;UBERON:0000117!1.57e-07!14;UBERON:0000171!1.57e-07!14;UBERON:0000170!1.57e-07!14;UBERON:0005597!1.57e-07!14;UBERON:0000118!1.57e-07!14;UBERON:0000468!5.09e-07!333;UBERON:0000922!7.76e-07!320
|tfbs_overrepresentation_for_novel_motifs=0.557864,0.612204,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.310789,0.115752,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,0.397593,0.283802,0.185796,0.489529,0.145201,0.727684,0.404661,0.537749,0.757752,0.274609,0.641282,0.456327,0.227599,0.626183,1.03545,0.395107,0.253145,0.425309,0.454919,0.384813,0.699032,0.360612,0.328675,1.03785,0.631725,0.134724,0.426986,0.4934,0.591277,0.847828,0.658142,0.115788,0.459555,0.912738,0.786094,0.220111,1.18062,1.19842,0.73621,0.469329,0.689304,0.26467,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.30684,0.152094,1.23259,0.257421,0.245132,0.253065,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.796301,1.1148,0.0793594,0.0882907,0.645625,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.3366,0.806207,1.05152,0.848095,0.20438,0.384901,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,0.491483,0.550229,1.16464,0.495367,0.674448,1.41481,0.399936,0.0998646,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,3.16898,0.44142,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,0.230371,0.133815,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.997706,0.701187,0.0513167
|tfbs_overrepresentation_jaspar=MA0003.1;0.0185483,MA0004.1;0.603793,MA0006.1;0.419915,MA0007.1;0.587678,MA0009.1;1.06266,MA0014.1;0.0502051,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;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;1.71065,MA0069.1;1.08414,MA0070.1;1.07418,MA0071.1;0.644448,MA0072.1;1.06547,MA0073.1;3.73882,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;0.148348,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;0.248108,MA0106.1;0.809991,MA0107.1;1.15122,MA0108.2;0.897859,MA0109.1;0,MA0111.1;0.582193,MA0113.1;1.83629,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;0.295945,MA0140.1;0.695713,MA0141.1;0.482463,MA0142.1;0.950155,MA0143.1;0.797553,MA0144.1;0.365053,MA0145.1;0.157686,MA0146.1;0.0604336,MA0147.1;0.378658,MA0148.1;1.50563,MA0149.1;0.529387,MA0062.2;0.254018,MA0035.2;0.700704,MA0039.2;0.0511423,MA0138.2;0.861035,MA0002.2;0.299191,MA0137.2;0.479301,MA0104.2;0.315156,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;0.203217,MA0155.1;0.173445,MA0156.1;0.469089,MA0157.1;0.91689,MA0158.1;0,MA0159.1;1.01146,MA0160.1;0.624415,MA0161.1;0,MA0162.1;0.0699535,MA0163.1;0.230013,MA0164.1;0.729558,MA0080.2;0.455167,MA0018.2;0.739807,MA0099.2;0.854449,MA0079.2;0.967156,MA0102.2;1.79669,MA0258.1;0.346619,MA0259.1;0.366802,MA0442.1;0
}}

Latest revision as of 17:31, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr4:57885681..57885689,+p@chr4:57885681..57885689
+
Mm9::chr4:57905792..57905813,+p@chr4:57905792..57905813
+
Mm9::chr4:57905869..57905880,+p@chr4:57905869..57905880
+
Mm9::chr4:57906592..57906605,+p@chr4:57906592..57906605
+
Mm9::chr8:37631781..37631786,-p@chr8:37631781..37631786
-


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:0030036actin cytoskeleton organization and biogenesis0.00300527903998777
GO:0030029actin filament-based process0.00300527903998777
GO:0048041focal adhesion formation0.0110705550622698
GO:0007010cytoskeleton organization and biogenesis0.0110705550622698
GO:0051018protein kinase A binding0.0129707221430816
GO:0005100Rho GTPase activator activity0.0185255414448508
GO:0021575hindbrain morphogenesis0.0185255414448508
GO:0006996organelle organization and biogenesis0.0230730798064303
GO:0003007heart morphogenesis0.0230730798064303
GO:0007015actin filament organization0.0230730798064303
GO:0030902hindbrain development0.0230730798064303
GO:0001843neural tube closure0.0230730798064303
GO:0014020primary neural tube formation0.0230730798064303
GO:0005099Ras GTPase activator activity0.0230730798064303
GO:0019901protein kinase binding0.0230730798064303
GO:0019900kinase binding0.0230730798064303
GO:0001841neural tube formation0.0230730798064303
GO:0001839neural plate morphogenesis0.0230730798064303
GO:0001840neural plate development0.0230730798064303
GO:0001838embryonic epithelial tube formation0.0230730798064303
GO:0007160cell-matrix adhesion0.0235769978571226
GO:0021915neural tube development0.0235769978571226
GO:0031589cell-substrate adhesion0.0235769978571226
GO:0016331morphogenesis of embryonic epithelium0.0246139683323876
GO:0007178transmembrane receptor protein serine/threonine kinase signaling pathway0.0248944883805912
GO:0007266Rho protein signal transduction0.0248944883805912
GO:0030900forebrain development0.0299491345571582
GO:0002009morphogenesis of an epithelium0.0354993707898815
GO:0019899enzyme binding0.0358622256579649
GO:0016043cellular component organization and biogenesis0.0358622256579649
GO:0035239tube morphogenesis0.0358622256579649
GO:0007265Ras protein signal transduction0.0358622256579649
GO:0005083small GTPase regulator activity0.0358622256579649
GO:0005096GTPase activator activity0.0358622256579649
GO:0007507heart development0.0392006300624062
GO:0007420brain development0.0412344423135765
GO:0048598embryonic morphogenesis0.0417653652618351
GO:0035295tube development0.0417653652618351
GO:0008047enzyme activator activity0.0417653652618351
GO:0016337cell-cell adhesion0.041923842515526
GO:0043009chordate embryonic development0.0429798586251968
GO:0009792embryonic development ending in birth or egg hatching0.0429798586251968
GO:0007417central nervous system development0.043283859516484
GO:0007167enzyme linked receptor protein signaling pathway0.0486622483649315



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
cardiovascular system6.40e-1123
circulatory system6.40e-1123
splanchnic layer of lateral plate mesoderm7.47e-1133
primary circulatory organ1.23e-1018
heart1.23e-1018
primitive heart tube1.23e-1018
primary heart field1.23e-1018
anterior lateral plate mesoderm1.23e-1018
heart tube1.23e-1018
heart primordium1.23e-1018
cardiac mesoderm1.23e-1018
cardiogenic plate1.23e-1018
heart rudiment1.23e-1018
compound organ9.73e-0843
lung1.57e-0714
respiratory tube1.57e-0714
respiration organ1.57e-0714
pair of lungs1.57e-0714
lung primordium1.57e-0714
lung bud1.57e-0714
multi-cellular organism5.09e-07333
embryo7.76e-07320


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)
MA0003.10.0185483
MA0004.10.603793
MA0006.10.419915
MA0007.10.587678
MA0009.11.06266
MA0014.10.0502051
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
MA0048.10.205696
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
MA0068.11.71065
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.13.73882
MA0074.10.708108
MA0076.10.470037
MA0077.11.04318
MA0078.10.801834
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.10.148348
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
MA0105.10.248108
MA0106.10.809991
MA0107.11.15122
MA0108.20.897859
MA0109.10
MA0111.10.582193
MA0113.11.83629
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
MA0139.10.295945
MA0140.10.695713
MA0141.10.482463
MA0142.10.950155
MA0143.10.797553
MA0144.10.365053
MA0145.10.157686
MA0146.10.0604336
MA0147.10.378658
MA0148.11.50563
MA0149.10.529387
MA0062.20.254018
MA0035.20.700704
MA0039.20.0511423
MA0138.20.861035
MA0002.20.299191
MA0137.20.479301
MA0104.20.315156
MA0047.20.75686
MA0112.20.157681
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
MA0159.11.01146
MA0160.10.624415
MA0161.10
MA0162.10.0699535
MA0163.10.230013
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.20.967156
MA0102.21.79669
MA0258.10.346619
MA0259.10.366802
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:1805&oldid=3073804"