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MCL coexpression mm9:1355: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0046935;1-phosphatidylinositol-3-kinase regulator activity;0.0246534816194598;18710!GO:0007169;transmembrane receptor protein tyrosine kinase signaling pathway;0.0308033469676536;18710,12927!GO:0048008;platelet-derived growth factor receptor signaling pathway;0.0308033469676536;12927!GO:0035014;phosphoinositide 3-kinase regulator activity;0.0308033469676536;18710!GO:0007167;enzyme linked receptor protein signaling pathway;0.0351845416805496;18710,12927!GO:0005942;phosphoinositide 3-kinase complex;0.0351845416805496;18710!GO:0016339;calcium-dependent cell-cell adhesion;0.0351845416805496;93706!GO:0030054;cell junction;0.0473742144187332;12927,93706!}}
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junction;0.0473742144187332;12927,93706!|ontology_enrichment_celltype=CL:0002319!5.92e-13!43;CL:0000221!5.97e-13!44;CL:0000133!5.97e-13!44;CL:0000055!1.55e-12!49;CL:0000117!4.22e-12!23;CL:0000337!4.22e-12!23;CL:0000540!1.10e-11!33;CL:0000047!1.10e-11!33;CL:0000031!1.10e-11!33;CL:0000404!1.10e-11!33;CL:0000393!4.23e-11!39;CL:0000211!4.23e-11!39|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0001017!5.92e-26!73;UBERON:0001016!7.83e-26!75;UBERON:0004121!1.42e-24!95;UBERON:0000924!1.42e-24!95;UBERON:0006601!1.42e-24!95;UBERON:0002346!5.70e-24!64;UBERON:0003075!5.70e-24!64;UBERON:0007284!5.70e-24!64;UBERON:0001049!2.53e-23!52;UBERON:0005068!2.53e-23!52;UBERON:0006241!2.53e-23!52;UBERON:0007135!2.53e-23!52;UBERON:0000073!6.14e-23!54;UBERON:0010371!2.15e-21!73;UBERON:0010314!2.33e-21!92;UBERON:0000955!2.81e-20!47;UBERON:0006238!2.81e-20!47;UBERON:0002616!6.47e-20!46;UBERON:0002020!1.36e-18!34;UBERON:0003056!2.25e-18!49;UBERON:0003080!1.06e-17!40;UBERON:0002780!3.47e-17!39;UBERON:0001890!3.47e-17!39;UBERON:0006240!3.47e-17!39;UBERON:0003528!1.31e-15!29;UBERON:0002791!1.31e-15!29;UBERON:0001893!1.31e-15!29;UBERON:0000956!2.17e-12!21;UBERON:0001869!2.17e-12!21;UBERON:0000203!2.17e-12!21;UBERON:0000025!8.09e-11!114;UBERON:0004111!3.01e-10!122;UBERON:0002619!5.06e-10!17;UBERON:0000468!7.65e-08!333|tfbs_overrepresentation_for_novel_motifs=0.491922,0.819928,1.17362,0.535892,0.346849,0.550971,0.645383,0.247459,0.257202,1.48899,0.599767,0.632897,0.692139,0.6581,0.364314,0,0.856992,0.338549,0.656199,0.442204,0.426133,0.713088,0.657163,0.345236,0.472505,0.686615,0.223823,0.572827,1.02135,0.534301,0.558142,0.960397,0.336199,0.204204,0.364821,0.144368,0.326478,1.52228,0.303703,0.752287,0.342638,0.56353,0.0995018,0.366415,0.659176,0.524258,0.77511,0.589246,0.284064,1.02809,0.839084,0.714419,0.517905,1.10437,1.12205,0.66551,0.406788,0.619643,0.614918,0.663395,0.939962,0.724164,0.742129,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,1.1311,0.70565,0.740068,1.156,1.13013,0.19692,0.204132,0.763395,0.922432,0.430551,0.254777,0.874787,0.722675,0.676326,1.03903,2.18121,0.0610418,0.534643,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.2995,0.281222,0.244935,0.976308,0.775372,0.483322,0.326561,0.960112,1.08669,0.839694,0.838613,1.38336,0.8998,0.585058,0.435642,1.09461,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,0.902522,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.106956,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.920761,0.183562,0.0987301,1.10596,0.783181,0.678689,1.18867,0.71546,0.376898,0.48935,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.325308,0.63125,0.131395|tfbs_overrepresentation_jaspar=MA0003.1;1.03722,MA0004.1;1.3269,MA0006.1;0.359699,MA0007.1;1.29371,MA0009.1;0.987341,MA0014.1;1.71935,MA0017.1;0.387481,MA0019.1;0.800946,MA0024.1;0.942716,MA0025.1;1.22395,MA0027.1;2.64231,MA0028.1;0.370592,MA0029.1;0.920529,MA0030.1;0.927235,MA0031.1;0.890871,MA0038.1;0.686534,MA0040.1;1.00009,MA0041.1;0.457338,MA0042.1;0.443591,MA0043.1;1.08567,MA0046.1;1.02391,MA0048.1;0.486223,MA0050.1;0.57678,MA0051.1;0.695779,MA0052.1;1.00829,MA0055.1;0.212634,MA0056.1;0,MA0057.1;1.43735,MA0058.1;1.11298,MA0059.1;1.14076,MA0060.1;0.275911,MA0061.1;0.307097,MA0063.1;0,MA0066.1;1.61836,MA0067.1;1.33603,MA0068.1;0.153907,MA0069.1;1.00864,MA0070.1;0.998765,MA0071.1;0.575909,MA0072.1;0.990133,MA0073.1;0.270597,MA0074.1;0.638014,MA0076.1;0.407465,MA0077.1;0.968053,MA0078.1;0.729877,MA0081.1;0.473489,MA0083.1;1.08487,MA0084.1;1.66561,MA0087.1;1.04109,MA0088.1;1.19273,MA0089.1;0,MA0090.1;0.500693,MA0091.1;0.55008,MA0092.1;0.501022,MA0093.1;0.988233,MA0095.1;0,MA0098.1;0,MA0100.1;0.626021,MA0101.1;0.458688,MA0103.1;0.398766,MA0105.1;0.199622,MA0106.1;0.737893,MA0107.1;0.392331,MA0108.2;0.824407,MA0109.1;0,MA0111.1;0.515457,MA0113.1;0.708789,MA0114.1;0.304661,MA0115.1;1.08851,MA0116.1;0.359483,MA0117.1;1.05576,MA0119.1;0.459301,MA0122.1;1.07591,MA0124.1;1.28237,MA0125.1;1.20757,MA0130.1;0,MA0131.1;0.796279,MA0132.1;0,MA0133.1;0,MA0135.1;1.1226,MA0136.1;0.658622,MA0139.1;0.243463,MA0140.1;0.625902,MA0141.1;0.419361,MA0142.1;0.876028,MA0143.1;0.725672,MA0144.1;0.307873,MA0145.1;1.24552,MA0146.1;0.990842,MA0147.1;0.858298,MA0148.1;0.553294,MA0149.1;0.464445,MA0062.2;0.204999,MA0035.2;0.630778,MA0039.2;1.76222,MA0138.2;0.788113,MA0002.2;0.689262,MA0137.2;0.416331,MA0104.2;1.33199,MA0047.2;0.685741,MA0112.2;0.37938,MA0065.2;0.119561,MA0150.1;0.520653,MA0151.1;0,MA0152.1;0.685852,MA0153.1;1.13945,MA0154.1;0.480757,MA0155.1;1.33283,MA0156.1;0.406559,MA0157.1;0.843181,MA0158.1;0,MA0159.1;0.331229,MA0160.1;0.556423,MA0161.1;0,MA0162.1;1.53386,MA0163.1;1.4645,MA0164.1;0.658997,MA0080.2;0.393257,MA0018.2;0.669032,MA0099.2;0.781628,MA0079.2;1.5775,MA0102.2;1.7182,MA0258.1;0.290587,MA0259.1;1.5079,MA0442.1;0}}

Latest revision as of 16:48, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr14:121434731..121434742,+p7@Farp1
Mm9::chr18:37966664..37966677,+p@chr18:37966664..37966677
+
Mm9::chr1:95532218..95532229,-p4@Stk25
Mm9::chr4:115894226..115894237,+p3@Pik3r3
Mm9::chr8:114267768..114267787,-p3@Bcar1
Mm9::chr8:127187311..127187332,-p4@2310022B05Rik


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:00469351-phosphatidylinositol-3-kinase regulator activity0.0246534816194598
GO:0007169transmembrane receptor protein tyrosine kinase signaling pathway0.0308033469676536
GO:0048008platelet-derived growth factor receptor signaling pathway0.0308033469676536
GO:0035014phosphoinositide 3-kinase regulator activity0.0308033469676536
GO:0007167enzyme linked receptor protein signaling pathway0.0351845416805496
GO:0005942phosphoinositide 3-kinase complex0.0351845416805496
GO:0016339calcium-dependent cell-cell adhesion0.0351845416805496
GO:0030054cell junction0.0473742144187332



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
central nervous system5.92e-2673
nervous system7.83e-2675
ectoderm-derived structure1.42e-2495
ectoderm1.42e-2495
presumptive ectoderm1.42e-2495
neurectoderm5.70e-2464
neural plate5.70e-2464
presumptive neural plate5.70e-2464
neural tube2.53e-2352
neural rod2.53e-2352
future spinal cord2.53e-2352
neural keel2.53e-2352
regional part of nervous system6.14e-2354
ecto-epithelium2.15e-2173
structure with developmental contribution from neural crest2.33e-2192
brain2.81e-2047
future brain2.81e-2047
regional part of brain6.47e-2046
gray matter1.36e-1834
pre-chordal neural plate2.25e-1849
anterior neural tube1.06e-1740
regional part of forebrain3.47e-1739
forebrain3.47e-1739
future forebrain3.47e-1739
brain grey matter1.31e-1529
regional part of telencephalon1.31e-1529
telencephalon1.31e-1529
cerebral cortex2.17e-1221
cerebral hemisphere2.17e-1221
pallium2.17e-1221
tube8.09e-11114
anatomical conduit3.01e-10122
regional part of cerebral cortex5.06e-1017
multi-cellular organism7.65e-08333


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)
MA0003.11.03722
MA0004.11.3269
MA0006.10.359699
MA0007.11.29371
MA0009.10.987341
MA0014.11.71935
MA0017.10.387481
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.370592
MA0029.10.920529
MA0030.10.927235
MA0031.10.890871
MA0038.10.686534
MA0040.11.00009
MA0041.10.457338
MA0042.10.443591
MA0043.11.08567
MA0046.11.02391
MA0048.10.486223
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.212634
MA0056.10
MA0057.11.43735
MA0058.11.11298
MA0059.11.14076
MA0060.10.275911
MA0061.10.307097
MA0063.10
MA0066.11.61836
MA0067.11.33603
MA0068.10.153907
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.10.270597
MA0074.10.638014
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.11.19273
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.10.501022
MA0093.10.988233
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.10.458688
MA0103.10.398766
MA0105.10.199622
MA0106.10.737893
MA0107.10.392331
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.304661
MA0115.11.08851
MA0116.10.359483
MA0117.11.05576
MA0119.10.459301
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.10.796279
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.10.658622
MA0139.10.243463
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.11.24552
MA0146.10.990842
MA0147.10.858298
MA0148.10.553294
MA0149.10.464445
MA0062.20.204999
MA0035.20.630778
MA0039.21.76222
MA0138.20.788113
MA0002.20.689262
MA0137.20.416331
MA0104.21.33199
MA0047.20.685741
MA0112.20.37938
MA0065.20.119561
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.480757
MA0155.11.33283
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.11.53386
MA0163.11.4645
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.21.5775
MA0102.21.7182
MA0258.10.290587
MA0259.11.5079
MA0442.10
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