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MCL coexpression mm9:2165: Difference between revisions

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{{MCL_coexpression_mm9
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099146531,0.232248715859676,0.238257510563801,0.319514988439541,0.260123047271308,0.226953780456906,0.244527676310416,0.204343226098226,0.280188057556759,0.406863532209059,0.209439279369182,0.358625807932077,0.185660734839627,0.647567312725935,0.465375341689751,0.71774397069283|gostat_on_MCL_coexpression=GO:0030934;anchoring collagen;6.20334193880936e-08;12841,12840!GO:0005593;FACIT collagen;6.20334193880936e-08;12841,12840!GO:0005594;collagen type IX;6.20334193880936e-08;12841,12840!GO:0030020;extracellular matrix structural constituent conferring tensile strength;1.88891762036745e-05;12841,12840!GO:0005581;collagen;2.21459307215495e-05;12841,12840!GO:0005201;extracellular matrix structural constituent;5.4899576158463e-05;12841,12840!GO:0044420;extracellular matrix part;0.00011128795438224;12841,12840!GO:0005578;proteinaceous extracellular matrix;0.000902144263983623;12841,12840!GO:0022610;biological adhesion;0.00321168103534753;12841,12840!GO:0007155;cell adhesion;0.00321168103534753;12841,12840!GO:0006817;phosphate transport;0.0206515964031062;12840!GO:0005615;extracellular space;0.0300779114333823;12841,12840!GO:0044421;extracellular region part;0.0311908040996588;12841,12840!GO:0015698;inorganic anion transport;0.0338376794407204;12840!GO:0006820;anion transport;0.0374202582905894;12840!GO:0001501;skeletal 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|gostat_on_MCL_coexpression=GO:0030934;anchoring collagen;6.20334193880936e-08;12841,12840!GO:0005593;FACIT collagen;6.20334193880936e-08;12841,12840!GO:0005594;collagen type IX;6.20334193880936e-08;12841,12840!GO:0030020;extracellular matrix structural constituent conferring tensile strength;1.88891762036745e-05;12841,12840!GO:0005581;collagen;2.21459307215495e-05;12841,12840!GO:0005201;extracellular matrix structural constituent;5.4899576158463e-05;12841,12840!GO:0044420;extracellular matrix part;0.00011128795438224;12841,12840!GO:0005578;proteinaceous extracellular matrix;0.000902144263983623;12841,12840!GO:0022610;biological adhesion;0.00321168103534753;12841,12840!GO:0007155;cell adhesion;0.00321168103534753;12841,12840!GO:0006817;phosphate transport;0.0206515964031062;12840!GO:0005615;extracellular space;0.0300779114333823;12841,12840!GO:0044421;extracellular region part;0.0311908040996588;12841,12840!GO:0015698;inorganic anion transport;0.0338376794407204;12840!GO:0006820;anion transport;0.0374202582905894;12840!GO:0001501;skeletal development;0.0380255168127235;12840!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000026!3.53e-07!12;UBERON:0004708!3.53e-07!12;UBERON:0002101!3.53e-07!12;UBERON:0004357!3.53e-07!12;UBERON:0004347!3.53e-07!12;UBERON:0005732!3.53e-07!12;UBERON:0005733!3.53e-07!12;UBERON:0002102!5.66e-07!7;UBERON:0004710!5.66e-07!7;UBERON:0005419!5.66e-07!7;UBERON:0005417!5.66e-07!7;UBERON:0005729!5.66e-07!7
|tfbs_overrepresentation_for_novel_motifs=0.641384,1.30284,0.612053,0.688265,0.483253,0.704257,0.803568,0.96814,0.381467,0.489964,0.755749,0.790506,0.96877,0.81685,0.502646,0,1.02248,0.473993,0.352304,0.24402,0.570433,0.57409,0.815872,0.481455,0.620553,0.846564,0.342316,0.727368,0.535752,0.790816,0.711848,1.12823,0.471365,0.318879,0.503207,0.30022,0.460474,0.786577,0.434783,0.40068,0.478558,1.70641,0.185353,0.504971,0.325217,0.675898,0.938241,0.744678,0.162985,1.3327,1.0041,0.875451,0.282443,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,0.205546,1.32691,0.323563,0.310084,0.318792,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,1.69489,1.20828,0.758875,0.129654,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,0.938512,0.264911,1.16494,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,0.143825,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,1.2358,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,1.21803,0.293812,0.542121,1.27621,0.416214,0.838313,1.35996,0.87653,1.28473,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,0.589293
|tfbs_overrepresentation_jaspar=MA0003.1;0.600426,MA0004.1;0.6888,MA0006.1;0.497533,MA0007.1;0.672186,MA0009.1;1.15569,MA0014.1;0.276754,MA0017.1;0.528196,MA0019.1;0.964875,MA0024.1;1.11019,MA0025.1;1.39562,MA0027.1;2.81824,MA0028.1;0.509589,MA0029.1;1.08753,MA0030.1;1.09438,MA0031.1;1.05719,MA0038.1;0.846479,MA0040.1;1.16866,MA0041.1;0.604221,MA0042.1;0.589368,MA0043.1;1.25564,MA0046.1;1.1929,MA0048.1;1.35097,MA0050.1;0.731539,MA0051.1;0.856094,MA0052.1;1.17701,MA0055.1;1.28762,MA0056.1;0,MA0057.1;0.251896,MA0058.1;0.581673,MA0059.1;0.59559,MA0060.1;0.403071,MA0061.1;0.438628,MA0063.1;0,MA0066.1;0.834648,MA0067.1;1.50873,MA0068.1;0.713436,MA0069.1;1.17737,MA0070.1;1.16732,MA0071.1;0.73062,MA0072.1;1.15853,MA0073.1;0.0471131,MA0074.1;0.795862,MA0076.1;0.550092,MA0077.1;1.13603,MA0078.1;0.891476,MA0081.1;0.621611,MA0083.1;1.25482,MA0084.1;1.84013,MA0087.1;1.21037,MA0088.1;0.582815,MA0089.1;0,MA0090.1;0.650768,MA0091.1;0.703314,MA0092.1;0.651119,MA0093.1;0.519148,MA0095.1;0,MA0098.1;0,MA0100.1;0.783305,MA0101.1;0.605676,MA0103.1;1.33576,MA0105.1;0.313353,MA0106.1;0.899777,MA0107.1;1.3208,MA0108.2;0.989014,MA0109.1;0,MA0111.1;0.666525,MA0113.1;2.01975,MA0114.1;0.43587,MA0115.1;1.25852,MA0116.1;0.497293,MA0117.1;1.22527,MA0119.1;0.606338,MA0122.1;1.24573,MA0124.1;1.45461,MA0125.1;1.37907,MA0130.1;0,MA0131.1;0.960068,MA0132.1;0,MA0133.1;0,MA0135.1;1.29308,MA0136.1;0.817395,MA0139.1;0.365453,MA0140.1;0.78318,MA0141.1;0.563066,MA0142.1;1.04199,MA0143.1;0.887119,MA0144.1;0.439506,MA0145.1;1.14526,MA0146.1;0.313734,MA0147.1;1.15069,MA0148.1;0.706718,MA0149.1;0.611881,MA0062.2;0.319836,MA0035.2;0.788288,MA0039.2;1.07321,MA0138.2;0.951653,MA0002.2;0.965577,MA0137.2;0.559766,MA0104.2;1.0034,MA0047.2;0.845655,MA0112.2;1.14524,MA0065.2;0.212467,MA0150.1;0.67206,MA0151.1;0,MA0152.1;0.84577,MA0153.1;1.31015,MA0154.1;0.263609,MA0155.1;1.21457,MA0156.1;0.549102,MA0157.1;1.0083,MA0158.1;0,MA0159.1;0.465802,MA0160.1;0.71003,MA0161.1;0,MA0162.1;0.704935,MA0163.1;0.327769,MA0164.1;0.817786,MA0080.2;0.534538,MA0018.2;0.828253,MA0099.2;0.944966,MA0079.2;0.440842,MA0102.2;1.8929,MA0258.1;1.07695,MA0259.1;0.441366,MA0442.1;0
}}

Latest revision as of 18:06, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr15:97808303..97808319,-p@chr15:97808303..97808319
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Mm9::chr2:180332932..180332956,+p1@Col9a3
Mm9::chr3:24757119..24757131,-p@chr3:24757119..24757131
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Mm9::chr4:120712306..120712317,+p3@Col9a2


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:0030934anchoring collagen6.20334193880936e-08
GO:0005593FACIT collagen6.20334193880936e-08
GO:0005594collagen type IX6.20334193880936e-08
GO:0030020extracellular matrix structural constituent conferring tensile strength1.88891762036745e-05
GO:0005581collagen2.21459307215495e-05
GO:0005201extracellular matrix structural constituent5.4899576158463e-05
GO:0044420extracellular matrix part0.00011128795438224
GO:0005578proteinaceous extracellular matrix0.000902144263983623
GO:0022610biological adhesion0.00321168103534753
GO:0007155cell adhesion0.00321168103534753
GO:0006817phosphate transport0.0206515964031062
GO:0005615extracellular space0.0300779114333823
GO:0044421extracellular region part0.0311908040996588
GO:0015698inorganic anion transport0.0338376794407204
GO:0006820anion transport0.0374202582905894
GO:0001501skeletal development0.0380255168127235



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
appendage3.53e-0712
paired limb/fin3.53e-0712
limb3.53e-0712
paired limb/fin bud3.53e-0712
limb bud3.53e-0712
limb/fin field3.53e-0712
limb field3.53e-0712
forelimb5.66e-077
pectoral appendage5.66e-077
pectoral appendage bud5.66e-077
forelimb bud5.66e-077
forelimb/pectoral fin field5.66e-077


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)
MA0003.10.600426
MA0004.10.6888
MA0006.10.497533
MA0007.10.672186
MA0009.11.15569
MA0014.10.276754
MA0017.10.528196
MA0019.10.964875
MA0024.11.11019
MA0025.11.39562
MA0027.12.81824
MA0028.10.509589
MA0029.11.08753
MA0030.11.09438
MA0031.11.05719
MA0038.10.846479
MA0040.11.16866
MA0041.10.604221
MA0042.10.589368
MA0043.11.25564
MA0046.11.1929
MA0048.11.35097
MA0050.10.731539
MA0051.10.856094
MA0052.11.17701
MA0055.11.28762
MA0056.10
MA0057.10.251896
MA0058.10.581673
MA0059.10.59559
MA0060.10.403071
MA0061.10.438628
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.10.713436
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.10.0471131
MA0074.10.795862
MA0076.10.550092
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.10.582815
MA0089.10
MA0090.10.650768
MA0091.10.703314
MA0092.10.651119
MA0093.10.519148
MA0095.10
MA0098.10
MA0100.10.783305
MA0101.10.605676
MA0103.11.33576
MA0105.10.313353
MA0106.10.899777
MA0107.11.3208
MA0108.20.989014
MA0109.10
MA0111.10.666525
MA0113.12.01975
MA0114.10.43587
MA0115.11.25852
MA0116.10.497293
MA0117.11.22527
MA0119.10.606338
MA0122.11.24573
MA0124.11.45461
MA0125.11.37907
MA0130.10
MA0131.10.960068
MA0132.10
MA0133.10
MA0135.11.29308
MA0136.10.817395
MA0139.10.365453
MA0140.10.78318
MA0141.10.563066
MA0142.11.04199
MA0143.10.887119
MA0144.10.439506
MA0145.11.14526
MA0146.10.313734
MA0147.11.15069
MA0148.10.706718
MA0149.10.611881
MA0062.20.319836
MA0035.20.788288
MA0039.21.07321
MA0138.20.951653
MA0002.20.965577
MA0137.20.559766
MA0104.21.0034
MA0047.20.845655
MA0112.21.14524
MA0065.20.212467
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.10.263609
MA0155.11.21457
MA0156.10.549102
MA0157.11.0083
MA0158.10
MA0159.10.465802
MA0160.10.71003
MA0161.10
MA0162.10.704935
MA0163.10.327769
MA0164.10.817786
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.20.440842
MA0102.21.8929
MA0258.11.07695
MA0259.10.441366
MA0442.10
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