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MCL coexpression mm9:2170: Difference between revisions

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{{MCL_coexpression_mm9
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furrow;0.00300407238992677;59069!GO:0002102;podosome;0.00300407238992677;59069!GO:0005862;muscle thin filament tropomyosin;0.00300407238992677;59069!GO:0032153;cell division site;0.00300407238992677;59069!GO:0032155;cell division site part;0.00300407238992677;59069!GO:0031941;filamentous actin;0.00300407238992677;59069!GO:0030426;growth cone;0.00437736262532187;59069!GO:0030427;site of polarized growth;0.00437736262532187;59069!GO:0005865;striated muscle thin filament;0.00437736262532187;59069!GO:0030863;cortical cytoskeleton;0.00437736262532187;59069!GO:0005884;actin filament;0.00538392194558304;59069!GO:0044448;cell cortex part;0.00600814477985354;59069!GO:0006937;regulation of muscle contraction;0.00653633333192858;59069!GO:0005938;cell cortex;0.00864437157101377;59069!GO:0030017;sarcomere;0.0106859146441681;59069!GO:0044449;contractile fiber part;0.0106859146441681;59069!GO:0030016;myofibril;0.0106859146441681;59069!GO:0043292;contractile fiber;0.0106859146441681;59069!GO:0003012;muscle system process;0.0106859146441681;59069!GO:0006936;muscle contraction;0.0106859146441681;59069!GO:0043005;neuron projection;0.0142233631523063;59069!GO:0015629;actin cytoskeleton;0.0222379384708865;59069!GO:0003779;actin binding;0.0270926280135011;59069!GO:0051239;regulation of multicellular organismal process;0.0298261472999872;59069!GO:0008092;cytoskeletal protein binding;0.0344009203966471;59069!GO:0042995;cell projection;0.0360488686791213;59069!GO:0044430;cytoskeletal part;0.0495910362781562;59069!|ontology_enrichment_celltype=|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0000970!1.91e-09!9;UBERON:0000019!1.91e-09!9;UBERON:0000047!1.91e-09!9;UBERON:0010312!1.91e-09!9;UBERON:0004088!1.91e-09!9;UBERON:0002104!1.91e-09!9;UBERON:0001456!1.91e-09!9;UBERON:0003072!1.91e-09!9;UBERON:0004128!1.91e-09!9;UBERON:0003071!1.91e-09!9;UBERON:0001444!6.06e-09!11;UBERON:0000020!5.37e-08!12;UBERON:0001032!5.37e-08!12;UBERON:0004456!5.37e-08!12;UBERON:0005418!5.80e-08!5;UBERON:0002472!5.80e-08!5;UBERON:0008784!5.80e-08!5;UBERON:0006058!5.80e-08!5;UBERON:0004709!5.80e-08!5;UBERON:0002529!5.80e-08!5;UBERON:0010538!5.80e-08!5;UBERON:0005420!5.80e-08!5;UBERON:0010758!5.80e-08!5;UBERON:0000978!5.80e-08!5;UBERON:0002103!5.80e-08!5;UBERON:0000376!5.80e-08!5;UBERON:0000154!5.80e-08!5;UBERON:0010709!5.80e-08!5;UBERON:0005730!5.80e-08!5;UBERON:0000033!3.37e-07!13|tfbs_overrepresentation_for_novel_motifs=0.641384,0.128156,0.612053,0.688265,0.483253,0.704257,0.803568,0.96814,0.381467,0.162942,0.755749,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,0.352304,0.24402,0.570433,0.197567,0.815872,0.481455,0.620553,0.846564,0.342316,0.727368,0.535752,0.290745,0.711848,1.12823,0.471365,0.318879,0.503207,0.30022,0.460474,0.786577,0.434783,0.40068,0.478558,0.717547,0.544696,0.504971,0.0986756,0.675898,0.938241,0.744678,0.49007,0.539131,1.0041,0.875451,0.282443,1.2746,1.29252,0.82458,0.549352,0.776619,0.882473,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,0.205546,1.32691,0.323563,0.310084,0.854076,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,0.11855,0.129654,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,0.143825,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,1.2358,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.293812,0.184289,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,0.0824127|tfbs_overrepresentation_jaspar=MA0003.1;0.142214,MA0004.1;0.6888,MA0006.1;0.497533,MA0007.1;0.672186,MA0009.1;1.15569,MA0014.1;0.0809287,MA0017.1;1.30949,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;0.266382,MA0050.1;0.731539,MA0051.1;0.856094,MA0052.1;1.17701,MA0055.1;0.396346,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;0.256913,MA0069.1;1.17737,MA0070.1;1.16732,MA0071.1;0.73062,MA0072.1;1.15853,MA0073.1;0.0140887,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;0.540576,MA0105.1;0.841866,MA0106.1;0.899777,MA0107.1;0.533522,MA0108.2;0.989014,MA0109.1;0,MA0111.1;0.666525,MA0113.1;0.869608,MA0114.1;0.43587,MA0115.1;1.25852,MA0116.1;1.24367,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;2.36797,MA0142.1;1.04199,MA0143.1;0.887119,MA0144.1;0.439506,MA0145.1;0.21199,MA0146.1;0.0944145,MA0147.1;0.453952,MA0148.1;0.706718,MA0149.1;0.611881,MA0062.2;0.319836,MA0035.2;1.85264,MA0039.2;0.0959929,MA0138.2;0.951653,MA0002.2;0.368961,MA0137.2;0.559766,MA0104.2;0.386166,MA0047.2;0.845655,MA0112.2;0.608441,MA0065.2;0.212467,MA0150.1;0.67206,MA0151.1;0,MA0152.1;0.84577,MA0153.1;1.31015,MA0154.1;2.06517,MA0155.1;0.230016,MA0156.1;0.549102,MA0157.1;1.0083,MA0158.1;0,MA0159.1;0.465802,MA0160.1;1.69082,MA0161.1;0,MA0162.1;0.10667,MA0163.1;0.327769,MA0164.1;0.817786,MA0080.2;0.534538,MA0018.2;0.828253,MA0099.2;0.944966,MA0079.2;0.0234849,MA0102.2;1.8929,MA0258.1;1.07695,MA0259.1;0.441366,MA0442.1;0}}
|coexpression_dpi_cluster_scores_mean=0,0,0,0,0,0,0,0,0.0578638045997903,0.0841310747884862,0,0,0,0,0,0,0,0,0,0,0.0563496998792963,0.0102781632737099,0,0,0.0224241218442176,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0215620259804927,0,0,0,0.016840500553487,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0284524349013718,0,0,0,0,0,0,0,0,0,0,0,0,0,0.00950470588951562,0,0,0,0,0,0.0289037142393673,0,0.00792543589561178,0,0,0,0,0,0,0,0.678816818929796,0,0,0,0,0,0,0,0,0,0,0.292027986017235,0,0,0,0.123929725269165,0.0943125795306435,0.142431457493128,0.233729221619637,0,0,0.17264165884689,0.570863220209654,0.948912043366693,0.944889902760871,0.697439133579094,0,0,0.0379874431891978,0,0,0,0,0,0,0,0,0.0247228100670125,0,0.0163240725348775,0.167241235186208,0.473896445297869,0,0.711371327821744,0.0251133913248857,0.26164255961951,0.364382345749376,0.470390571100044,0.530715520698399,0.589602609059449,0.590641897869534,1.03593319630664,0,0,0.0460204192907362,0.161505446528942,0.0946102069649822,0.528101289108969,0.400189339109636,0,0,0,0,0,0,0,0,0,0.0155765805041843,0.0453994444268803,0.0258032210994128,0.0347779712212284,0,0.0308268981088045,0.0163143899467127,0.0148150998392991,0,0.0136730251847535,0,0,0.0309970919167852,0,0,0,0.062189722598514,0,0.0218013851437485,0.0189073241480204,0,0,0,0.0197008540950864,0.0193387133502521,0,0,0,0.0349175022149708,0.0704848083681528,0,0.0370968768038467,0,0.0142520807299197,0.0349240684395732,0.028085910286319,0.0720618796479733,0.0239487044583413,0,0,0,0.0220218002973959,0.0369747247109252,0.0427380058052035,0.0762573717031963,0,0.0542749320626107,0.261066640036857,0.306421006940047,0.204591353511385,0.25763330290303,0.0244512709958093,0.319414841446803,0,0,0,0.0327833179115153,0,0,0,0.042278009573524,0.145852370267931,0.0807328422560968,0,0.0160634527744164,0.043412361703945,0.0495057727218439,0.0146680888560183,0,0,0.183617515271478,0,0,0.0120338674974764,0,1.15623688941048,0,0,0,0,0,0,0,0,0,0,0,0.20035718461956,0.237701568045944,0,0,0,0,0,0.110690917480782,0,0.0249571184854793,0,0.375046159155119,0,0,0,0.0933088682265462,0,0,0,0.105354448708231,0.0509442784527464,0.0549089711906035,0.0516342805282582,0,0,0,0.0309443373300435,0.203057669468376,0.118511434859811,0.050816827526439,0.0434729614721253,0,0.090336424791172,0,0.0203716502675842,0.0342109703182358,0,0,0,0,0,0,0.0727683962091365,0,0.0517036636843165,0,0,0,0,0.0437271454500332,0.164847757985063,0,0.0524684783235278,0.0485378687462348,0,0,0.0192921017140294,0.0131888542903607,0.0169495527659021,0.0417871483033413,0.0132892469734015,0.0108267482772483,0,0.215796283016061,0.0298148897980265,0.0515833702241262,0.0106154224983411,0.02507899012669,0.0357618192777494,0.0507612193472217,0.0823457548391716,0.0770784855873102,0.0486977726063285,0.0313499622201701,0.020859375746038,0.0201939307380272,0,0.0348084535911198,0.0443745609988697,0,0,0,0,0.0186750870991491,0,0.0539163383726255,0,0,0,0,0.0172183009384173,0,0,0,0,0,0,0.0377005721513428,0,0.0670079898709182,0.328654076782035,0.242391716717443,0.314404324073525,0.475566831661427,0.559489249778209,0.480418153517271,0.495961230974502,0.512318732783751,0.526558106927801,0.514285295770548,0.517772190073505,0.495302662492853,0.492229352701812,0.567740080544417,0.478988751700118,0.568119717126648,0.516325626403229,0.493200282108258,0.52112426309406,0.495020657352334,0.491537575284564,0.526631381091205,0.514911642023995,0.527499947002231,0.523032087673268,0.531879773085336,0.41409700331585,0.569943243917679,0.497830722652159,0.527462486282063,0.536488713099117,0.432447215777634,0.315856274897913,0.444754156417719,0.636474254152288,0.79342376181188,0.929524774503132,1.02397049120248
|gostat_on_MCL_coexpression=GO:0032154;cleavage furrow;0.00300407238992677;59069!GO:0002102;podosome;0.00300407238992677;59069!GO:0005862;muscle thin filament tropomyosin;0.00300407238992677;59069!GO:0032153;cell division site;0.00300407238992677;59069!GO:0032155;cell division site part;0.00300407238992677;59069!GO:0031941;filamentous actin;0.00300407238992677;59069!GO:0030426;growth cone;0.00437736262532187;59069!GO:0030427;site of polarized growth;0.00437736262532187;59069!GO:0005865;striated muscle thin filament;0.00437736262532187;59069!GO:0030863;cortical cytoskeleton;0.00437736262532187;59069!GO:0005884;actin filament;0.00538392194558304;59069!GO:0044448;cell cortex part;0.00600814477985354;59069!GO:0006937;regulation of muscle contraction;0.00653633333192858;59069!GO:0005938;cell cortex;0.00864437157101377;59069!GO:0030017;sarcomere;0.0106859146441681;59069!GO:0044449;contractile fiber part;0.0106859146441681;59069!GO:0030016;myofibril;0.0106859146441681;59069!GO:0043292;contractile fiber;0.0106859146441681;59069!GO:0003012;muscle system process;0.0106859146441681;59069!GO:0006936;muscle contraction;0.0106859146441681;59069!GO:0043005;neuron projection;0.0142233631523063;59069!GO:0015629;actin cytoskeleton;0.0222379384708865;59069!GO:0003779;actin binding;0.0270926280135011;59069!GO:0051239;regulation of multicellular organismal process;0.0298261472999872;59069!GO:0008092;cytoskeletal protein binding;0.0344009203966471;59069!GO:0042995;cell projection;0.0360488686791213;59069!GO:0044430;cytoskeletal part;0.0495910362781562;59069!
}}

Latest revision as of 18:06, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr16:19883954..19883965,-p4@A930003A15Rik
Mm9::chr17:25257732..25257748,+p1@Ptx4
Mm9::chr3:89876563..89876579,+p3@Tpm3
Mm9::chr5:137165168..137165170,+p@chr5:137165168..137165170
+


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:0032154cleavage furrow0.00300407238992677
GO:0002102podosome0.00300407238992677
GO:0005862muscle thin filament tropomyosin0.00300407238992677
GO:0032153cell division site0.00300407238992677
GO:0032155cell division site part0.00300407238992677
GO:0031941filamentous actin0.00300407238992677
GO:0030426growth cone0.00437736262532187
GO:0030427site of polarized growth0.00437736262532187
GO:0005865striated muscle thin filament0.00437736262532187
GO:0030863cortical cytoskeleton0.00437736262532187
GO:0005884actin filament0.00538392194558304
GO:0044448cell cortex part0.00600814477985354
GO:0006937regulation of muscle contraction0.00653633333192858
GO:0005938cell cortex0.00864437157101377
GO:0030017sarcomere0.0106859146441681
GO:0044449contractile fiber part0.0106859146441681
GO:0030016myofibril0.0106859146441681
GO:0043292contractile fiber0.0106859146441681
GO:0003012muscle system process0.0106859146441681
GO:0006936muscle contraction0.0106859146441681
GO:0043005neuron projection0.0142233631523063
GO:0015629actin cytoskeleton0.0222379384708865
GO:0003779actin binding0.0270926280135011
GO:0051239regulation of multicellular organismal process0.0298261472999872
GO:0008092cytoskeletal protein binding0.0344009203966471
GO:0042995cell projection0.0360488686791213
GO:0044430cytoskeletal part0.0495910362781562



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
eye1.91e-099
camera-type eye1.91e-099
simple eye1.91e-099
immature eye1.91e-099
ocular region1.91e-099
visual system1.91e-099
face1.91e-099
optic cup1.91e-099
optic vesicle1.91e-099
eye primordium1.91e-099
subdivision of head6.06e-0911
sense organ5.37e-0812
sensory system5.37e-0812
entire sense organ system5.37e-0812
hindlimb bud5.80e-085
stylopod5.80e-085
lower limb segment5.80e-085
multi-limb segment region5.80e-085
pelvic appendage5.80e-085
limb segment5.80e-085
paired limb/fin segment5.80e-085
pelvic appendage bud5.80e-085
subdivision of organism along appendicular axis5.80e-085
leg5.80e-085
hindlimb5.80e-085
hindlimb stylopod5.80e-085
posterior region of body5.80e-085
pelvic complex5.80e-085
hindlimb/pelvic fin field5.80e-085
head3.37e-0713


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)
MA0003.10.142214
MA0004.10.6888
MA0006.10.497533
MA0007.10.672186
MA0009.11.15569
MA0014.10.0809287
MA0017.11.30949
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
MA0048.10.266382
MA0050.10.731539
MA0051.10.856094
MA0052.11.17701
MA0055.10.396346
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
MA0068.10.256913
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.10.0140887
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
MA0103.10.540576
MA0105.10.841866
MA0106.10.899777
MA0107.10.533522
MA0108.20.989014
MA0109.10
MA0111.10.666525
MA0113.10.869608
MA0114.10.43587
MA0115.11.25852
MA0116.11.24367
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
MA0141.12.36797
MA0142.11.04199
MA0143.10.887119
MA0144.10.439506
MA0145.10.21199
MA0146.10.0944145
MA0147.10.453952
MA0148.10.706718
MA0149.10.611881
MA0062.20.319836
MA0035.21.85264
MA0039.20.0959929
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.20.386166
MA0047.20.845655
MA0112.20.608441
MA0065.20.212467
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.12.06517
MA0155.10.230016
MA0156.10.549102
MA0157.11.0083
MA0158.10
MA0159.10.465802
MA0160.11.69082
MA0161.10
MA0162.10.10667
MA0163.10.327769
MA0164.10.817786
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.20.0234849
MA0102.21.8929
MA0258.11.07695
MA0259.10.441366
MA0442.10
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