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MCL coexpression mm9:1037: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=UBERON:0000058!9.77e-20!7;UBERON:0000080!3.55e-13!4;UBERON:0005904!3.55e-13!4;UBERON:0006947!3.55e-13!4;UBERON:0002120!3.55e-13!4;UBERON:0004054!3.55e-13!4;UBERON:0004875!3.55e-13!4;UBERON:0004876!3.55e-13!4;UBERON:0005721!3.55e-13!4;UBERON:0005754!3.55e-13!4;UBERON:0007297!3.55e-13!4;UBERON:0010147!1.05e-12!2;UBERON:0003937!1.05e-12!2;UBERON:0005399!1.05e-12!2;UBERON:0004766!6.40e-12!2;UBERON:0008193!6.40e-12!2;UBERON:0005913!6.40e-12!2;UBERON:0011158!6.40e-12!2;UBERON:0005744!6.40e-12!2;UBERON:0003457!6.40e-12!2;UBERON:0008001!6.40e-12!2;UBERON:0007497!6.40e-12!2;UBERON:0009955!6.40e-12!2;UBERON:0003067!6.40e-12!2;UBERON:0002546!6.40e-12!2;UBERON:0007914!6.40e-12!2;UBERON:0005253!6.40e-12!2;UBERON:0002227!6.40e-12!2;UBERON:0001846!6.40e-12!2;UBERON:0004339!6.40e-12!2;UBERON:0002105!6.40e-12!2;UBERON:0001678!6.40e-12!2;UBERON:0003128!6.40e-12!2;UBERON:0001694!6.40e-12!2;UBERON:0004681!6.40e-12!2;UBERON:0001839!6.40e-12!2;UBERON:0001690!6.40e-12!2;UBERON:0001844!6.40e-12!2;UBERON:0001849!6.40e-12!2;UBERON:0002499!6.40e-12!2;UBERON:0001855!6.40e-12!2;UBERON:0011137!6.40e-12!2;UBERON:0001703!6.40e-12!2;UBERON:0010323!6.40e-12!2;UBERON:0003129!6.40e-12!2;UBERON:0003069!6.40e-12!2;UBERON:0003051!6.40e-12!2;UBERON:0004637!6.40e-12!2;UBERON:0004761!6.40e-12!2;UBERON:0010113!6.40e-12!2;UBERON:0009123!6.40e-12!2;UBERON:0010351!6.40e-12!2;UBERON:0009617!6.40e-12!2;UBERON:0005641!6.40e-12!2;UBERON:0010349!6.40e-12!2;UBERON:0000033!6.47e-11!13;UBERON:0001301!3.92e-08!3;UBERON:0006555!3.92e-08!3;UBERON:0005103!3.92e-08!3;UBERON:0000083!3.92e-08!3;UBERON:0009201!3.92e-08!3;UBERON:0004819!3.92e-08!3;UBERON:0006553!3.92e-08!3;UBERON:0003074!3.92e-08!3;UBERON:0003060!3.92e-08!3;UBERON:0000020!8.31e-08!12;UBERON:0001032!8.31e-08!12;UBERON:0004456!8.31e-08!12;UBERON:0000998!2.75e-07!1;UBERON:0007194!2.75e-07!1;UBERON:0006868!2.75e-07!1;UBERON:0005085!3.23e-07!13;UBERON:0001044!4.10e-07!1;UBERON:0001736!4.10e-07!1;UBERON:0003293!4.10e-07!1;UBERON:0003294!4.10e-07!1;UBERON:0001829!4.10e-07!1;UBERON:0010047!4.10e-07!1;UBERON:0000167!4.10e-07!1;UBERON:0006298!4.10e-07!1;UBERON:0002367!4.68e-07!1;UBERON:0009846!4.68e-07!1;UBERON:0003353!4.68e-07!1;UBERON:0004902!4.68e-07!1;UBERON:0003820!4.68e-07!1;UBERON:0009847!4.68e-07!1
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.0418382,0.411716,1.20801,0.810002,0.495263,0.587291,0.206208,1.15776,0.0609112,0.542749,0.575086,0.59526,0.599731,0.847296,0,0.795315,0.291368,0.19222,0.361892,0.374752,0.27937,0.598814,0.29769,0.419327,0.62766,1.0368,0.516511,0.344372,0.446946,1.25421,0.897561,0.78719,0.964228,0.316253,0.248902,0.279977,0.57142,0.717242,0.652422,0.295233,0.507468,0.258106,0.851774,2.10004,0.469348,0.714592,0.532496,0.82704,0.347313,0.777641,0.654933,0.431711,1.04034,1.0579,0.606984,0.356236,0.56214,1.00328,0.604914,0.877332,0.664501,0.226529,0.766235,0.618279,0.807219,2.68153,1.54543,0.872612,1.39786,0.392734,0.608073,0.0869413,2.47226,0.17012,0.159969,0.498755,0.703064,2.00003,0.98764,1.14907,0.812889,0.663039,0.200155,0.975495,0.146394,0.164297,0.447265,0.719558,1.70793,1.26498,2.24635,2.10343,0.305079,0.254625,1.24315,0.203879,0.913319,0.71485,0.127063,0.7665,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,0.430942,1.02459,0.380122,0.547992,1.27206,1.45003,0.187586,0.484437,0.796633,1.38758,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,1.19218,1.16374,0.620831,1.29374,0.275843,0.446555,1.26843,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.147909,0.0736236,1.04192,0.243291,0.619892,1.12411,0.655955,0.874089,0.435579,0.446272,1.25393,2.23437,0.864173,0.428662,0.767269,0.612377,0.278874,0.573477,0.0206035
|tfbs_overrepresentation_jaspar=MA0003.1;0.0861444,MA0004.1;0.481116,MA0006.1;0.311391,MA0007.1;0.465969,MA0009.1;0.92425,MA0014.1;0.0200028,MA0017.1;0.337808,MA0019.1;0.740036,MA0024.1;0.880057,MA0025.1;1.15921,MA0027.1;2.57545,MA0028.1;0.321735,MA0029.1;0.858105,MA0030.1;0.864739,MA0031.1;0.828781,MA0038.1;0.62758,MA0040.1;0.936879,MA0041.1;0.404721,MA0042.1;0.391504,MA0043.1;1.02178,MA0046.1;0.960497,MA0048.1;0.128106,MA0050.1;0.520357,MA0051.1;0.636645,MA0052.1;0.945011,MA0055.1;0.0406078,MA0056.1;0,MA0057.1;0.376102,MA0058.1;0.384683,MA0059.1;0.397033,MA0060.1;0.232592,MA0061.1;0.261749,MA0063.1;0,MA0066.1;0.616444,MA0067.1;1.27078,MA0068.1;0.121435,MA0069.1;0.945354,MA0070.1;0.93557,MA0071.1;0.519509,MA0072.1;0.927016,MA0073.1;4.19963e-05,MA0074.1;0.580087,MA0076.1;0.356883,MA0077.1;0.905143,MA0078.1;0.670113,MA0081.1;0.420276,MA0083.1;1.02098,MA0084.1;1.59945,MA0087.1;0.977537,MA0088.1;0.285759,MA0089.1;0,MA0090.1;1.1347,MA0091.1;2.14241,MA0092.1;0.446857,MA0093.1;0.329976,MA0095.1;0,MA0098.1;0,MA0100.1;1.39455,MA0101.1;0.406019,MA0103.1;0.348572,MA0105.1;0.162418,MA0106.1;0.677988,MA0107.1;0.342432,MA0108.2;0.763162,MA0109.1;0,MA0111.1;0.460823,MA0113.1;0.649407,MA0114.1;0.259463,MA0115.1;1.0246,MA0116.1;0.311187,MA0117.1;0.992087,MA0119.1;0.40661,MA0122.1;1.01209,MA0124.1;1.21735,MA0125.1;1.14291,MA0130.1;0,MA0131.1;0.735438,MA0132.1;0,MA0133.1;0,MA0135.1;1.05845,MA0136.1;0.600242,MA0139.1;0.202522,MA0140.1;0.568252,MA0141.1;0.964041,MA0142.1;0.814115,MA0143.1;0.665982,MA0144.1;0.262477,MA0145.1;0.304732,MA0146.1;0.108739,MA0147.1;0.274511,MA0148.1;0.49752,MA0149.1;0.411562,MA0062.2;0.167299,MA0035.2;0.573016,MA0039.2;0.113749,MA0138.2;0.727395,MA0002.2;0.592533,MA0137.2;0.365364,MA0104.2;0.218974,MA0047.2;0.626803,MA0112.2;0.0910939,MA0065.2;0.305574,MA0150.1;0.465855,MA0151.1;0,MA0152.1;0.626912,MA0153.1;1.07519,MA0154.1;2.52797,MA0155.1;0.336768,MA0156.1;0.356017,MA0157.1;0.781683,MA0158.1;0,MA0159.1;0.284457,MA0160.1;1.25065,MA0161.1;0,MA0162.1;0.0312493,MA0163.1;0.0280055,MA0164.1;0.600609,MA0080.2;0.343316,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;0.00878868,MA0102.2;1.65195,MA0258.1;0.246285,MA0259.1;0.26402,MA0442.1;0
}}

Latest revision as of 16:17, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:69522935..69522942,+p@chr10:69522935..69522942
+
Mm9::chr2:105239751..105239799,-p5@Rcn1
Mm9::chr6:142271461..142271477,-p4@Slco1a5
Mm9::chr6:142271487..142271497,-p6@Slco1a5
Mm9::chr6:142271498..142271527,-p1@Slco1a5
Mm9::chr9:45197960..45197965,+p@chr9:45197960..45197965
+
Mm9::chr9:45197974..45197989,+p@chr9:45197974..45197989
+


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:0015125bile acid transmembrane transporter activity0.0315434894871784
GO:0008028monocarboxylic acid transmembrane transporter activity0.0315434894871784



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
duct9.77e-207
mesonephros3.55e-134
duct of male reproductive system3.55e-134
male genital duct3.55e-134
pronephros3.55e-134
internal male genitalia3.55e-134
nephrogenic cord3.55e-134
urogenital ridge3.55e-134
pronephric mesoderm3.55e-134
rostral part of nephrogenic cord3.55e-134
presumptive pronephric mesoderm3.55e-134
male accessory sex gland1.05e-122
sex gland1.05e-122
male reproductive gland1.05e-122
cranial bone6.40e-122
pneumatized bone6.40e-122
zone of bone organ6.40e-122
primary subdivision of skull6.40e-122
cranial conduit6.40e-122
head bone6.40e-122
irregular bone6.40e-122
developing epithelial placode6.40e-122
neurogenic placode6.40e-122
dorsolateral placode6.40e-122
cranial placode6.40e-122
head or neck bone6.40e-122
head mesenchyme6.40e-122
spiral organ of cochlea6.40e-122
internal ear6.40e-122
calvarium6.40e-122
vestibulo-auditory system6.40e-122
temporal bone6.40e-122
cranium6.40e-122
petrous part of temporal bone6.40e-122
vestibular system6.40e-122
bony labyrinth6.40e-122
ear6.40e-122
cochlea6.40e-122
membranous labyrinth6.40e-122
cochlear labyrinth6.40e-122
cochlear duct of membranous labyrinth6.40e-122
axial skeletal system6.40e-122
neurocranium6.40e-122
cranial skeletal system6.40e-122
skull6.40e-122
otic placode6.40e-122
ear vesicle6.40e-122
otic capsule6.40e-122
cartilaginous neurocranium6.40e-122
future membranous labyrinth6.40e-122
otic cup6.40e-122
otic capsule cartilage condensation6.40e-122
head paraxial mesoderm6.40e-122
otocyst epithelium6.40e-122
otic capsule pre-cartilage condensation6.40e-122
head6.47e-1113
epididymis3.92e-083
excretory tube3.92e-083
mesonephric epithelium3.92e-083
mesonephric tubule3.92e-083
nephric duct3.92e-083
kidney epithelium3.92e-083
renal duct3.92e-083
mesonephric duct3.92e-083
pronephric duct3.92e-083
sense organ8.31e-0812
sensory system8.31e-0812
entire sense organ system8.31e-0812
seminal vesicle2.75e-071
vesicular gland2.75e-071
seminal fluid secreting gland2.75e-071
ectodermal placode3.23e-0713
saliva-secreting gland4.10e-071
submandibular gland4.10e-071
gland of oral region4.10e-071
gland of foregut4.10e-071
major salivary gland4.10e-071
oral gland4.10e-071
oral cavity4.10e-071
submandibular gland primordium4.10e-071
prostate gland4.68e-071
embryonic cloacal epithelium4.68e-071
epithelium of hindgut4.68e-071
urogenital sinus epithelium4.68e-071
prostate bud4.68e-071
prostate field4.68e-071


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)
MA0003.10.0861444
MA0004.10.481116
MA0006.10.311391
MA0007.10.465969
MA0009.10.92425
MA0014.10.0200028
MA0017.10.337808
MA0019.10.740036
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.10.321735
MA0029.10.858105
MA0030.10.864739
MA0031.10.828781
MA0038.10.62758
MA0040.10.936879
MA0041.10.404721
MA0042.10.391504
MA0043.11.02178
MA0046.10.960497
MA0048.10.128106
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.0406078
MA0056.10
MA0057.10.376102
MA0058.10.384683
MA0059.10.397033
MA0060.10.232592
MA0061.10.261749
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.121435
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.14.19963e-05
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.10.285759
MA0089.10
MA0090.11.1347
MA0091.12.14241
MA0092.10.446857
MA0093.10.329976
MA0095.10
MA0098.10
MA0100.11.39455
MA0101.10.406019
MA0103.10.348572
MA0105.10.162418
MA0106.10.677988
MA0107.10.342432
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.259463
MA0115.11.0246
MA0116.10.311187
MA0117.10.992087
MA0119.10.40661
MA0122.11.01209
MA0124.11.21735
MA0125.11.14291
MA0130.10
MA0131.10.735438
MA0132.10
MA0133.10
MA0135.11.05845
MA0136.10.600242
MA0139.10.202522
MA0140.10.568252
MA0141.10.964041
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.10.304732
MA0146.10.108739
MA0147.10.274511
MA0148.10.49752
MA0149.10.411562
MA0062.20.167299
MA0035.20.573016
MA0039.20.113749
MA0138.20.727395
MA0002.20.592533
MA0137.20.365364
MA0104.20.218974
MA0047.20.626803
MA0112.20.0910939
MA0065.20.305574
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.12.52797
MA0155.10.336768
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.10.284457
MA0160.11.25065
MA0161.10
MA0162.10.0312493
MA0163.10.0280055
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.20.00878868
MA0102.21.65195
MA0258.10.246285
MA0259.10.26402
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:1037&oldid=3073036"