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MCL coexpression mm9:270: Difference between revisions

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{{MCL_coexpression_mm9
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constituent of myelin sheath;0.0439582683660776;17196!GO:0000015;phosphopyruvate hydratase complex;0.0439582683660776;13807!GO:0004634;phosphopyruvate hydratase activity;0.0439582683660776;13807!GO:0043209;myelin sheath;0.0439582683660776;17196!GO:0044265;cellular macromolecule catabolic process;0.0439582683660776;13807,78651!GO:0019894;kinesin binding;0.0439582683660776;60597!GO:0008191;metalloendopeptidase inhibitor activity;0.0439582683660776;110595!GO:0030295;protein kinase activator activity;0.0439582683660776;60597!GO:0009057;macromolecule catabolic process;0.0468695565507533;13807,78651!GO:0019209;kinase activator activity;0.0468695565507533;60597!GO:0007267;cell-cell 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|coexpression_dpi_cluster_scores_mean=0.0382767661028666,0.00942030579312388,0.00831696367587751,-0.00219031156874675,-0.00219031156874675,-1.61841352954162e-05,0.000750940394580307,0.0202299672197958,0.00150034772735435,0.00664883699814559,0.00223792884987739,-0.00219031156874675,0.0201207104476657,0.0195926620880665,0.00899027319019268,0.000392790125869945,0.00523991362876612,0.024242721858997,0.021788544444565,0.0187146726554703,0.131363629926049,0.00700933330144563,0.0101998959766097,0.0196871619258721,0.0259004634192329,0.0168808554940656,0.0028279915253849,0.00556345800531432,-0.00219031156874675,-0.00219031156874675,0.0057574458709422,-0.00219031156874675,0.00904614317945958,-0.00219031156874675,0.00775253484882652,0.00613965896088354,0.00260669221737735,-0.00219031156874675,-0.00219031156874675,-0.00219031156874675,-0.00219031156874675,-0.00219031156874675,0.00335406529891229,-0.000529066674369593,-0.00219031156874675,-0.00219031156874675,0.0470664964540767,0.0746326134192992,0.0275400541750837,0.0200566667038476,0.0344790791008301,0.0667153086956653,0.0266750305658529,0.0256501717594991,0.0195145814424861,0.00683225595179061,0.00768608411842372,0.0176666894072191,0.0372220973864722,0.0523980788797956,0.0425511691320259,0.00598582709200467,-0.00219031156874675,0.0212244497090668,0.032400140737336,0.00532962487298281,0.234127292123151,0.401775705325299,0.00784693830447015,0.00668035516615649,0.00733708402385763,0.811481131854062,0.818483753418932,0.020382573196801,0.0117255918372851,0.0160757843117926,0.831720211227641,0.717422958482364,0.723723205615904,0.0358682035363416,0.0390175800118211,0.0354339209540642,1.05370288079826,0.756575368090107,0.770746094096889,0.33465973112431,0.342881031940829,0.0498397940311995,0.226397935205165,0.0852538091557715,0.0121609413018245,-0.00219031156874675,0.00507749072734951,0.0141121523937484,0.00482340105500361,0.00677261263291248,0.0569781899705779,1.43840641269259e-05,0.00428044838696281,0.00628754531460035,0.184462396540412,-0.00219031156874675,-0.00219031156874675,-0.00219031156874675,0.0186172451403786,0.00889382043923058,0.0190353762806905,0.0394758003469705,0.0010356336707167,0.0143678704862331,0.01040345752168,0.0119194493484309,0.0138976914908629,0.0259119368371108,0.0125553071551407,0.0107253345584641,-0.00219031156874675,0.0202199609770471,-0.00219031156874675,0.00621213747441555,0.0258550197858021,0.0184536749957349,-0.00219031156874675,0.241470663212791,0.446357404240983,0.00737115890953796,0.00931384941358176,0.00439335229360306,0.00691885581361285,0.42076443305176,0.432147651959559,0.0431982257726971,0.264246669243604,0.309076381491951,0.57535439386244,0.565152257482106,-0.000831657254659487,0.0139970517567793,0.000966300282830468,0.025951471368929,0.00600426461280798,0.00600856443367781,0.00617995148173733,0.0106594538812537,0.0129483313911511,0.020397184086514,0.0238986099988692,0.122502792593337,-0.00219031156874675,0.000236159391348001,-0.00219031156874675,0.000586250812850529,-0.00219031156874675,0.00940085294894354,0.000431264093497194,-0.00219031156874675,-0.00219031156874675,0.00422616993024702,0.00832133244977736,0.000446866571669319,0.00371293114204481,0.0024487108950325,0.000786464895500303,-0.00219031156874675,0.00559671199520826,0.00366768126052814,0.00113913631504845,0.0093830987263777,-5.60595356944228e-05,0.00914087827846063,0.0182289145297535,0.0307107677724186,0.0137501126987302,0.0271781696117394,0.313330335246938,0.0192867253731736,0.00580893795816556,0.00438400168239171,0.000518204299565939,0.00658653966628814,0.00102224068398403,0.00553131168244897,-0.00219031156874675,0.00268899788880691,0.00715887522018874,-0.00219031156874675,-0.00219031156874675,0.00543582550031895,0.00280032413454412,-0.00219031156874675,-0.00219031156874675,0.0126831188078138,0.00024277694154149,0.000840789271686735,0.00838334276817373,0.00300328193305894,0.000293141481984711,0.00338692869250002,-0.00133128278446341,0.00166739036219103,0.00367831442231825,0.00252995104333266,0.0014469997891918,-2.85951520326969e-05,0.000323692170641587,0.00585396575970954,0.00705671713721383,-0.00219031156874675,0.000987566883059445,0.00135205594721351,0.00567915226357434,0.0012084228267268,0.0102928194670722,0.00224190536088945,0.00161440795728796,0.000964691140389929,0.00243292527080817,0.0033251128329579,0.0233983310808038,0.000240698455168697,0.00203979396822297,0.00410100329221172,0.00371665733807299,0.00807516878026284,0.00924788023306117,0.00492306844330273,0.00528538413376985,-0.00219031156874675,0.00195509559884458,0.0158860119748007,0.0145088274180036,0.00831158703754729,0.0106907348456357,0.0235348731557057,0.00901615306433512,0.00967292233018867,0.676599593881408,0.753410673357725,-0.00219031156874675,0.066619238522367,0.00714065325895903,0.0276187272237703,0.0252012788065665,0.0280825630055887,0.027303228406391,0.0145707170582111,0.0267801951233809,0.0359925241167816,0.0250937142660723,0.175625947203382,0.0213212080480358,0.0113218214432024,0.002037914260682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|gostat_on_MCL_coexpression=GO:0019911;structural constituent of myelin sheath;0.0439582683660776;17196!GO:0000015;phosphopyruvate hydratase complex;0.0439582683660776;13807!GO:0004634;phosphopyruvate hydratase activity;0.0439582683660776;13807!GO:0043209;myelin sheath;0.0439582683660776;17196!GO:0044265;cellular macromolecule catabolic process;0.0439582683660776;13807,78651!GO:0019894;kinesin binding;0.0439582683660776;60597!GO:0008191;metalloendopeptidase inhibitor activity;0.0439582683660776;110595!GO:0030295;protein kinase activator activity;0.0439582683660776;60597!GO:0009057;macromolecule catabolic process;0.0468695565507533;13807,78651!GO:0019209;kinase activator activity;0.0468695565507533;60597!GO:0007267;cell-cell signaling;0.048916634562752;14618,17196!
}}

Latest revision as of 15:00, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:100442103..100442128,+p@chr11:100442103..100442128
+
Mm9::chr11:100442142..100442165,+p@chr11:100442142..100442165
+
Mm9::chr11:100442597..100442612,+p@chr11:100442597..100442612
+
Mm9::chr14:68705447..68705460,-p@chr14:68705447..68705460
-
Mm9::chr15:82086621..82086634,+p3@1500009C09Rik
Mm9::chr15:89284538..89284545,+p8@Mapk8ip2
Mm9::chr18:82742238..82742272,-p@chr18:82742238..82742272
-
Mm9::chr18:82744988..82745004,+p@chr18:82744988..82745004
+
Mm9::chr18:82748407..82748411,+p@chr18:82748407..82748411
+
Mm9::chr18:82753500..82753517,+p12@Mbp
Mm9::chr18:82753633..82753676,-p@chr18:82753633..82753676
-
Mm9::chr18:82753891..82753908,+p@chr18:82753891..82753908
+
Mm9::chr18:82753905..82753933,-p@chr18:82753905..82753933
-
Mm9::chr18:82753941..82753954,+p@chr18:82753941..82753954
+
Mm9::chr18:82753999..82754008,+p@chr18:82753999..82754008
+
Mm9::chr18:82754039..82754053,+p@chr18:82754039..82754053
+
Mm9::chr18:82754092..82754126,+p@chr18:82754092..82754126
+
Mm9::chr18:82754173..82754194,+p@chr18:82754173..82754194
+
Mm9::chr18:82754208..82754223,+p@chr18:82754208..82754223
+
Mm9::chr18:82754410..82754428,+p@chr18:82754410..82754428
+
Mm9::chr18:82754517..82754531,+p@chr18:82754517..82754531
+
Mm9::chr18:82754558..82754580,+p@chr18:82754558..82754580
+
Mm9::chr18:82754581..82754615,+p@chr18:82754581..82754615
+
Mm9::chr18:82754675..82754700,-p@chr18:82754675..82754700
-
Mm9::chr2:29701161..29701165,-p1@Mir219-2
Mm9::chr6:115202281..115202317,-p2@Timp4
Mm9::chr6:124713083..124713094,-p5@Eno2
Mm9::chr6:125168999..125169012,+p@chr6:125168999..125169012
+
Mm9::chr7:107793432..107793445,-p@chr7:107793432..107793445
-
Mm9::chr8:81334181..81334194,-p8@Lsm6
Mm9::chrX:98579120..98579141,+p6@Gjb1


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:0019911structural constituent of myelin sheath0.0439582683660776
GO:0000015phosphopyruvate hydratase complex0.0439582683660776
GO:0004634phosphopyruvate hydratase activity0.0439582683660776
GO:0043209myelin sheath0.0439582683660776
GO:0044265cellular macromolecule catabolic process0.0439582683660776
GO:0019894kinesin binding0.0439582683660776
GO:0008191metalloendopeptidase inhibitor activity0.0439582683660776
GO:0030295protein kinase activator activity0.0439582683660776
GO:0009057macromolecule catabolic process0.0468695565507533
GO:0019209kinase activator activity0.0468695565507533
GO:0007267cell-cell signaling0.048916634562752



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>

Cell Type
Ontology termp-valuen
CNS neuron (sensu Vertebrata)2.43e-0823
neuroblast (sensu Vertebrata)2.43e-0823
neuron of the substantia nigra4.23e-083
raphe nuclei neuron6.38e-083
ectodermal cell7.02e-0844
neurectodermal cell7.02e-0844
neural cell4.74e-0743

Uber Anatomy
Ontology termp-valuen
regional part of nervous system2.35e-3054
nervous system2.71e-3075
central nervous system1.16e-2773
neural tube7.51e-2752
neural rod7.51e-2752
future spinal cord7.51e-2752
neural keel7.51e-2752
ectoderm-derived structure3.81e-2595
ectoderm3.81e-2595
presumptive ectoderm3.81e-2595
neurectoderm4.08e-2264
neural plate4.08e-2264
presumptive neural plate4.08e-2264
brain6.84e-2147
future brain6.84e-2147
gray matter7.74e-2134
ecto-epithelium5.52e-2073
regional part of brain1.23e-1946
occipital lobe6.20e-1910
visual cortex6.20e-1910
neocortex6.20e-1910
brain grey matter2.87e-1529
regional part of telencephalon2.87e-1529
telencephalon2.87e-1529
anterior neural tube4.71e-1540
structure with developmental contribution from neural crest2.45e-1492
posterior neural tube8.10e-1412
chordal neural plate8.10e-1412
regional part of forebrain1.02e-1339
forebrain1.02e-1339
future forebrain1.02e-1339
pre-chordal neural plate9.47e-1349
regional part of cerebral cortex1.59e-1217
cerebral cortex1.33e-1121
cerebral hemisphere1.33e-1121
pallium1.33e-1121
regional part of midbrain5.29e-104
midbrain5.29e-104
presumptive midbrain5.29e-104
midbrain neural tube5.29e-104
spinal cord1.98e-096
dorsal region element1.98e-096
dorsum1.98e-096
tube1.74e-08114
anatomical conduit2.98e-08122
substantia nigra4.23e-083
telencephalic nucleus4.23e-083
midbrain nucleus4.23e-083
neural nucleus4.23e-083
nucleus of brain4.23e-083
raphe nuclei6.38e-083
reticular formation6.38e-083
regional part of spinal cord1.91e-075
gray matter of spinal cord1.91e-075
organ system subdivision3.18e-07194


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)
MA0003.10.082789
MA0004.10.275884
MA0006.10.0992039
MA0007.10.257336
MA0009.13.5347
MA0014.10.00733366
MA0017.10.0294752
MA0019.10.229805
MA0024.10.884334
MA0025.10.564682
MA0027.11.93116
MA0028.10.107755
MA0029.10.315482
MA0030.10.320542
MA0031.10.293406
MA0038.10.157421
MA0040.10.377038
MA0041.10.0501054
MA0042.10.0455676
MA0043.10.446565
MA0046.10.396073
MA0048.10.25078
MA0050.10.0989764
MA0051.10.162867
MA0052.10.383564
MA0055.10.203373
MA0056.10
MA0057.11.53009
MA0058.10.378396
MA0059.10.179276
MA0060.10.262455
MA0061.10.166845
MA0063.10
MA0066.10.4599
MA0067.10.664516
MA0068.11.92116
MA0069.10.383839
MA0070.10.37599
MA0071.11.10769
MA0072.10.369163
MA0073.10.72025
MA0074.10.130125
MA0076.10.0347575
MA0077.10.351866
MA0078.10.183594
MA0081.10.783797
MA0083.12.94574
MA0084.10.971934
MA0087.10.409958
MA0088.10.189004
MA0089.10
MA0090.10.505079
MA0091.10.0866349
MA0092.10.505756
MA0093.10.114799
MA0095.10
MA0098.10
MA0100.10.391104
MA0101.10.18882
MA0103.10.895358
MA0105.10.121213
MA0106.10.188607
MA0107.10.125829
MA0108.20.245881
MA0109.10
MA0111.10.0718182
MA0113.10.170658
MA0114.10.326395
MA0115.10.448923
MA0116.10.24435
MA0117.10.42191
MA0119.15.43902
MA0122.10.438479
MA0124.10.616327
MA0125.10.55037
MA0130.10
MA0131.10.64304
MA0132.10
MA0133.10
MA0135.10.477472
MA0136.10.141449
MA0139.10.0907756
MA0140.10.781633
MA0141.11.39315
MA0142.10.282551
MA0143.10.180984
MA0144.10.561038
MA0145.10.00228986
MA0146.10.00208601
MA0147.10.36415
MA0148.10.296488
MA0149.10.0525422
MA0062.20.0557565
MA0035.20.126246
MA0039.20.00341659
MA0138.20.221177
MA0002.20.57298
MA0137.20.147294
MA0104.20.407689
MA0047.20.156958
MA0112.20.0663097
MA0065.21.42324
MA0150.10.257198
MA0151.10
MA0152.10.475315
MA0153.10.491737
MA0154.12.78374
MA0155.10.0880378
MA0156.10.138367
MA0157.10.259017
MA0158.10
MA0159.10.956073
MA0160.10.089496
MA0161.10
MA0162.10.00115095
MA0163.11.58136
MA0164.10.141659
MA0080.20.300456
MA0018.20.147322
MA0099.20.216863
MA0079.20.00969592
MA0102.21.0223
MA0258.10.50247
MA0259.10.064381
MA0442.10
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