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MCL coexpression mm9:168: Difference between revisions

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{{MCL_coexpression_mm9
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pathway;0.000457623209854216;270192,18191,20614,18190!GO:0007269;neurotransmitter secretion;0.000457623209854216;18191,20614,18190!GO:0032940;secretion by cell;0.000457623209854216;270192,18191,20614,18190!GO:0045055;regulated secretory pathway;0.000457623209854216;18191,20614,18190!GO:0005246;calcium channel regulator activity;0.000597317262859314;18191,18190!GO:0046903;secretion;0.000597317262859314;270192,18191,20614,18190!GO:0003001;generation of a signal involved in cell-cell signaling;0.000597317262859314;18191,20614,18190!GO:0001505;regulation of neurotransmitter levels;0.000597317262859314;18191,20614,18190!GO:0042734;presynaptic membrane;0.000599258709996223;18191,18190!GO:0016247;channel regulator activity;0.000779172411882122;18191,18190!GO:0015457;auxiliary transport protein activity;0.000779172411882122;18191,18190!GO:0044456;synapse part;0.000959641592216027;242425,18191,18190!GO:0007416;synaptogenesis;0.000959641592216027;18191,18190!GO:0007268;synaptic transmission;0.00336985056220335;18191,20614,18190!GO:0050808;synapse organization and biogenesis;0.00484547315251145;18191,18190!GO:0019226;transmission of nerve impulse;0.00484547315251145;18191,20614,18190!GO:0016081;synaptic vesicle docking during exocytosis;0.00787713265980194;20614!GO:0007154;cell communication;0.00787713265980194;270192,232975,432530,18190,12315,242425,18191,20614!GO:0051649;establishment of cellular localization;0.00953371527333145;270192,18191,20614,18190!GO:0051641;cellular localization;0.00964482068496454;270192,18191,20614,18190!GO:0007267;cell-cell signaling;0.0107642795175801;18191,20614,18190!GO:0043062;extracellular structure organization and biogenesis;0.0170006521667474;18191,18190!GO:0006890;retrograde vesicle-mediated transport, Golgi to ER;0.0170006521667474;270192!GO:0004965;GABA-B receptor activity;0.0170006521667474;242425!GO:0035235;ionotropic glutamate receptor signaling pathway;0.0217542782711481;232975!GO:0001504;neurotransmitter uptake;0.0365726831518397;20614!GO:0016020;membrane;0.0381004874793611;73340,66797,270192,232975,432530,18190,12315,242425,18191,20614!GO:0007215;glutamate signaling pathway;0.0466392475381137;232975!GO:0005391;sodium:potassium-exchanging ATPase activity;0.0466392475381137;232975!GO:0007399;nervous system development;0.0466392475381137;109934,18191,18190!GO:0016079;synaptic vesicle exocytosis;0.0466392475381137;20614!GO:0004016;adenylate cyclase activity;0.0466392475381137;432530!GO:0007190;adenylate cyclase activation;0.0489652615281346;432530!GO:0045762;positive regulation of adenylate cyclase activity;0.0489652615281346;432530!GO:0031281;positive regulation of cyclase activity;0.0489652615281346;432530!GO:0051349;positive regulation of lyase 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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.179051645532617,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.147562843172839,0.18440492317299,0.213207239280454,0,0,0,0,0,0,0,0.0818436986734574,0.103807782330171,0.0829019901297716,0.330941898710929,0.323116468687679,0.0951629323478916,0.0761636383140293,0,0.428477360389439,0.483301582624407,0.49837830748604,0.144779277929812,0.190030631017894,0.182104477852721,0.468647462304843,0.429475765992591,0.402774059390807,0.486061930039393,0.454971602226302,0.192901363035279,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0469568706916304,0,0,0,0,0,0,0.0482820047261801,0,0,0,0,0,0,0,0,0.273774759912798,1.01594921528684,0,0,0,0,0.311443277314482,0.36884287281064,0.138922288373465,0.378505927175087,0.403856780142017,0.389965922625323,0.257967923814717,0,0,0,0.069874145690564,0,0,0,0.0609639314262262,0.055406237837571,0.0523528812100954,0.074598306112166,0.0999233952154288,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.31206088192539,0.116844694267823,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.332948128165414,0.312791786774663,0,0,0,0,0,0,0,0,0,0,0,0.41607548758856,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0661577744756082,0.0324884813795483,0,0,0,0,0,0,0,0,0,0.324807369180142,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.513085342652956,0.518727899922476,0.517404685814234,0.56978032349625,0.485046405834616,0.514040340140897,0.568212287967179,0.568427876181492,0.449103283876296,0.554949444870281,0,0,0,0,0,0,0,0,0,0,0,0,0.0388749848471105,0.0269518943326477,0.0242538736058389,0,0,0,0,0.0596387295197733,0,0,0,0,0.0390607415003592,0.0352754493378881,0,0,0,0,0.0486884105045233,0.0408018333703219,0,0,0,0.0968441960560167,0,0.0845301845292944,0.0760168881589905,0,0
|gostat_on_MCL_coexpression=GO:0045045;secretory pathway;0.000457623209854216;270192,18191,20614,18190!GO:0007269;neurotransmitter secretion;0.000457623209854216;18191,20614,18190!GO:0032940;secretion by cell;0.000457623209854216;270192,18191,20614,18190!GO:0045055;regulated secretory pathway;0.000457623209854216;18191,20614,18190!GO:0005246;calcium channel regulator activity;0.000597317262859314;18191,18190!GO:0046903;secretion;0.000597317262859314;270192,18191,20614,18190!GO:0003001;generation of a signal involved in cell-cell signaling;0.000597317262859314;18191,20614,18190!GO:0001505;regulation of neurotransmitter levels;0.000597317262859314;18191,20614,18190!GO:0042734;presynaptic membrane;0.000599258709996223;18191,18190!GO:0016247;channel regulator activity;0.000779172411882122;18191,18190!GO:0015457;auxiliary transport protein activity;0.000779172411882122;18191,18190!GO:0044456;synapse part;0.000959641592216027;242425,18191,18190!GO:0007416;synaptogenesis;0.000959641592216027;18191,18190!GO:0007268;synaptic transmission;0.00336985056220335;18191,20614,18190!GO:0050808;synapse organization and biogenesis;0.00484547315251145;18191,18190!GO:0019226;transmission of nerve impulse;0.00484547315251145;18191,20614,18190!GO:0016081;synaptic vesicle docking during exocytosis;0.00787713265980194;20614!GO:0007154;cell communication;0.00787713265980194;270192,232975,432530,18190,12315,242425,18191,20614!GO:0051649;establishment of cellular localization;0.00953371527333145;270192,18191,20614,18190!GO:0051641;cellular localization;0.00964482068496454;270192,18191,20614,18190!GO:0007267;cell-cell signaling;0.0107642795175801;18191,20614,18190!GO:0043062;extracellular structure organization and biogenesis;0.0170006521667474;18191,18190!GO:0006890;retrograde vesicle-mediated transport, Golgi to ER;0.0170006521667474;270192!GO:0004965;GABA-B receptor activity;0.0170006521667474;242425!GO:0035235;ionotropic glutamate receptor signaling pathway;0.0217542782711481;232975!GO:0001504;neurotransmitter uptake;0.0365726831518397;20614!GO:0016020;membrane;0.0381004874793611;73340,66797,270192,232975,432530,18190,12315,242425,18191,20614!GO:0007215;glutamate signaling pathway;0.0466392475381137;232975!GO:0005391;sodium:potassium-exchanging ATPase activity;0.0466392475381137;232975!GO:0007399;nervous system development;0.0466392475381137;109934,18191,18190!GO:0016079;synaptic vesicle exocytosis;0.0466392475381137;20614!GO:0004016;adenylate cyclase activity;0.0466392475381137;432530!GO:0007190;adenylate cyclase activation;0.0489652615281346;432530!GO:0045762;positive regulation of adenylate cyclase activity;0.0489652615281346;432530!GO:0031281;positive regulation of cyclase activity;0.0489652615281346;432530!GO:0051349;positive regulation of lyase activity;0.0489652615281346;432530!
}}

Latest revision as of 14:49, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:59595669..59595709,+p@chr10:59595669..59595709
+
Mm9::chr11:118374668..118374689,-p7@Rbfox3
Mm9::chr11:68904443..68904452,+p@chr11:68904443..68904452
+
Mm9::chr11:68904523..68904540,+p@chr11:68904523..68904540
+
Mm9::chr11:6963404..6963407,+p3@Adcy1
Mm9::chr11:76384765..76384775,-p36@Abr
Mm9::chr12:90033250..90033264,+p11@LOC100505240
p12@Nrxn3
Mm9::chr12:90033455..90033478,+p12@LOC100505240
p13@Nrxn3
Mm9::chr13:54860735..54860764,-p@chr13:54860735..54860764
-
Mm9::chr14:124842838..124842872,-p@chr14:124842838..124842872
-
Mm9::chr15:79619471..79619487,-p@chr15:79619471..79619487
-
Mm9::chr16:28159955..28159960,-p1@uc012adx.1
Mm9::chr16:96747106..96747170,+p@chr16:96747106..96747170
+
Mm9::chr16:96747205..96747216,+p@chr16:96747205..96747216
+
Mm9::chr17:35374840..35374863,+p@chr17:35374840..35374863
+
Mm9::chr17:35375112..35375126,+p@chr17:35375112..35375126
+
Mm9::chr17:57219785..57219838,-p@chr17:57219785..57219838
-
Mm9::chr19:6497674..6497687,+p10@Nrxn2
Mm9::chr19:6498024..6498037,+p7@Nrxn2
Mm9::chr2:136581807..136581878,+p@chr2:136581807..136581878
+
Mm9::chr2:158201991..158202031,+p@chr2:158201991..158202031
+
Mm9::chr2:25172399..25172412,-p@chr2:25172399..25172412
-
Mm9::chr2:28063675..28063687,+p@chr2:28063675..28063687
+
Mm9::chr2:28069659..28069675,+p@chr2:28069659..28069675
+
Mm9::chr2:28084644..28084656,+p@chr2:28084644..28084656
+
Mm9::chr2:32167682..32167722,-p@chr2:32167682..32167722
-
Mm9::chr3:80683618..80683637,-p@chr3:80683618..80683637
-
Mm9::chr4:126429259..126429266,-p@chr4:126429259..126429266
-
Mm9::chr4:47004694..47004703,-p8@Gabbr2
Mm9::chr5:108949049..108949074,-p@chr5:108949049..108949074
-
Mm9::chr5:49140574..49140590,-p@chr5:49140574..49140590
-
Mm9::chr6:45010099..45010108,+p13@Cntnap2
Mm9::chr7:105059616..105059642,+p@chr7:105059616..105059642
+
Mm9::chr7:134096524..134096540,+p@chr7:134096524..134096540
+
Mm9::chr7:134161986..134162037,-p@chr7:134161986..134162037
-
Mm9::chr7:134162092..134162110,-p@chr7:134162092..134162110
-
Mm9::chr7:134950140..134950151,-p@chr7:134950140..134950151
-
Mm9::chr7:16502686..16502782,-p@chr7:16502686..16502782
-
Mm9::chr7:17502235..17502264,-p@chr7:17502235..17502264
-
Mm9::chr7:25763334..25763361,-p@chr7:25763334..25763361
-
Mm9::chr7:25763366..25763383,-p@chr7:25763366..25763383
-
Mm9::chr7:25763409..25763419,-p@chr7:25763409..25763419
-
Mm9::chr7:25763428..25763438,-p@chr7:25763428..25763438
-
Mm9::chr7:25763452..25763455,-p@chr7:25763452..25763455
-
Mm9::chr7:25763531..25763540,-p@chr7:25763531..25763540
-
Mm9::chr7:25782256..25782270,-p@chr7:25782256..25782270
-
Mm9::chr7:25782591..25782655,-p@chr7:25782591..25782655
-
Mm9::chr7:25785732..25785765,-p@chr7:25785732..25785765
-
Mm9::chr7:31092226..31092249,+p@chr7:31092226..31092249
+
Mm9::chr7:31220215..31220234,-p@chr7:31220215..31220234
-
Mm9::chr7:31227273..31227296,-p@chr7:31227273..31227296
-
Mm9::chr7:3366466..3366480,+p@chr7:3366466..3366480
+
Mm9::chr7:3366529..3366586,+p@chr7:3366529..3366586
+
Mm9::chr7:67128313..67128327,-p@chr7:67128313..67128327
-
Mm9::chr8:73009616..73009639,-p@chr8:73009616..73009639
-
Mm9::chr8:73282007..73282033,+p@chr8:73282007..73282033
+
Mm9::chr8:73282082..73282099,+p@chr8:73282082..73282099
+
Mm9::chr8:98237247..98237264,+p@chr8:98237247..98237264
+
Mm9::chr9:103014393..103014398,+p10@Rab6b
Mm9::chr9:108041696..108041708,-p@chr9:108041696..108041708
-
Mm9::chr9:58488544..58488566,+p@chr9:58488544..58488566
+
Mm9::chrX:10172828..10172913,+p@chrX:10172828..10172913
+
Mm9::chrX:10173130..10173156,+p@chrX:10173130..10173156
+
Mm9::chrX:58436727..58436738,+p@chrX:58436727..58436738
+
Mm9::chrX:7229008..7229027,+p@chrX:7229008..7229027
+


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:0045045secretory pathway0.000457623209854216
GO:0007269neurotransmitter secretion0.000457623209854216
GO:0032940secretion by cell0.000457623209854216
GO:0045055regulated secretory pathway0.000457623209854216
GO:0005246calcium channel regulator activity0.000597317262859314
GO:0046903secretion0.000597317262859314
GO:0003001generation of a signal involved in cell-cell signaling0.000597317262859314
GO:0001505regulation of neurotransmitter levels0.000597317262859314
GO:0042734presynaptic membrane0.000599258709996223
GO:0016247channel regulator activity0.000779172411882122
GO:0015457auxiliary transport protein activity0.000779172411882122
GO:0044456synapse part0.000959641592216027
GO:0007416synaptogenesis0.000959641592216027
GO:0007268synaptic transmission0.00336985056220335
GO:0050808synapse organization and biogenesis0.00484547315251145
GO:0019226transmission of nerve impulse0.00484547315251145
GO:0016081synaptic vesicle docking during exocytosis0.00787713265980194
GO:0007154cell communication0.00787713265980194
GO:0051649establishment of cellular localization0.00953371527333145
GO:0051641cellular localization0.00964482068496454
GO:0007267cell-cell signaling0.0107642795175801
GO:0043062extracellular structure organization and biogenesis0.0170006521667474
GO:0006890retrograde vesicle-mediated transport, Golgi to ER0.0170006521667474
GO:0004965GABA-B receptor activity0.0170006521667474
GO:0035235ionotropic glutamate receptor signaling pathway0.0217542782711481
GO:0001504neurotransmitter uptake0.0365726831518397
GO:0016020membrane0.0381004874793611
GO:0007215glutamate signaling pathway0.0466392475381137
GO:0005391sodium:potassium-exchanging ATPase activity0.0466392475381137
GO:0007399nervous system development0.0466392475381137
GO:0016079synaptic vesicle exocytosis0.0466392475381137
GO:0004016adenylate cyclase activity0.0466392475381137
GO:0007190adenylate cyclase activation0.0489652615281346
GO:0045762positive regulation of adenylate cyclase activity0.0489652615281346
GO:0031281positive regulation of cyclase activity0.0489652615281346
GO:0051349positive regulation of lyase activity0.0489652615281346



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
regional part of nervous system4.61e-4254
neurectoderm1.55e-3964
neural plate1.55e-3964
presumptive neural plate1.55e-3964
neural tube5.55e-3952
neural rod5.55e-3952
future spinal cord5.55e-3952
neural keel5.55e-3952
central nervous system1.54e-3673
gray matter8.87e-3634
nervous system3.42e-3575
ecto-epithelium5.56e-3373
ectoderm-derived structure7.01e-3395
ectoderm7.01e-3395
presumptive ectoderm7.01e-3395
brain1.71e-3247
future brain1.71e-3247
regional part of brain3.60e-3146
pre-chordal neural plate8.12e-3149
brain grey matter3.63e-2929
regional part of telencephalon3.63e-2929
telencephalon3.63e-2929
anterior neural tube6.43e-2840
regional part of forebrain9.38e-2739
forebrain9.38e-2739
future forebrain9.38e-2739
structure with developmental contribution from neural crest1.46e-2492
cerebral cortex1.34e-1921
cerebral hemisphere1.34e-1921
pallium1.34e-1921
occipital lobe4.70e-1610
visual cortex4.70e-1610
neocortex4.70e-1610
regional part of cerebral cortex1.46e-1517
tube3.03e-11114
posterior neural tube4.94e-1112
chordal neural plate4.94e-1112
basal ganglion1.23e-108
nuclear complex of neuraxis1.23e-108
aggregate regional part of brain1.23e-108
collection of basal ganglia1.23e-108
cerebral subcortex1.23e-108
anatomical conduit8.97e-10122
spinal cord8.17e-096
dorsal region element8.17e-096
dorsum8.17e-096
regional part of spinal cord1.19e-075
gray matter of spinal cord1.19e-075
organ part4.93e-0799
corpus striatum9.17e-075
striatum9.17e-075
ventral part of telencephalon9.17e-075
future corpus striatum9.17e-075


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)
MA0003.10.114859
MA0004.10.052639
MA0006.10.023578
MA0007.11.00351
MA0009.10.160008
MA0014.10.233806
MA0017.10.662865
MA0019.10.542391
MA0024.10.136175
MA0025.10.312699
MA0027.11.61241
MA0028.10.070568
MA0029.10.125003
MA0030.10.128331
MA0031.10.357432
MA0038.10.147549
MA0040.10.966531
MA0041.10.491425
MA0042.11.23711
MA0043.10.218486
MA0046.10.180835
MA0048.10.212688
MA0050.10.369143
MA0051.10.356522
MA0052.10.511731
MA0055.10.0692889
MA0056.10
MA0057.11.50142
MA0058.10.0604986
MA0059.10.692236
MA0060.10.00112439
MA0061.10.129085
MA0063.10
MA0066.10.323968
MA0067.10.397426
MA0068.10.182419
MA0069.10.171998
MA0070.10.963471
MA0071.10.187661
MA0072.10.161558
MA0073.13.86115
MA0074.10.501007
MA0076.10.0439233
MA0077.10.893139
MA0078.10.184832
MA0081.11.42644
MA0083.10.217977
MA0084.10.676467
MA0087.10.191005
MA0088.10.453428
MA0089.10
MA0090.10.230817
MA0091.10.317185
MA0092.10.0381485
MA0093.10.0309119
MA0095.10
MA0098.10
MA0100.10.102771
MA0101.10.0754506
MA0103.10.498741
MA0105.10.69487
MA0106.10.192185
MA0107.10.036574
MA0108.20.0821349
MA0109.10
MA0111.10.443356
MA0113.10.377765
MA0114.10.333946
MA0115.10.628067
MA0116.11.59125
MA0117.10.199875
MA0119.10.0758923
MA0122.10.212337
MA0124.10.35604
MA0125.10.300895
MA0130.10
MA0131.10.0713666
MA0132.10
MA0133.10
MA0135.10.24238
MA0136.10.0307086
MA0139.10.671048
MA0140.10.102691
MA0141.10.812029
MA0142.10.104015
MA0143.10.18103
MA0144.11.15315
MA0145.10.167947
MA0146.10.145848
MA0147.10.0126688
MA0148.10.0606046
MA0149.10.00459441
MA0062.20.00872224
MA0035.20.258662
MA0039.20.137923
MA0138.20.518074
MA0002.20.0973547
MA0137.20.221616
MA0104.20.0123631
MA0047.20.146907
MA0112.21.57915
MA0065.20.99016
MA0150.10.456843
MA0151.10
MA0152.10.615133
MA0153.10.253603
MA0154.11.92129
MA0155.11.2092
MA0156.10.012816
MA0157.10.625308
MA0158.10
MA0159.12.73793
MA0160.10.165189
MA0161.10
MA0162.10.0296111
MA0163.16.09427
MA0164.10.126099
MA0080.20.0911242
MA0018.20.314542
MA0099.20.0660857
MA0079.23.10455
MA0102.20.723908
MA0258.10.591756
MA0259.10.507279
MA0442.10
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