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MCL coexpression mm9:168: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9
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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!
|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!
}}
}}

Revision as of 12:37, 11 October 2012


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>disease_data<br>

Cell Type
Ontology termp-valuen

Uber Anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen


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)

{{{tfbs_overrepresentation_jaspar}}}

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