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MCL coexpression mm9:601: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0.59159224115328,1.04924373800262,0.957821341702156,0.539584426555989,0.331586633844282,0.21524561219591,0.157487597443535,0,0.0447857898258226,0,0.119078361648301,0.0558041721483835,0,0,0.965301187240608,1.08499316545066,0.0644551523736777,0,0,0,0,0,0,0,0,0,0,0,0,0,0.075919512117871,0.2507456850819,0,0.100456901012675,0.226095853111613,0.233283434786145,0,0,0,0,0,0,0,0,0,0.122210736921952,0.389294454188438,0.174560973302262,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.154563335474484,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0234784353458152,0.181236227563129,0,0,0,0,0,0,0,0,0.0586534975690397,0,0,0.0413012308433057,0,0,0,0,0.049400930804471,0.170044660063349,0,0.0983461768813133,0,0,0,0,0,0,0,0,0.0509235292940968,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0146648352254805,0,0,0.0497277316172017,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0401075634450079,0,0.049257116002996,0,0.0652566657696677,0,0,0,0,0,0,0,0.0736278867910527,0,0,0,0,0,0,0,0,0,0,0.0659019793256198,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0331417600494206,0,0.00249397163134728,0.0244872863598586,0,0,0,0.127668937363575,0,0.0737896374598673,0.106901036464273,0.104960908225686,0,0.322868857438944,0.193070533481811,0.278076890983579,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.182078428252277,0.147815532899656,0.148325002318,0.121628269860045,0.132916844396872,0.112006449694472,0.110266795188488,0.159286971335735,0.147325594122017,0.0789923888605098,0.173873861735699,0.15767882076776,0.182511593142912,0.245198985460805,0,0,0,0,0,0.0373501741982983,0,0.0387498733264616,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0388749848471105,0,0.0242538736058389,0,0,0,0,0,0,0,0,0,0.0195303707501796,0,0,0,0,0,0,0,0,0,0.0383032227056179,0,0.0599055350463703,0,0,0,0
|gostat_on_MCL_coexpression=GO:0045069;regulation of viral genome replication;0.0119145437698286;12043!GO:0050792;regulation of viral reproduction;0.0119145437698286;12043!GO:0019079;viral genome replication;0.0119145437698286;12043!GO:0046902;regulation of mitochondrial membrane permeability;0.0119145437698286;12043!GO:0019058;viral infectious cycle;0.0119145437698286;12043!GO:0051881;regulation of mitochondrial membrane potential;0.0119145437698286;12043!GO:0004652;polynucleotide adenylyltransferase activity;0.0136158753894981;216578!GO:0022415;viral reproductive process;0.0148915477320502;12043!GO:0016032;viral reproduction;0.0158834472390889;12043!GO:0001836;release of cytochrome c from mitochondria;0.0238186440108132;12043!GO:0043631;RNA polyadenylation;0.0238186440108132;216578!GO:0007006;mitochondrial membrane organization and biogenesis;0.0256466306647956;12043!GO:0031069;hair follicle morphogenesis;0.0256466306647956;12043!GO:0031123;RNA 3'-end processing;0.0289131305174863;216578!GO:0008637;apoptotic mitochondrial changes;0.0301570578102471;12043!GO:0006839;mitochondrial transport;0.0322040377729354;12043!GO:0043524;negative regulation of neuron apoptosis;0.0322040377729354;12043!GO:0043523;regulation of neuron apoptosis;0.0408962687220554;12043!GO:0051402;neuron apoptosis;0.0408962687220554;12043!GO:0022404;molting cycle process;0.0408962687220554;12043!GO:0001942;hair follicle development;0.0408962687220554;12043!GO:0022405;hair cycle process;0.0408962687220554;12043!GO:0042391;regulation of membrane potential;0.0408962687220554;12043!GO:0042633;hair cycle;0.0408962687220554;12043!GO:0042303;molting cycle;0.0408962687220554;12043!GO:0008632;apoptotic program;0.0421101746110773;12043!GO:0048730;epidermis morphogenesis;0.0421101746110773;12043!GO:0016772;transferase activity, transferring phosphorus-containing groups;0.0421101746110773;216578,18712!GO:0046982;protein heterodimerization activity;0.0483232202533136;12043!GO:0005634;nucleus;0.0483232202533136;216578,18712,12043!
|gostat_on_MCL_coexpression=GO:0045069;regulation of viral genome replication;0.0119145437698286;12043!GO:0050792;regulation of viral reproduction;0.0119145437698286;12043!GO:0019079;viral genome replication;0.0119145437698286;12043!GO:0046902;regulation of mitochondrial membrane permeability;0.0119145437698286;12043!GO:0019058;viral infectious cycle;0.0119145437698286;12043!GO:0051881;regulation of mitochondrial membrane potential;0.0119145437698286;12043!GO:0004652;polynucleotide adenylyltransferase activity;0.0136158753894981;216578!GO:0022415;viral reproductive process;0.0148915477320502;12043!GO:0016032;viral reproduction;0.0158834472390889;12043!GO:0001836;release of cytochrome c from mitochondria;0.0238186440108132;12043!GO:0043631;RNA polyadenylation;0.0238186440108132;216578!GO:0007006;mitochondrial membrane organization and biogenesis;0.0256466306647956;12043!GO:0031069;hair follicle morphogenesis;0.0256466306647956;12043!GO:0031123;RNA 3'-end processing;0.0289131305174863;216578!GO:0008637;apoptotic mitochondrial changes;0.0301570578102471;12043!GO:0006839;mitochondrial transport;0.0322040377729354;12043!GO:0043524;negative regulation of neuron apoptosis;0.0322040377729354;12043!GO:0043523;regulation of neuron apoptosis;0.0408962687220554;12043!GO:0051402;neuron apoptosis;0.0408962687220554;12043!GO:0022404;molting cycle process;0.0408962687220554;12043!GO:0001942;hair follicle development;0.0408962687220554;12043!GO:0022405;hair cycle process;0.0408962687220554;12043!GO:0042391;regulation of membrane potential;0.0408962687220554;12043!GO:0042633;hair cycle;0.0408962687220554;12043!GO:0042303;molting cycle;0.0408962687220554;12043!GO:0008632;apoptotic program;0.0421101746110773;12043!GO:0048730;epidermis morphogenesis;0.0421101746110773;12043!GO:0016772;transferase activity, transferring phosphorus-containing groups;0.0421101746110773;216578,18712!GO:0046982;protein heterodimerization activity;0.0483232202533136;12043!GO:0005634;nucleus;0.0483232202533136;216578,18712,12043!
}}
}}

Revision as of 12:44, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr11:23795175..23795189,-p2@Papolg
Mm9::chr15:5187479..5187496,+p@chr15:5187479..5187496
+
Mm9::chr16:49856460..49856493,-p@chr16:49856460..49856493
-
Mm9::chr16:49856709..49856732,+p@chr16:49856709..49856732
+
Mm9::chr17:29629982..29630050,+p3@Pim1
Mm9::chr17:29630059..29630073,+p8@Pim1
Mm9::chr17:29630077..29630088,+p9@Pim1
Mm9::chr17:29630114..29630128,+p@chr17:29630114..29630128
+
Mm9::chr1:108610492..108610501,-p4@Bcl2
Mm9::chr3:58902298..58902304,-p@chr3:58902298..58902304
-
Mm9::chr6:129185107..129185119,+p@chr6:129185107..129185119
+
Mm9::chr7:31941253..31941263,-p@chr7:31941253..31941263
-


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:0045069regulation of viral genome replication0.0119145437698286
GO:0050792regulation of viral reproduction0.0119145437698286
GO:0019079viral genome replication0.0119145437698286
GO:0046902regulation of mitochondrial membrane permeability0.0119145437698286
GO:0019058viral infectious cycle0.0119145437698286
GO:0051881regulation of mitochondrial membrane potential0.0119145437698286
GO:0004652polynucleotide adenylyltransferase activity0.0136158753894981
GO:0022415viral reproductive process0.0148915477320502
GO:0016032viral reproduction0.0158834472390889
GO:0001836release of cytochrome c from mitochondria0.0238186440108132
GO:0043631RNA polyadenylation0.0238186440108132
GO:0007006mitochondrial membrane organization and biogenesis0.0256466306647956
GO:0031069hair follicle morphogenesis0.0256466306647956
GO:0031123RNA 3'-end processing0.0289131305174863
GO:0008637apoptotic mitochondrial changes0.0301570578102471
GO:0006839mitochondrial transport0.0322040377729354
GO:0043524negative regulation of neuron apoptosis0.0322040377729354
GO:0043523regulation of neuron apoptosis0.0408962687220554
GO:0051402neuron apoptosis0.0408962687220554
GO:0022404molting cycle process0.0408962687220554
GO:0001942hair follicle development0.0408962687220554
GO:0022405hair cycle process0.0408962687220554
GO:0042391regulation of membrane potential0.0408962687220554
GO:0042633hair cycle0.0408962687220554
GO:0042303molting cycle0.0408962687220554
GO:0008632apoptotic program0.0421101746110773
GO:0048730epidermis morphogenesis0.0421101746110773
GO:0016772transferase activity, transferring phosphorus-containing groups0.0421101746110773
GO:0046982protein heterodimerization activity0.0483232202533136
GO:0005634nucleus0.0483232202533136



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}}}