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MCL coexpression mm9:1028: Difference between revisions

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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0354470656487682,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.877753318668592,0.817944053113571,0.633856272871215,0,0,0,0.142658407030909,0,0,0,0,0,0.099424903790252,0.109421078997306,0.180605254120548,0,0,0,0,0,0,0,0,0,0.141204588184303,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.127383644231484,0.100296779313498,0,0,0.358556276484448,0,0.909056572608405,0.0851089148667383,0.245532308442916,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0509235292940968,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0623063220167371,0,0,0.0479619276176895,0,0,0.0338533374824575,0.0592603993571966,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.046982063026719,0,0,0.0769870445726752,0.0294389011296462,0,0,0.0633328814307688,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.136564059910207,0,0,0,0,0,0,0.0774164737207147,0,0,0,0,0.0691813633419548,0,0,0,0,0,0,0,0,0,0,0,0,0.0930603692915911,0,0,0,0,0,0,0.108524491213051,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.083442441818608,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.034489466458534,0,0,0,0,0,0,0,0.0527554171614426,0,0,0,0.0433069931089932,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0767094571656325,0,0.0730404042754446,0.0843504501108034,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0242538736058389,0,0,0,0,0.0596387295197733,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0354470656487682,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.877753318668592,0.817944053113571,0.633856272871215,0,0,0,0.142658407030909,0,0,0,0,0,0.099424903790252,0.109421078997306,0.180605254120548,0,0,0,0,0,0,0,0,0,0.141204588184303,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.127383644231484,0.100296779313498,0,0,0.358556276484448,0,0.909056572608405,0.0851089148667383,0.245532308442916,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0509235292940968,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0623063220167371,0,0,0.0479619276176895,0,0,0.0338533374824575,0.0592603993571966,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.046982063026719,0,0,0.0769870445726752,0.0294389011296462,0,0,0.0633328814307688,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.136564059910207,0,0,0,0,0,0,0.0774164737207147,0,0,0,0,0.0691813633419548,0,0,0,0,0,0,0,0,0,0,0,0,0.0930603692915911,0,0,0,0,0,0,0.108524491213051,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.083442441818608,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.034489466458534,0,0,0,0,0,0,0,0.0527554171614426,0,0,0,0.0433069931089932,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0767094571656325,0,0.0730404042754446,0.0843504501108034,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0242538736058389,0,0,0,0,0.0596387295197733,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=GO:0005176;ErbB-2 class receptor binding;0.0258495539819157;211323!GO:0046579;positive regulation of Ras protein signal transduction;0.0258495539819157;211323!GO:0045213;neurotransmitter receptor metabolic process;0.0258495539819157;211323!GO:0051057;positive regulation of small GTPase mediated signal transduction;0.0258495539819157;211323!GO:0043624;cellular protein complex disassembly;0.0258495539819157;211323!GO:0043241;protein complex disassembly;0.0258495539819157;211323!GO:0032984;macromolecular complex disassembly;0.0258495539819157;211323!GO:0007416;synaptogenesis;0.0269185018583432;211323!GO:0048663;neuron fate commitment;0.0269185018583432;211323!GO:0022411;cellular component disassembly;0.0269185018583432;211323!GO:0007422;peripheral nervous system development;0.0269185018583432;211323!GO:0043112;receptor metabolic process;0.0269185018583432;211323!GO:0010001;glial cell differentiation;0.0377552695103153;211323!GO:0042063;gliogenesis;0.0378231262427327;211323!GO:0050808;synapse organization and biogenesis;0.037881510381851;211323!
|gostat_on_MCL_coexpression=GO:0005176;ErbB-2 class receptor binding;0.0258495539819157;211323!GO:0046579;positive regulation of Ras protein signal transduction;0.0258495539819157;211323!GO:0045213;neurotransmitter receptor metabolic process;0.0258495539819157;211323!GO:0051057;positive regulation of small GTPase mediated signal transduction;0.0258495539819157;211323!GO:0043624;cellular protein complex disassembly;0.0258495539819157;211323!GO:0043241;protein complex disassembly;0.0258495539819157;211323!GO:0032984;macromolecular complex disassembly;0.0258495539819157;211323!GO:0007416;synaptogenesis;0.0269185018583432;211323!GO:0048663;neuron fate commitment;0.0269185018583432;211323!GO:0022411;cellular component disassembly;0.0269185018583432;211323!GO:0007422;peripheral nervous system development;0.0269185018583432;211323!GO:0043112;receptor metabolic process;0.0269185018583432;211323!GO:0010001;glial cell differentiation;0.0377552695103153;211323!GO:0042063;gliogenesis;0.0378231262427327;211323!GO:0050808;synapse organization and biogenesis;0.037881510381851;211323!
|ontology_enrichment_celltype=CL:0000680!6.13e-16!6;CL:0000183!6.13e-16!6;CL:0000187!6.13e-16!6;CL:0000056!6.13e-16!6;CL:0000222!1.52e-13!7;CL:0000355!2.37e-10!9;CL:0000192!4.24e-09!3;CL:0000359!4.24e-09!3;CL:0002539!4.24e-09!3;CL:0000514!4.24e-09!3;CL:0002494!1.81e-08!3;CL:0000737!1.81e-08!3;CL:0000746!1.81e-08!3;CL:0000513!1.81e-08!3
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001134!2.37e-10!9;UBERON:0002036!2.37e-10!9;UBERON:0002385!2.37e-10!9;UBERON:0000486!2.37e-10!9;UBERON:0007503!2.37e-10!9;UBERON:0001015!2.37e-10!9;UBERON:0002329!2.37e-10!9;UBERON:0003082!2.37e-10!9;UBERON:0003059!2.37e-10!9;UBERON:0007282!2.37e-10!9;UBERON:0004290!2.37e-10!9;UBERON:0009618!2.37e-10!9;UBERON:0000383!3.11e-09!10;UBERON:0001135!4.24e-09!3;UBERON:0004237!4.24e-09!3;UBERON:0004695!4.24e-09!3;UBERON:0002111!4.24e-09!3;UBERON:0004178!4.24e-09!3;UBERON:0003103!5.45e-09!43;UBERON:0004535!5.65e-09!23;UBERON:0001009!5.65e-09!23;UBERON:0007524!2.56e-08!11;UBERON:0003077!2.56e-08!11;UBERON:0007285!2.56e-08!11;UBERON:0004872!2.86e-08!33;UBERON:0000947!6.87e-07!4;UBERON:0001637!6.87e-07!4;UBERON:0004573!6.87e-07!4;UBERON:0003509!6.87e-07!4;UBERON:0004571!6.87e-07!4;UBERON:0010191!6.87e-07!4;UBERON:0004572!6.87e-07!4
}}
}}

Revision as of 16:12, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:58071854..58071882,+p@chr10:58071854..58071882
+
Mm9::chr1:127573438..127573451,+p5@Gpr39
Mm9::chr1:127573708..127573719,+p9@Gpr39
Mm9::chr1:127573773..127573786,+p6@Gpr39
Mm9::chr1:137662814..137662817,+p5@Phlda3
Mm9::chr2:50152414..50152430,+p2@ENSMUST00000123699
Mm9::chr8:33119942..33119952,-p4@Nrg1


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:0005176ErbB-2 class receptor binding0.0258495539819157
GO:0046579positive regulation of Ras protein signal transduction0.0258495539819157
GO:0045213neurotransmitter receptor metabolic process0.0258495539819157
GO:0051057positive regulation of small GTPase mediated signal transduction0.0258495539819157
GO:0043624cellular protein complex disassembly0.0258495539819157
GO:0043241protein complex disassembly0.0258495539819157
GO:0032984macromolecular complex disassembly0.0258495539819157
GO:0007416synaptogenesis0.0269185018583432
GO:0048663neuron fate commitment0.0269185018583432
GO:0022411cellular component disassembly0.0269185018583432
GO:0007422peripheral nervous system development0.0269185018583432
GO:0043112receptor metabolic process0.0269185018583432
GO:0010001glial cell differentiation0.0377552695103153
GO:0042063gliogenesis0.0378231262427327
GO:0050808synapse organization and biogenesis0.037881510381851



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
skeletal muscle tissue2.37e-109
striated muscle tissue2.37e-109
muscle tissue2.37e-109
multilaminar epithelium2.37e-109
epithelial vesicle2.37e-109
musculature2.37e-109
somite2.37e-109
myotome2.37e-109
presomitic mesoderm2.37e-109
presumptive segmental plate2.37e-109
dermomyotome2.37e-109
trunk paraxial mesoderm2.37e-109
musculature of body3.11e-0910
smooth muscle tissue4.24e-093
blood vessel smooth muscle4.24e-093
arterial system smooth muscle4.24e-093
artery smooth muscle tissue4.24e-093
aorta smooth muscle tissue4.24e-093
compound organ5.45e-0943
cardiovascular system5.65e-0923
circulatory system5.65e-0923
dense mesenchyme tissue2.56e-0811
paraxial mesoderm2.56e-0811
presumptive paraxial mesoderm2.56e-0811
splanchnic layer of lateral plate mesoderm2.86e-0833
aorta6.87e-074
artery6.87e-074
systemic artery6.87e-074
arterial blood vessel6.87e-074
systemic arterial system6.87e-074
aortic system6.87e-074
arterial system6.87e-074


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}}}