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MCL coexpression mm9:2739: Difference between revisions

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|gostat_on_MCL_coexpression=GO:0005891;voltage-gated calcium channel complex;0.0488632521975829;12291!GO:0005509;calcium ion binding;0.0488632521975829;12291,16443!GO:0005245;voltage-gated calcium channel activity;0.0488632521975829;12291!GO:0030027;lamellipodium;0.0488632521975829;16443!GO:0019717;synaptosome;0.0488632521975829;16443!GO:0005089;Rho guanyl-nucleotide exchange factor activity;0.0488632521975829;16443!GO:0035023;regulation of Rho protein signal transduction;0.0488632521975829;16443!GO:0044459;plasma membrane part;0.0488632521975829;12291,16443!GO:0005088;Ras guanyl-nucleotide exchange factor activity;0.0488632521975829;16443!GO:0005262;calcium channel activity;0.0488632521975829;12291!GO:0031252;leading edge;0.0488632521975829;16443!GO:0007266;Rho protein signal transduction;0.0488632521975829;16443!GO:0005886;plasma membrane;0.0488632521975829;12291,16443!GO:0046578;regulation of Ras protein signal transduction;0.0488632521975829;16443!GO:0006816;calcium ion transport;0.0488632521975829;12291!GO:0022843;voltage-gated cation channel activity;0.0488632521975829;12291!GO:0005085;guanyl-nucleotide exchange factor activity;0.0488632521975829;16443!GO:0051056;regulation of small GTPase mediated signal transduction;0.0488632521975829;16443!GO:0015674;di-, tri-valent inorganic cation transport;0.0488632521975829;12291!GO:0006810;transport;0.0488632521975829;12291,16443!GO:0051234;establishment of localization;0.0488632521975829;12291,16443!GO:0007265;Ras protein signal transduction;0.0488632521975829;16443!GO:0005083;small GTPase regulator activity;0.0488632521975829;16443!GO:0022832;voltage-gated channel activity;0.0488632521975829;12291!GO:0005244;voltage-gated ion channel activity;0.0488632521975829;12291!GO:0010324;membrane invagination;0.0488632521975829;16443!GO:0006897;endocytosis;0.0488632521975829;16443!
|gostat_on_MCL_coexpression=GO:0005891;voltage-gated calcium channel complex;0.0488632521975829;12291!GO:0005509;calcium ion binding;0.0488632521975829;12291,16443!GO:0005245;voltage-gated calcium channel activity;0.0488632521975829;12291!GO:0030027;lamellipodium;0.0488632521975829;16443!GO:0019717;synaptosome;0.0488632521975829;16443!GO:0005089;Rho guanyl-nucleotide exchange factor activity;0.0488632521975829;16443!GO:0035023;regulation of Rho protein signal transduction;0.0488632521975829;16443!GO:0044459;plasma membrane part;0.0488632521975829;12291,16443!GO:0005088;Ras guanyl-nucleotide exchange factor activity;0.0488632521975829;16443!GO:0005262;calcium channel activity;0.0488632521975829;12291!GO:0031252;leading edge;0.0488632521975829;16443!GO:0007266;Rho protein signal transduction;0.0488632521975829;16443!GO:0005886;plasma membrane;0.0488632521975829;12291,16443!GO:0046578;regulation of Ras protein signal transduction;0.0488632521975829;16443!GO:0006816;calcium ion transport;0.0488632521975829;12291!GO:0022843;voltage-gated cation channel activity;0.0488632521975829;12291!GO:0005085;guanyl-nucleotide exchange factor activity;0.0488632521975829;16443!GO:0051056;regulation of small GTPase mediated signal transduction;0.0488632521975829;16443!GO:0015674;di-, tri-valent inorganic cation transport;0.0488632521975829;12291!GO:0006810;transport;0.0488632521975829;12291,16443!GO:0051234;establishment of localization;0.0488632521975829;12291,16443!GO:0007265;Ras protein signal transduction;0.0488632521975829;16443!GO:0005083;small GTPase regulator activity;0.0488632521975829;16443!GO:0022832;voltage-gated channel activity;0.0488632521975829;12291!GO:0005244;voltage-gated ion channel activity;0.0488632521975829;12291!GO:0010324;membrane invagination;0.0488632521975829;16443!GO:0006897;endocytosis;0.0488632521975829;16443!
|ontology_enrichment_celltype=CL:0000117!7.29e-11!23;CL:0000337!7.29e-11!23;CL:0000540!3.19e-08!33;CL:0000047!3.19e-08!33;CL:0000031!3.19e-08!33;CL:0000404!3.19e-08!33
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!8.13e-21!54;UBERON:0002346!1.36e-20!64;UBERON:0003075!1.36e-20!64;UBERON:0007284!1.36e-20!64;UBERON:0010371!2.38e-19!73;UBERON:0001017!2.47e-19!73;UBERON:0010314!3.09e-19!92;UBERON:0001049!3.69e-19!52;UBERON:0005068!3.69e-19!52;UBERON:0006241!3.69e-19!52;UBERON:0007135!3.69e-19!52;UBERON:0004121!1.09e-18!95;UBERON:0000924!1.09e-18!95;UBERON:0006601!1.09e-18!95;UBERON:0001016!6.01e-18!75;UBERON:0000955!2.17e-16!47;UBERON:0006238!2.17e-16!47;UBERON:0003056!5.70e-16!49;UBERON:0002616!8.73e-16!46;UBERON:0002020!5.98e-15!34;UBERON:0003080!1.26e-13!40;UBERON:0002780!4.71e-13!39;UBERON:0001890!4.71e-13!39;UBERON:0006240!4.71e-13!39;UBERON:0003528!3.63e-12!29;UBERON:0002791!3.63e-12!29;UBERON:0001893!3.63e-12!29;UBERON:0000025!8.24e-10!114;UBERON:0000468!1.32e-09!333;UBERON:0004111!4.74e-09!122;UBERON:0000956!4.53e-08!21;UBERON:0001869!4.53e-08!21;UBERON:0000203!4.53e-08!21;UBERON:0000922!2.00e-07!320;UBERON:0002021!2.57e-07!10;UBERON:0000411!2.57e-07!10;UBERON:0001950!2.57e-07!10;UBERON:0002619!3.03e-07!17
}}
}}

Revision as of 18:57, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr11:94335638..94335661,-p6@Cacna1g
Mm9::chr11:94335672..94335699,-p1@Cacna1g
Mm9::chr16:91729681..91729719,+p4@Itsn1


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:0005891voltage-gated calcium channel complex0.0488632521975829
GO:0005509calcium ion binding0.0488632521975829
GO:0005245voltage-gated calcium channel activity0.0488632521975829
GO:0030027lamellipodium0.0488632521975829
GO:0019717synaptosome0.0488632521975829
GO:0005089Rho guanyl-nucleotide exchange factor activity0.0488632521975829
GO:0035023regulation of Rho protein signal transduction0.0488632521975829
GO:0044459plasma membrane part0.0488632521975829
GO:0005088Ras guanyl-nucleotide exchange factor activity0.0488632521975829
GO:0005262calcium channel activity0.0488632521975829
GO:0031252leading edge0.0488632521975829
GO:0007266Rho protein signal transduction0.0488632521975829
GO:0005886plasma membrane0.0488632521975829
GO:0046578regulation of Ras protein signal transduction0.0488632521975829
GO:0006816calcium ion transport0.0488632521975829
GO:0022843voltage-gated cation channel activity0.0488632521975829
GO:0005085guanyl-nucleotide exchange factor activity0.0488632521975829
GO:0051056regulation of small GTPase mediated signal transduction0.0488632521975829
GO:0015674di-, tri-valent inorganic cation transport0.0488632521975829
GO:0006810transport0.0488632521975829
GO:0051234establishment of localization0.0488632521975829
GO:0007265Ras protein signal transduction0.0488632521975829
GO:0005083small GTPase regulator activity0.0488632521975829
GO:0022832voltage-gated channel activity0.0488632521975829
GO:0005244voltage-gated ion channel activity0.0488632521975829
GO:0010324membrane invagination0.0488632521975829
GO:0006897endocytosis0.0488632521975829



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)7.29e-1123
neuroblast (sensu Vertebrata)7.29e-1123
neuron3.19e-0833
neuronal stem cell3.19e-0833
neuroblast3.19e-0833
electrically signaling cell3.19e-0833

Uber Anatomy
Ontology termp-valuen
regional part of nervous system8.13e-2154
neurectoderm1.36e-2064
neural plate1.36e-2064
presumptive neural plate1.36e-2064
ecto-epithelium2.38e-1973
central nervous system2.47e-1973
structure with developmental contribution from neural crest3.09e-1992
neural tube3.69e-1952
neural rod3.69e-1952
future spinal cord3.69e-1952
neural keel3.69e-1952
ectoderm-derived structure1.09e-1895
ectoderm1.09e-1895
presumptive ectoderm1.09e-1895
nervous system6.01e-1875
brain2.17e-1647
future brain2.17e-1647
pre-chordal neural plate5.70e-1649
regional part of brain8.73e-1646
gray matter5.98e-1534
anterior neural tube1.26e-1340
regional part of forebrain4.71e-1339
forebrain4.71e-1339
future forebrain4.71e-1339
brain grey matter3.63e-1229
regional part of telencephalon3.63e-1229
telencephalon3.63e-1229
tube8.24e-10114
multi-cellular organism1.32e-09333
anatomical conduit4.74e-09122
cerebral cortex4.53e-0821
cerebral hemisphere4.53e-0821
pallium4.53e-0821
embryo2.00e-07320
occipital lobe2.57e-0710
visual cortex2.57e-0710
neocortex2.57e-0710
regional part of cerebral cortex3.03e-0717


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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