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MCL coexpression mm9:2050: Difference between revisions

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|gostat_on_MCL_coexpression=GO:0015985;energy coupled proton transport, down electrochemical gradient;0.0417526751697796;66144!GO:0015986;ATP synthesis coupled proton transport;0.0417526751697796;66144!GO:0006754;ATP biosynthetic process;0.0417526751697796;66144!GO:0006753;nucleoside phosphate metabolic process;0.0417526751697796;66144!GO:0046933;hydrogen ion transporting ATP synthase activity, rotational mechanism;0.0417526751697796;66144!GO:0016469;proton-transporting two-sector ATPase complex;0.0417526751697796;66144!GO:0046961;hydrogen ion transporting ATPase activity, rotational mechanism;0.0417526751697796;66144!GO:0044249;cellular biosynthetic process;0.0417526751697796;66144,67994!GO:0046034;ATP metabolic process;0.0417526751697796;66144!GO:0009206;purine ribonucleoside triphosphate biosynthetic process;0.0417526751697796;66144!GO:0009201;ribonucleoside triphosphate biosynthetic process;0.0417526751697796;66144!GO:0009145;purine nucleoside triphosphate biosynthetic process;0.0417526751697796;66144!GO:0019829;cation-transporting ATPase activity;0.0417526751697796;66144!GO:0009142;nucleoside triphosphate biosynthetic process;0.0417526751697796;66144!GO:0009205;purine ribonucleoside triphosphate metabolic process;0.0417526751697796;66144!GO:0009199;ribonucleoside triphosphate metabolic process;0.0417526751697796;66144!GO:0009144;purine nucleoside triphosphate metabolic process;0.0417526751697796;66144!GO:0006119;oxidative phosphorylation;0.0417526751697796;66144!GO:0015992;proton transport;0.0417526751697796;66144!GO:0006752;group transfer coenzyme metabolic process;0.0417526751697796;66144!GO:0009141;nucleoside triphosphate metabolic process;0.0417526751697796;66144!GO:0009152;purine ribonucleotide biosynthetic process;0.0417526751697796;66144!GO:0006818;hydrogen transport;0.0417526751697796;66144!GO:0009260;ribonucleotide biosynthetic process;0.0417526751697796;66144!GO:0009150;purine ribonucleotide metabolic process;0.0417526751697796;66144!GO:0006164;purine nucleotide biosynthetic process;0.0417526751697796;66144!GO:0009058;biosynthetic process;0.0417526751697796;66144,67994!GO:0009259;ribonucleotide metabolic process;0.0417526751697796;66144!GO:0006163;purine nucleotide metabolic process;0.0426071727823965;66144!GO:0042625;ATPase activity, coupled to transmembrane movement of ions;0.0446838862837438;66144!GO:0009108;coenzyme biosynthetic process;0.0446838862837438;66144!GO:0015078;hydrogen ion transmembrane transporter activity;0.0470887349534143;66144!GO:0015077;monovalent inorganic cation transmembrane transporter activity;0.0470887349534143;66144!GO:0051188;cofactor biosynthetic process;0.0470887349534143;66144!
|gostat_on_MCL_coexpression=GO:0015985;energy coupled proton transport, down electrochemical gradient;0.0417526751697796;66144!GO:0015986;ATP synthesis coupled proton transport;0.0417526751697796;66144!GO:0006754;ATP biosynthetic process;0.0417526751697796;66144!GO:0006753;nucleoside phosphate metabolic process;0.0417526751697796;66144!GO:0046933;hydrogen ion transporting ATP synthase activity, rotational mechanism;0.0417526751697796;66144!GO:0016469;proton-transporting two-sector ATPase complex;0.0417526751697796;66144!GO:0046961;hydrogen ion transporting ATPase activity, rotational mechanism;0.0417526751697796;66144!GO:0044249;cellular biosynthetic process;0.0417526751697796;66144,67994!GO:0046034;ATP metabolic process;0.0417526751697796;66144!GO:0009206;purine ribonucleoside triphosphate biosynthetic process;0.0417526751697796;66144!GO:0009201;ribonucleoside triphosphate biosynthetic process;0.0417526751697796;66144!GO:0009145;purine nucleoside triphosphate biosynthetic process;0.0417526751697796;66144!GO:0019829;cation-transporting ATPase activity;0.0417526751697796;66144!GO:0009142;nucleoside triphosphate biosynthetic process;0.0417526751697796;66144!GO:0009205;purine ribonucleoside triphosphate metabolic process;0.0417526751697796;66144!GO:0009199;ribonucleoside triphosphate metabolic process;0.0417526751697796;66144!GO:0009144;purine nucleoside triphosphate metabolic process;0.0417526751697796;66144!GO:0006119;oxidative phosphorylation;0.0417526751697796;66144!GO:0015992;proton transport;0.0417526751697796;66144!GO:0006752;group transfer coenzyme metabolic process;0.0417526751697796;66144!GO:0009141;nucleoside triphosphate metabolic process;0.0417526751697796;66144!GO:0009152;purine ribonucleotide biosynthetic process;0.0417526751697796;66144!GO:0006818;hydrogen transport;0.0417526751697796;66144!GO:0009260;ribonucleotide biosynthetic process;0.0417526751697796;66144!GO:0009150;purine ribonucleotide metabolic process;0.0417526751697796;66144!GO:0006164;purine nucleotide biosynthetic process;0.0417526751697796;66144!GO:0009058;biosynthetic process;0.0417526751697796;66144,67994!GO:0009259;ribonucleotide metabolic process;0.0417526751697796;66144!GO:0006163;purine nucleotide metabolic process;0.0426071727823965;66144!GO:0042625;ATPase activity, coupled to transmembrane movement of ions;0.0446838862837438;66144!GO:0009108;coenzyme biosynthetic process;0.0446838862837438;66144!GO:0015078;hydrogen ion transmembrane transporter activity;0.0470887349534143;66144!GO:0015077;monovalent inorganic cation transmembrane transporter activity;0.0470887349534143;66144!GO:0051188;cofactor biosynthetic process;0.0470887349534143;66144!
|ontology_enrichment_celltype=CL:0000055!3.40e-23!49;CL:0000221!1.70e-21!44;CL:0000133!1.70e-21!44;CL:0002319!2.51e-21!43;CL:0000393!1.33e-16!39;CL:0000211!1.33e-16!39;CL:0002371!2.91e-15!118;CL:0000540!7.76e-15!33;CL:0000047!7.76e-15!33;CL:0000031!7.76e-15!33;CL:0000404!7.76e-15!33;CL:0000723!1.69e-14!91;CL:0000048!1.69e-14!91;CL:0000548!2.75e-14!115;CL:0000255!2.75e-14!115;CL:0002321!3.51e-14!70;CL:0000034!5.61e-14!97;CL:0000117!5.15e-13!23;CL:0000337!5.15e-13!23;CL:0000333!1.58e-07!10;CL:0000095!1.58e-07!10;CL:0000243!1.58e-07!10;CL:0000123!1.58e-07!10;CL:0000125!1.58e-07!10;CL:0000030!1.58e-07!10;CL:0000339!1.58e-07!10
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001016!1.45e-31!75;UBERON:0001017!2.49e-30!73;UBERON:0004121!4.94e-22!95;UBERON:0000924!4.94e-22!95;UBERON:0006601!4.94e-22!95;UBERON:0000073!5.17e-22!54;UBERON:0001049!8.56e-21!52;UBERON:0005068!8.56e-21!52;UBERON:0006241!8.56e-21!52;UBERON:0007135!8.56e-21!52;UBERON:0002346!3.22e-19!64;UBERON:0003075!3.22e-19!64;UBERON:0007284!3.22e-19!64;UBERON:0010314!3.66e-19!92;UBERON:0000955!4.25e-18!47;UBERON:0006238!4.25e-18!47;UBERON:0002616!9.28e-18!46;UBERON:0002020!1.70e-16!34;UBERON:0003080!7.11e-16!40;UBERON:0002780!8.74e-16!39;UBERON:0001890!8.74e-16!39;UBERON:0006240!8.74e-16!39;UBERON:0010371!1.97e-14!73;UBERON:0003528!5.90e-14!29;UBERON:0002791!5.90e-14!29;UBERON:0001893!5.90e-14!29;UBERON:0003056!2.20e-13!49;UBERON:0000956!7.47e-10!21;UBERON:0001869!7.47e-10!21;UBERON:0000203!7.47e-10!21;UBERON:0002619!2.15e-08!17
}}
}}

Revision as of 17:51, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr12:8928823..8928834,+p@chr12:8928823..8928834
+
Mm9::chr2:118305373..118305423,-p1@LOC100504988
p1@Srp14
Mm9::chr6:29417733..29417764,+p2@Atp6v1f
Mm9::chr7:85928189..85928227,+p2@Mrps11


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:0015985energy coupled proton transport, down electrochemical gradient0.0417526751697796
GO:0015986ATP synthesis coupled proton transport0.0417526751697796
GO:0006754ATP biosynthetic process0.0417526751697796
GO:0006753nucleoside phosphate metabolic process0.0417526751697796
GO:0046933hydrogen ion transporting ATP synthase activity, rotational mechanism0.0417526751697796
GO:0016469proton-transporting two-sector ATPase complex0.0417526751697796
GO:0046961hydrogen ion transporting ATPase activity, rotational mechanism0.0417526751697796
GO:0044249cellular biosynthetic process0.0417526751697796
GO:0046034ATP metabolic process0.0417526751697796
GO:0009206purine ribonucleoside triphosphate biosynthetic process0.0417526751697796
GO:0009201ribonucleoside triphosphate biosynthetic process0.0417526751697796
GO:0009145purine nucleoside triphosphate biosynthetic process0.0417526751697796
GO:0019829cation-transporting ATPase activity0.0417526751697796
GO:0009142nucleoside triphosphate biosynthetic process0.0417526751697796
GO:0009205purine ribonucleoside triphosphate metabolic process0.0417526751697796
GO:0009199ribonucleoside triphosphate metabolic process0.0417526751697796
GO:0009144purine nucleoside triphosphate metabolic process0.0417526751697796
GO:0006119oxidative phosphorylation0.0417526751697796
GO:0015992proton transport0.0417526751697796
GO:0006752group transfer coenzyme metabolic process0.0417526751697796
GO:0009141nucleoside triphosphate metabolic process0.0417526751697796
GO:0009152purine ribonucleotide biosynthetic process0.0417526751697796
GO:0006818hydrogen transport0.0417526751697796
GO:0009260ribonucleotide biosynthetic process0.0417526751697796
GO:0009150purine ribonucleotide metabolic process0.0417526751697796
GO:0006164purine nucleotide biosynthetic process0.0417526751697796
GO:0009058biosynthetic process0.0417526751697796
GO:0009259ribonucleotide metabolic process0.0417526751697796
GO:0006163purine nucleotide metabolic process0.0426071727823965
GO:0042625ATPase activity, coupled to transmembrane movement of ions0.0446838862837438
GO:0009108coenzyme biosynthetic process0.0446838862837438
GO:0015078hydrogen ion transmembrane transporter activity0.0470887349534143
GO:0015077monovalent inorganic cation transmembrane transporter activity0.0470887349534143
GO:0051188cofactor biosynthetic process0.0470887349534143



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
non-terminally differentiated cell3.40e-2349
ectodermal cell1.70e-2144
neurectodermal cell1.70e-2144
neural cell2.51e-2143
electrically responsive cell1.33e-1639
electrically active cell1.33e-1639
somatic cell2.91e-15118
neuron7.76e-1533
neuronal stem cell7.76e-1533
neuroblast7.76e-1533
electrically signaling cell7.76e-1533
somatic stem cell1.69e-1491
multi fate stem cell1.69e-1491
animal cell2.75e-14115
eukaryotic cell2.75e-14115
embryonic cell3.51e-1470
stem cell5.61e-1497
CNS neuron (sensu Vertebrata)5.15e-1323
neuroblast (sensu Vertebrata)5.15e-1323
migratory neural crest cell1.58e-0710
neuron associated cell1.58e-0710
glial cell (sensu Vertebrata)1.58e-0710
neuron associated cell (sensu Vertebrata)1.58e-0710
glial cell1.58e-0710
glioblast1.58e-0710
glioblast (sensu Vertebrata)1.58e-0710

Uber Anatomy
Ontology termp-valuen
nervous system1.45e-3175
central nervous system2.49e-3073
ectoderm-derived structure4.94e-2295
ectoderm4.94e-2295
presumptive ectoderm4.94e-2295
regional part of nervous system5.17e-2254
neural tube8.56e-2152
neural rod8.56e-2152
future spinal cord8.56e-2152
neural keel8.56e-2152
neurectoderm3.22e-1964
neural plate3.22e-1964
presumptive neural plate3.22e-1964
structure with developmental contribution from neural crest3.66e-1992
brain4.25e-1847
future brain4.25e-1847
regional part of brain9.28e-1846
gray matter1.70e-1634
anterior neural tube7.11e-1640
regional part of forebrain8.74e-1639
forebrain8.74e-1639
future forebrain8.74e-1639
ecto-epithelium1.97e-1473
brain grey matter5.90e-1429
regional part of telencephalon5.90e-1429
telencephalon5.90e-1429
pre-chordal neural plate2.20e-1349
cerebral cortex7.47e-1021
cerebral hemisphere7.47e-1021
pallium7.47e-1021
regional part of cerebral cortex2.15e-0817


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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