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MCL coexpression mm9:491: Difference between revisions

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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.202843190349958,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0583821828293117,0,0.0568996784870888,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.342106802711204,0.391218457651958,0,0,0,0.349063385543086,0.323116468687679,0,0,0,0.991636709896498,0.717185272729006,0.823869696355722,0,0,0,0.736713084825951,0.948348234470256,0.830966875433846,0.21016670557241,0.268163623204797,0.00783579303708656,0,0,0,0,0,0,0,0,0.101245098008666,0,0,0,0,0,0,0,0,0,0,0.0469568706916304,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.391623779964764,0.264295134298998,0,0,0,0,0.727860642262913,0.516866159673758,0,0.486056691420592,0.35766376392443,0.635946818970111,0.627859817173333,0,0,0.0978549673988937,0,0,0,0,0,0,0,0,0.0999233952154288,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0197889407591105,0,0,0,0.461289813759464,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.614061914935632,0.539257487858814,0,0,0,0,0,0,0,0,0,0,0,0.358940419539848,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.507483923817102,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.194445471641185,0.376754964798171,0.331587424856164,0.361164718034908,0.485046405834616,0.514040340140897,0.480735069848811,0.347566289184351,0.420244759041355,0.407098602473158,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0352754493378881,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.037468938902345
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|gostat_on_MCL_coexpression=GO:0016492;neurotensin receptor activity, G-protein coupled;0.0394412483415015;18217!
|gostat_on_MCL_coexpression=GO:0016492;neurotensin receptor activity, G-protein coupled;0.0394412483415015;18217!
|ontology_enrichment_celltype=CL:0000117!5.46e-09!23;CL:0000337!5.46e-09!23;CL:0002614!6.43e-08!3;CL:0002610!7.10e-08!3;CL:0002319!2.62e-07!43;CL:0000221!4.58e-07!44;CL:0000133!4.58e-07!44
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!3.81e-33!54;UBERON:0001017!1.21e-31!73;UBERON:0001016!1.44e-30!75;UBERON:0001049!2.00e-29!52;UBERON:0005068!2.00e-29!52;UBERON:0006241!2.00e-29!52;UBERON:0007135!2.00e-29!52;UBERON:0002346!3.62e-24!64;UBERON:0003075!3.62e-24!64;UBERON:0007284!3.62e-24!64;UBERON:0002020!5.66e-24!34;UBERON:0004121!9.96e-24!95;UBERON:0000924!9.96e-24!95;UBERON:0006601!9.96e-24!95;UBERON:0000955!1.79e-22!47;UBERON:0006238!1.79e-22!47;UBERON:0002616!4.39e-21!46;UBERON:0010371!3.15e-20!73;UBERON:0002021!1.00e-18!10;UBERON:0000411!1.00e-18!10;UBERON:0001950!1.00e-18!10;UBERON:0003528!4.42e-17!29;UBERON:0002791!4.42e-17!29;UBERON:0001893!4.42e-17!29;UBERON:0003080!1.25e-16!40;UBERON:0010314!1.42e-15!92;UBERON:0002780!3.58e-15!39;UBERON:0001890!3.58e-15!39;UBERON:0006240!3.58e-15!39;UBERON:0003076!1.02e-14!12;UBERON:0003057!1.02e-14!12;UBERON:0002619!1.15e-14!17;UBERON:0003056!5.17e-14!49;UBERON:0000956!1.44e-13!21;UBERON:0001869!1.44e-13!21;UBERON:0000203!1.44e-13!21;UBERON:0000025!4.66e-11!114;UBERON:0002240!6.35e-11!6;UBERON:0005174!6.35e-11!6;UBERON:0001137!6.35e-11!6;UBERON:0002950!5.79e-10!4;UBERON:0001891!5.79e-10!4;UBERON:0009616!5.79e-10!4;UBERON:0010286!5.79e-10!4;UBERON:0004111!7.91e-10!122;UBERON:0001948!4.65e-09!5;UBERON:0002315!4.65e-09!5;UBERON:0002038!6.43e-08!3;UBERON:0009663!6.43e-08!3;UBERON:0009661!6.43e-08!3;UBERON:0000125!6.43e-08!3;UBERON:0002308!6.43e-08!3;UBERON:0004684!7.10e-08!3;UBERON:0002275!7.10e-08!3
}}
}}

Revision as of 20:46, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr12:16660339..16660350,+p@chr12:16660339..16660350
+
Mm9::chr12:16660375..16660389,+p@chr12:16660375..16660389
+
Mm9::chr12:16660410..16660434,+p@chr12:16660410..16660434
+
Mm9::chr12:16660574..16660581,+p@chr12:16660574..16660581
+
Mm9::chr12:16660603..16660614,+p@chr12:16660603..16660614
+
Mm9::chr15:99329929..99329942,-p@chr15:99329929..99329942
-
Mm9::chr18:25838692..25838704,-p@chr18:25838692..25838704
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Mm9::chr18:38456462..38456473,+p4@Rnf14
Mm9::chr19:7053625..7053649,-p@chr19:7053625..7053649
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Mm9::chr19:9209526..9209541,-p@chr19:9209526..9209541
-
Mm9::chr4:120689585..120689613,-p4@Smap2
Mm9::chr4:153400169..153400201,-p1@1190007F08Rik
Mm9::chr6:29346665..29346666,+p5@Ccdc136
Mm9::chr7:48157988..48158007,+p@chr7:48157988..48158007
+
Mm9::chr9:46721640..46721656,+p2@2900052N01Rik


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:0016492neurotensin receptor activity, G-protein coupled0.0394412483415015



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)5.46e-0923
neuroblast (sensu Vertebrata)5.46e-0923
neuron of the substantia nigra6.43e-083
raphe nuclei neuron7.10e-083
neural cell2.62e-0743
ectodermal cell4.58e-0744
neurectodermal cell4.58e-0744

Uber Anatomy
Ontology termp-valuen
regional part of nervous system3.81e-3354
central nervous system1.21e-3173
nervous system1.44e-3075
neural tube2.00e-2952
neural rod2.00e-2952
future spinal cord2.00e-2952
neural keel2.00e-2952
neurectoderm3.62e-2464
neural plate3.62e-2464
presumptive neural plate3.62e-2464
gray matter5.66e-2434
ectoderm-derived structure9.96e-2495
ectoderm9.96e-2495
presumptive ectoderm9.96e-2495
brain1.79e-2247
future brain1.79e-2247
regional part of brain4.39e-2146
ecto-epithelium3.15e-2073
occipital lobe1.00e-1810
visual cortex1.00e-1810
neocortex1.00e-1810
brain grey matter4.42e-1729
regional part of telencephalon4.42e-1729
telencephalon4.42e-1729
anterior neural tube1.25e-1640
structure with developmental contribution from neural crest1.42e-1592
regional part of forebrain3.58e-1539
forebrain3.58e-1539
future forebrain3.58e-1539
posterior neural tube1.02e-1412
chordal neural plate1.02e-1412
regional part of cerebral cortex1.15e-1417
pre-chordal neural plate5.17e-1449
cerebral cortex1.44e-1321
cerebral hemisphere1.44e-1321
pallium1.44e-1321
tube4.66e-11114
spinal cord6.35e-116
dorsal region element6.35e-116
dorsum6.35e-116
regional part of midbrain5.79e-104
midbrain5.79e-104
presumptive midbrain5.79e-104
midbrain neural tube5.79e-104
anatomical conduit7.91e-10122
regional part of spinal cord4.65e-095
gray matter of spinal cord4.65e-095
substantia nigra6.43e-083
telencephalic nucleus6.43e-083
midbrain nucleus6.43e-083
neural nucleus6.43e-083
nucleus of brain6.43e-083
raphe nuclei7.10e-083
reticular formation7.10e-083


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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