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MCL coexpression mm9:724: Difference between revisions

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|coexpression_dpi_cluster_scores_median=0.0851963648524105,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.11292479074727,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0284498392435444,0,0,0,0,0,0,0,0.113790818113665,0,0,0,0,0,0,0,0,0,0,0.0274990668782,0,0,0.12277748593221,0.0475814661739458,0.0747544186697619,0,0.322458878535173,0.343354607776394,0.388890291771039,0.0508344633540495,0.0817950768629885,0,0.321855166838861,0.096946505969497,0.324635241603009,0.156669685869194,0.175108315011765,0.0742309351586685,0.46002863917888,0.941777208694406,0,0,0,0,0,0,0,0,0,0,0.323872700473358,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.111524892460631,0.332318706535519,0,0,0,0,0.507263673214221,0.399517605699759,0.0514050548005424,0.250441710981523,0.519886345377306,0.44157679082602,0.411088878303785,0,0,0,0.0829439327499637,0.0265623655145556,0.0449352723065536,0.0719048733411253,0.057207008968797,0.126603576803416,0.12015570389087,0.165990606316977,0.181102009199648,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.309767051056041,0.0619082774837524,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.524682761327817,0.538275032834345,0,0,0,0,0,0,0,0,0,0,0,0.215543090236368,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0359522460741798,0,0,0,0,0.061778508975334,0,0,0,0.0432739443039237,0,0,0,0,0,0,0.516571369075515,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0972227358205925,0.283448337556827,0.196699873644339,0.128304374276845,0.113310586729352,0,0.112010322600128,0.161464196262218,0.162308177550168,0.181203192176975,0.0214427057787972,0,0,0,0,0,0,0.040679966067952,0,0,0,0.0750453505157095,0.0731992624220758,0.0396401807728516,0.0581328665260699,0,0.0476191773904887,0,0,0.0298193647598867,0,0.0709519923534245,0,0.0848798800014619,0.0390607415003592,0,0.0729583017401753,0.101427320830301,0.0553034373508932,0,0,0.0408018333703219,0,0,0,0,0,0.0422650922646472,0.0760168881589905,0.0865703124974023,0
|coexpression_dpi_cluster_scores_median=0.0851963648524105,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.11292479074727,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0284498392435444,0,0,0,0,0,0,0,0.113790818113665,0,0,0,0,0,0,0,0,0,0,0.0274990668782,0,0,0.12277748593221,0.0475814661739458,0.0747544186697619,0,0.322458878535173,0.343354607776394,0.388890291771039,0.0508344633540495,0.0817950768629885,0,0.321855166838861,0.096946505969497,0.324635241603009,0.156669685869194,0.175108315011765,0.0742309351586685,0.46002863917888,0.941777208694406,0,0,0,0,0,0,0,0,0,0,0.323872700473358,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.111524892460631,0.332318706535519,0,0,0,0,0.507263673214221,0.399517605699759,0.0514050548005424,0.250441710981523,0.519886345377306,0.44157679082602,0.411088878303785,0,0,0,0.0829439327499637,0.0265623655145556,0.0449352723065536,0.0719048733411253,0.057207008968797,0.126603576803416,0.12015570389087,0.165990606316977,0.181102009199648,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.309767051056041,0.0619082774837524,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.524682761327817,0.538275032834345,0,0,0,0,0,0,0,0,0,0,0,0.215543090236368,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0359522460741798,0,0,0,0,0.061778508975334,0,0,0,0.0432739443039237,0,0,0,0,0,0,0.516571369075515,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0972227358205925,0.283448337556827,0.196699873644339,0.128304374276845,0.113310586729352,0,0.112010322600128,0.161464196262218,0.162308177550168,0.181203192176975,0.0214427057787972,0,0,0,0,0,0,0.040679966067952,0,0,0,0.0750453505157095,0.0731992624220758,0.0396401807728516,0.0581328665260699,0,0.0476191773904887,0,0,0.0298193647598867,0,0.0709519923534245,0,0.0848798800014619,0.0390607415003592,0,0.0729583017401753,0.101427320830301,0.0553034373508932,0,0,0.0408018333703219,0,0,0,0,0,0.0422650922646472,0.0760168881589905,0.0865703124974023,0
|gostat_on_MCL_coexpression=GO:0045745;positive regulation of G-protein coupled receptor protein signaling pathway;0.0239826601982353;50876!GO:0005523;tropomyosin binding;0.0239826601982353;50876!GO:0045176;apical protein localization;0.0239826601982353;15165!GO:0008105;asymmetric protein localization;0.0239826601982353;15165!GO:0030552;cAMP binding;0.0239826601982353;15165!GO:0007190;adenylate cyclase activation;0.0239826601982353;11516!GO:0031281;positive regulation of cyclase activity;0.0239826601982353;11516!GO:0051349;positive regulation of lyase activity;0.0239826601982353;11516!GO:0045762;positive regulation of adenylate cyclase activity;0.0239826601982353;11516!GO:0016208;AMP binding;0.0239826601982353;15165!GO:0045761;regulation of adenylate cyclase activity;0.0239826601982353;11516!GO:0031279;regulation of cyclase activity;0.0239826601982353;11516!GO:0008277;regulation of G-protein coupled receptor protein signaling pathway;0.0239826601982353;50876!GO:0051339;regulation of lyase activity;0.0239826601982353;11516!GO:0005184;neuropeptide hormone activity;0.0239826601982353;11516!GO:0030551;cyclic nucleotide binding;0.0239826601982353;15165!GO:0007270;nerve-nerve synaptic transmission;0.0285040806208462;50876!GO:0005272;sodium channel activity;0.029160700324735;15165!GO:0007189;G-protein signaling, adenylate cyclase activating pathway;0.0371704040420905;11516!GO:0030425;dendrite;0.0483932198836574;15165!
|gostat_on_MCL_coexpression=GO:0045745;positive regulation of G-protein coupled receptor protein signaling pathway;0.0239826601982353;50876!GO:0005523;tropomyosin binding;0.0239826601982353;50876!GO:0045176;apical protein localization;0.0239826601982353;15165!GO:0008105;asymmetric protein localization;0.0239826601982353;15165!GO:0030552;cAMP binding;0.0239826601982353;15165!GO:0007190;adenylate cyclase activation;0.0239826601982353;11516!GO:0031281;positive regulation of cyclase activity;0.0239826601982353;11516!GO:0051349;positive regulation of lyase activity;0.0239826601982353;11516!GO:0045762;positive regulation of adenylate cyclase activity;0.0239826601982353;11516!GO:0016208;AMP binding;0.0239826601982353;15165!GO:0045761;regulation of adenylate cyclase activity;0.0239826601982353;11516!GO:0031279;regulation of cyclase activity;0.0239826601982353;11516!GO:0008277;regulation of G-protein coupled receptor protein signaling pathway;0.0239826601982353;50876!GO:0051339;regulation of lyase activity;0.0239826601982353;11516!GO:0005184;neuropeptide hormone activity;0.0239826601982353;11516!GO:0030551;cyclic nucleotide binding;0.0239826601982353;15165!GO:0007270;nerve-nerve synaptic transmission;0.0285040806208462;50876!GO:0005272;sodium channel activity;0.029160700324735;15165!GO:0007189;G-protein signaling, adenylate cyclase activating pathway;0.0371704040420905;11516!GO:0030425;dendrite;0.0483932198836574;15165!
|ontology_enrichment_celltype=CL:0000117!1.52e-10!23;CL:0000337!1.52e-10!23;CL:0000221!1.25e-07!44;CL:0000133!1.25e-07!44;CL:0000540!5.15e-07!33;CL:0000047!5.15e-07!33;CL:0000031!5.15e-07!33;CL:0000404!5.15e-07!33;CL:0002319!6.63e-07!43
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002346!1.39e-30!64;UBERON:0003075!1.39e-30!64;UBERON:0007284!1.39e-30!64;UBERON:0004121!1.01e-29!95;UBERON:0000924!1.01e-29!95;UBERON:0006601!1.01e-29!95;UBERON:0010371!2.70e-28!73;UBERON:0000073!1.32e-26!54;UBERON:0001016!1.66e-25!75;UBERON:0003056!1.41e-24!49;UBERON:0001049!2.77e-24!52;UBERON:0005068!2.77e-24!52;UBERON:0006241!2.77e-24!52;UBERON:0007135!2.77e-24!52;UBERON:0001017!3.70e-23!73;UBERON:0000955!6.89e-21!47;UBERON:0006238!6.89e-21!47;UBERON:0002616!7.99e-20!46;UBERON:0010314!1.47e-19!92;UBERON:0002020!4.03e-19!34;UBERON:0003080!1.03e-16!40;UBERON:0003528!5.17e-16!29;UBERON:0002791!5.17e-16!29;UBERON:0001893!5.17e-16!29;UBERON:0002780!1.38e-15!39;UBERON:0001890!1.38e-15!39;UBERON:0006240!1.38e-15!39;UBERON:0000956!2.53e-10!21;UBERON:0001869!2.53e-10!21;UBERON:0000203!2.53e-10!21;UBERON:0000020!3.26e-10!12;UBERON:0001032!3.26e-10!12;UBERON:0004456!3.26e-10!12;UBERON:0002619!3.38e-10!17;UBERON:0002021!1.04e-09!10;UBERON:0000411!1.04e-09!10;UBERON:0001950!1.04e-09!10;UBERON:0000970!2.76e-09!9;UBERON:0000019!2.76e-09!9;UBERON:0000047!2.76e-09!9;UBERON:0010312!2.76e-09!9;UBERON:0004088!2.76e-09!9;UBERON:0002104!2.76e-09!9;UBERON:0001456!2.76e-09!9;UBERON:0003072!2.76e-09!9;UBERON:0004128!2.76e-09!9;UBERON:0003071!2.76e-09!9;UBERON:0000033!3.21e-09!13;UBERON:0005085!3.21e-09!13;UBERON:0003076!2.68e-08!12;UBERON:0003057!2.68e-08!12;UBERON:0001444!3.03e-07!11;UBERON:0002420!3.78e-07!8;UBERON:0007245!3.78e-07!8;UBERON:0010009!3.78e-07!8;UBERON:0010011!3.78e-07!8;UBERON:0000454!3.78e-07!8
}}
}}

Revision as of 21:09, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr13:118391138..118391145,+p4@Hcn1
Mm9::chr17:93598348..93598373,+p3@Adcyap1
Mm9::chr3:34459134..34459146,+p1@ENSMUST00000172935
Mm9::chr3:34459266..34459272,+p4@ENSMUST00000172935
Mm9::chr3:34459282..34459308,+p1@Sox2ot
Mm9::chr3:34459548..34459568,+p@chr3:34459548..34459568
+
Mm9::chr5:82229760..82229765,+p@chr5:82229760..82229765
+
Mm9::chr9:75445450..75445463,-p8@Tmod2
Mm9::chr9:75445481..75445519,-p6@Tmod2
Mm9::chr9:75445524..75445545,-p9@Tmod2


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:0045745positive regulation of G-protein coupled receptor protein signaling pathway0.0239826601982353
GO:0005523tropomyosin binding0.0239826601982353
GO:0045176apical protein localization0.0239826601982353
GO:0008105asymmetric protein localization0.0239826601982353
GO:0030552cAMP binding0.0239826601982353
GO:0007190adenylate cyclase activation0.0239826601982353
GO:0031281positive regulation of cyclase activity0.0239826601982353
GO:0051349positive regulation of lyase activity0.0239826601982353
GO:0045762positive regulation of adenylate cyclase activity0.0239826601982353
GO:0016208AMP binding0.0239826601982353
GO:0045761regulation of adenylate cyclase activity0.0239826601982353
GO:0031279regulation of cyclase activity0.0239826601982353
GO:0008277regulation of G-protein coupled receptor protein signaling pathway0.0239826601982353
GO:0051339regulation of lyase activity0.0239826601982353
GO:0005184neuropeptide hormone activity0.0239826601982353
GO:0030551cyclic nucleotide binding0.0239826601982353
GO:0007270nerve-nerve synaptic transmission0.0285040806208462
GO:0005272sodium channel activity0.029160700324735
GO:0007189G-protein signaling, adenylate cyclase activating pathway0.0371704040420905
GO:0030425dendrite0.0483932198836574



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)1.52e-1023
neuroblast (sensu Vertebrata)1.52e-1023
ectodermal cell1.25e-0744
neurectodermal cell1.25e-0744
neuron5.15e-0733
neuronal stem cell5.15e-0733
neuroblast5.15e-0733
electrically signaling cell5.15e-0733
neural cell6.63e-0743

Uber Anatomy
Ontology termp-valuen
neurectoderm1.39e-3064
neural plate1.39e-3064
presumptive neural plate1.39e-3064
ectoderm-derived structure1.01e-2995
ectoderm1.01e-2995
presumptive ectoderm1.01e-2995
ecto-epithelium2.70e-2873
regional part of nervous system1.32e-2654
nervous system1.66e-2575
pre-chordal neural plate1.41e-2449
neural tube2.77e-2452
neural rod2.77e-2452
future spinal cord2.77e-2452
neural keel2.77e-2452
central nervous system3.70e-2373
brain6.89e-2147
future brain6.89e-2147
regional part of brain7.99e-2046
structure with developmental contribution from neural crest1.47e-1992
gray matter4.03e-1934
anterior neural tube1.03e-1640
brain grey matter5.17e-1629
regional part of telencephalon5.17e-1629
telencephalon5.17e-1629
regional part of forebrain1.38e-1539
forebrain1.38e-1539
future forebrain1.38e-1539
cerebral cortex2.53e-1021
cerebral hemisphere2.53e-1021
pallium2.53e-1021
sense organ3.26e-1012
sensory system3.26e-1012
entire sense organ system3.26e-1012
regional part of cerebral cortex3.38e-1017
occipital lobe1.04e-0910
visual cortex1.04e-0910
neocortex1.04e-0910
eye2.76e-099
camera-type eye2.76e-099
simple eye2.76e-099
immature eye2.76e-099
ocular region2.76e-099
visual system2.76e-099
face2.76e-099
optic cup2.76e-099
optic vesicle2.76e-099
eye primordium2.76e-099
head3.21e-0913
ectodermal placode3.21e-0913
posterior neural tube2.68e-0812
chordal neural plate2.68e-0812
subdivision of head3.03e-0711
basal ganglion3.78e-078
nuclear complex of neuraxis3.78e-078
aggregate regional part of brain3.78e-078
collection of basal ganglia3.78e-078
cerebral subcortex3.78e-078


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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