Personal tools

MCL coexpression mm9:328: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 3: Line 3:
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.190947417941288,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0400093965272457,0,0,0,0,0,0,0,0,0,0.0428469550828748,0.0549981337564001,0,0.109123086691028,0.0778422136256562,0.0501827898833331,0.0397493170902889,0,0,0.414188667563274,0.441759342938654,0.0538027986792206,0.0729756721489083,0,0,0,0.299229130252845,0.156669685869194,0.0578074284787346,0.0742309351586685,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.00390665681439922,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0825867363219064,0,0,0,0,0.223335400219127,0.484326482617181,0.118143376972179,0.669146045046306,0.595347723711218,0.262724437924219,0.417868291930509,0,0,0,0,0,0,0,0,0.0067970654923699,0.0523528812100954,0.0194494484574599,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.19329992230912,0.430951058285018,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.193086408031806,0.130859448321889,0,0,0,0,0,0,0,0,0,0,0,0.441317932710179,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.192086593839265,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.821086572151095,0.746969655386223,0.723370700919886,0.797186708038281,0.485046405834616,0.641774351669359,0.524473678907995,0.593355602481523,0.638062984050757,0.554949444870281,0,0,0,0,0,0,0,0,0,0,0,0,0.0388749848471105,0.0396401807728516,0.0242538736058389,0,0.0436633540262291,0,0,0.0298193647598867,0,0,0,0.0589368614163519,0.0390607415003592,0.0352754493378881,0,0,0.0553034373508932,0,0,0.0408018333703219,0,0.0269399430611312,0.0766064454112358,0,0,0.0422650922646472,0,0,0
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.190947417941288,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0400093965272457,0,0,0,0,0,0,0,0,0,0.0428469550828748,0.0549981337564001,0,0.109123086691028,0.0778422136256562,0.0501827898833331,0.0397493170902889,0,0,0.414188667563274,0.441759342938654,0.0538027986792206,0.0729756721489083,0,0,0,0.299229130252845,0.156669685869194,0.0578074284787346,0.0742309351586685,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.00390665681439922,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0825867363219064,0,0,0,0,0.223335400219127,0.484326482617181,0.118143376972179,0.669146045046306,0.595347723711218,0.262724437924219,0.417868291930509,0,0,0,0,0,0,0,0,0.0067970654923699,0.0523528812100954,0.0194494484574599,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.19329992230912,0.430951058285018,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.193086408031806,0.130859448321889,0,0,0,0,0,0,0,0,0,0,0,0.441317932710179,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.192086593839265,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.821086572151095,0.746969655386223,0.723370700919886,0.797186708038281,0.485046405834616,0.641774351669359,0.524473678907995,0.593355602481523,0.638062984050757,0.554949444870281,0,0,0,0,0,0,0,0,0,0,0,0,0.0388749848471105,0.0396401807728516,0.0242538736058389,0,0.0436633540262291,0,0,0.0298193647598867,0,0,0,0.0589368614163519,0.0390607415003592,0.0352754493378881,0,0,0.0553034373508932,0,0,0.0408018333703219,0,0.0269399430611312,0.0766064454112358,0,0,0.0422650922646472,0,0,0
|gostat_on_MCL_coexpression=GO:0021801;cerebral cortex radial glia guided migration;0.0156138716923246;13131!GO:0021799;cerebral cortex radially oriented cell migration;0.0156138716923246;13131!GO:0021589;cerebellum structural organization;0.0156138716923246;13131!GO:0021813;cell-cell adhesion involved in neuronal-glial interactions involved in cerebral cortex radial glia guided migration;0.0156138716923246;13131!GO:0021577;hindbrain structural organization;0.0156138716923246;13131!GO:0048532;organization of an anatomical structure;0.0156138716923246;13131!GO:0021812;neuronal-glial interaction involved in cerebral cortex radial glia guided migration;0.0156138716923246;13131!GO:0021942;radial glia guided migration of Purkinje cell;0.0156138716923246;13131!GO:0021932;hindbrain radial glia guided cell migration;0.0249760353894974;13131!GO:0007168;receptor guanylyl cyclase signaling pathway;0.0249760353894974;14708!GO:0005516;calmodulin binding;0.0307942104658189;12323,17919!GO:0021535;cell migration in hindbrain;0.0312123473389508;13131!GO:0021795;cerebral cortex cell migration;0.0384057263879851;13131!GO:0042169;SH2 domain binding;0.0415856935171347;13131!GO:0005083;small GTPase regulator activity;0.0415856935171347;105445,14708!GO:0005954;calcium- and calmodulin-dependent protein kinase complex;0.0415856935171347;12323!GO:0021885;forebrain cell migration;0.0415856935171347;13131!GO:0022029;telencephalon cell migration;0.0415856935171347;13131!GO:0004274;dipeptidyl-peptidase IV activity;0.0459518053958278;13483!GO:0021987;cerebral cortex development;0.0498455976785651;13131!GO:0015629;actin cytoskeleton;0.0498455976785651;83767,17919!
|gostat_on_MCL_coexpression=GO:0021801;cerebral cortex radial glia guided migration;0.0156138716923246;13131!GO:0021799;cerebral cortex radially oriented cell migration;0.0156138716923246;13131!GO:0021589;cerebellum structural organization;0.0156138716923246;13131!GO:0021813;cell-cell adhesion involved in neuronal-glial interactions involved in cerebral cortex radial glia guided migration;0.0156138716923246;13131!GO:0021577;hindbrain structural organization;0.0156138716923246;13131!GO:0048532;organization of an anatomical structure;0.0156138716923246;13131!GO:0021812;neuronal-glial interaction involved in cerebral cortex radial glia guided migration;0.0156138716923246;13131!GO:0021942;radial glia guided migration of Purkinje cell;0.0156138716923246;13131!GO:0021932;hindbrain radial glia guided cell migration;0.0249760353894974;13131!GO:0007168;receptor guanylyl cyclase signaling pathway;0.0249760353894974;14708!GO:0005516;calmodulin binding;0.0307942104658189;12323,17919!GO:0021535;cell migration in hindbrain;0.0312123473389508;13131!GO:0021795;cerebral cortex cell migration;0.0384057263879851;13131!GO:0042169;SH2 domain binding;0.0415856935171347;13131!GO:0005083;small GTPase regulator activity;0.0415856935171347;105445,14708!GO:0005954;calcium- and calmodulin-dependent protein kinase complex;0.0415856935171347;12323!GO:0021885;forebrain cell migration;0.0415856935171347;13131!GO:0022029;telencephalon cell migration;0.0415856935171347;13131!GO:0004274;dipeptidyl-peptidase IV activity;0.0459518053958278;13483!GO:0021987;cerebral cortex development;0.0498455976785651;13131!GO:0015629;actin cytoskeleton;0.0498455976785651;83767,17919!
|ontology_enrichment_celltype=CL:0000117!4.05e-12!23;CL:0000337!4.05e-12!23;CL:0000540!2.36e-07!33;CL:0000047!2.36e-07!33;CL:0000031!2.36e-07!33;CL:0000404!2.36e-07!33
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!2.86e-32!54;UBERON:0002020!6.42e-32!34;UBERON:0001049!1.64e-31!52;UBERON:0005068!1.64e-31!52;UBERON:0006241!1.64e-31!52;UBERON:0007135!1.64e-31!52;UBERON:0002346!1.60e-28!64;UBERON:0003075!1.60e-28!64;UBERON:0007284!1.60e-28!64;UBERON:0001017!4.23e-26!73;UBERON:0000955!3.32e-25!47;UBERON:0006238!3.32e-25!47;UBERON:0003528!3.88e-25!29;UBERON:0002791!3.88e-25!29;UBERON:0001893!3.88e-25!29;UBERON:0001016!3.99e-25!75;UBERON:0002616!7.98e-24!46;UBERON:0010371!9.42e-24!73;UBERON:0003080!3.50e-22!40;UBERON:0000956!9.24e-22!21;UBERON:0001869!9.24e-22!21;UBERON:0000203!9.24e-22!21;UBERON:0003056!3.25e-21!49;UBERON:0004121!3.96e-21!95;UBERON:0000924!3.96e-21!95;UBERON:0006601!3.96e-21!95;UBERON:0002780!7.02e-21!39;UBERON:0001890!7.02e-21!39;UBERON:0006240!7.02e-21!39;UBERON:0002619!5.11e-19!17;UBERON:0002021!1.92e-18!10;UBERON:0000411!1.92e-18!10;UBERON:0001950!1.92e-18!10;UBERON:0010314!9.00e-17!92;UBERON:0003076!1.13e-09!12;UBERON:0003057!1.13e-09!12;UBERON:0002240!1.90e-09!6;UBERON:0005174!1.90e-09!6;UBERON:0001137!1.90e-09!6;UBERON:0000025!2.59e-09!114;UBERON:0004111!3.94e-08!122;UBERON:0001948!4.81e-08!5;UBERON:0002315!4.81e-08!5
}}
}}

Revision as of 19:48, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:40603275..40603289,+p5@Wasf1
Mm9::chr10:40603299..40603314,+p3@Wasf1
Mm9::chr10:40603426..40603440,+p4@Wasf1
Mm9::chr10:80464083..80464115,-p3@Gng7
Mm9::chr11:5966357..5966368,-p14@Camk2b
Mm9::chr11:5966374..5966387,-p8@Camk2b
Mm9::chr13:55050724..55050747,+p2@Unc5a
Mm9::chr14:122137717..122137728,-p15@Dock9
Mm9::chr14:122137765..122137775,-p16@Dock9
Mm9::chr14:56130053..56130057,-p@chr14:56130053..56130057
-
Mm9::chr15:37447238..37447243,+p@chr15:37447238..37447243
+
Mm9::chr16:75447352..75447361,-p@chr16:75447352..75447361
-
Mm9::chr17:13044761..13044782,-p1@Mas1
Mm9::chr17:70871052..70871078,+p13@Dlgap1
Mm9::chr18:74874391..74874406,+p13@Myo5b
Mm9::chr18:74874419..74874428,+p18@Myo5b
Mm9::chr18:74874437..74874450,+p12@Myo5b
Mm9::chr19:28084383..28084396,-p@chr19:28084383..28084396
-
Mm9::chr4:103292185..103292197,+p9@Dab1
Mm9::chr5:27588740..27588750,+p19@Dpp6
Mm9::chr5:27588762..27588776,+p10@Dpp6
Mm9::chr7:3390657..3390678,+p@chr7:3390657..3390678
+
Mm9::chr7:3391221..3391241,+p@chr7:3391221..3391241
+
Mm9::chr7:3391251..3391262,+p@chr7:3391251..3391262
+


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:0021801cerebral cortex radial glia guided migration0.0156138716923246
GO:0021799cerebral cortex radially oriented cell migration0.0156138716923246
GO:0021589cerebellum structural organization0.0156138716923246
GO:0021813cell-cell adhesion involved in neuronal-glial interactions involved in cerebral cortex radial glia guided migration0.0156138716923246
GO:0021577hindbrain structural organization0.0156138716923246
GO:0048532organization of an anatomical structure0.0156138716923246
GO:0021812neuronal-glial interaction involved in cerebral cortex radial glia guided migration0.0156138716923246
GO:0021942radial glia guided migration of Purkinje cell0.0156138716923246
GO:0021932hindbrain radial glia guided cell migration0.0249760353894974
GO:0007168receptor guanylyl cyclase signaling pathway0.0249760353894974
GO:0005516calmodulin binding0.0307942104658189
GO:0021535cell migration in hindbrain0.0312123473389508
GO:0021795cerebral cortex cell migration0.0384057263879851
GO:0042169SH2 domain binding0.0415856935171347
GO:0005083small GTPase regulator activity0.0415856935171347
GO:0005954calcium- and calmodulin-dependent protein kinase complex0.0415856935171347
GO:0021885forebrain cell migration0.0415856935171347
GO:0022029telencephalon cell migration0.0415856935171347
GO:0004274dipeptidyl-peptidase IV activity0.0459518053958278
GO:0021987cerebral cortex development0.0498455976785651
GO:0015629actin cytoskeleton0.0498455976785651



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)4.05e-1223
neuroblast (sensu Vertebrata)4.05e-1223
neuron2.36e-0733
neuronal stem cell2.36e-0733
neuroblast2.36e-0733
electrically signaling cell2.36e-0733

Uber Anatomy
Ontology termp-valuen
regional part of nervous system2.86e-3254
gray matter6.42e-3234
neural tube1.64e-3152
neural rod1.64e-3152
future spinal cord1.64e-3152
neural keel1.64e-3152
neurectoderm1.60e-2864
neural plate1.60e-2864
presumptive neural plate1.60e-2864
central nervous system4.23e-2673
brain3.32e-2547
future brain3.32e-2547
brain grey matter3.88e-2529
regional part of telencephalon3.88e-2529
telencephalon3.88e-2529
nervous system3.99e-2575
regional part of brain7.98e-2446
ecto-epithelium9.42e-2473
anterior neural tube3.50e-2240
cerebral cortex9.24e-2221
cerebral hemisphere9.24e-2221
pallium9.24e-2221
pre-chordal neural plate3.25e-2149
ectoderm-derived structure3.96e-2195
ectoderm3.96e-2195
presumptive ectoderm3.96e-2195
regional part of forebrain7.02e-2139
forebrain7.02e-2139
future forebrain7.02e-2139
regional part of cerebral cortex5.11e-1917
occipital lobe1.92e-1810
visual cortex1.92e-1810
neocortex1.92e-1810
structure with developmental contribution from neural crest9.00e-1792
posterior neural tube1.13e-0912
chordal neural plate1.13e-0912
spinal cord1.90e-096
dorsal region element1.90e-096
dorsum1.90e-096
tube2.59e-09114
anatomical conduit3.94e-08122
regional part of spinal cord4.81e-085
gray matter of spinal cord4.81e-085


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}}}

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:328&oldid=2155599"