Personal tools

MCL coexpression mm9:624: 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=0.00579066519177055,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.266814200011828,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.113790818113665,0.18440492317299,0.213207239280454,0,0,0,0,0,0,0,0.210087710822348,0.147681830935052,0.152487072037699,0.152691370679199,0.262674241751994,0.28100227991434,0.258650118633401,0.429020773604989,0.322458878535173,0.245883191824323,0.297785784051744,0.101668926708099,0.135434985107224,0.0910522389263605,0.14980107127196,0.193893011938994,0.314696953870186,0.306607492965986,0.250815731227818,0.165254141453003,0.0158508717912236,0,0,0,0,0,0,0,0.0570741246689917,0,0,0,0.014052381161376,0,0,0,0,0,0,0.0234784353458152,0,0,0.0347388317801137,0,0,0.03048532897689,0.0482820047261801,0,0,0,0,0,0,0,0,0.111524892460631,0.151949772756791,0,0,0,0,0.324592939768638,0.375206552143423,0.537202817762492,0.706216536279587,0.776638123061556,0.44157679082602,0.554027361714163,0.0210591418683525,0,0,0.0414719663749819,0,0,0.0359524366705627,0.0876889746819101,0.0680361098787663,0.0523528812100954,0.074598306112166,0.181102009199648,0,0,0,0,0.0532734549622995,0.06488556341682,0.0812688455295622,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.817687151067068,0.708393610862107,0,0,0,0,0,0,0,0,0,0,0,0,0.0386774267005042,0,0,0,0,0.046982063026719,0,0,0,0.0147194505648231,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.193086408031806,0.165589315855097,0,0,0,0,0,0,0,0,0,0,0,1.22355844695475,0.0576433181427177,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0421696201982708,0.0709019855629759,0.0712812415377886,0.0948573962131381,0.057716207064756,0,0,0,0,0.0325029563895826,0.0254340553719351,0,0,0,0.136990127740213,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0332484050430722,0,0.0328560430895791,0,0.0285045896907187,0,0.0216534965544966,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.06728585421298,0.996062446524854,1.08522246183987,1.01825496464043,0.677208372863442,0.559218288128925,0.640989224902194,0.69652905559521,0.66512481471733,0.731971704573404,0,0,0.0980190734489225,0.17208118264908,0.152051658298929,0.163373524380168,0.159715578577694,0.115608096853184,0.168103334988355,0.137748206855213,0.171868938041193,0.0750453505157095,0.138165606837579,0.170215474877392,0.128597245627104,0.169172763866184,0.0905291472420136,0.141706336142815,0,0.130353389977647,0.128033729919821,0.131923786075207,0.131108301552488,0.218131378243292,0.219785036720782,0.190168443418861,0.135404897539632,0.18359421108913,0.241945346991933,0,0.16724639360867,0.0766218792953725,0.204343226098226,0.187614366711608,0.0766064454112358,0.271881217361352,0.166685587652774,0.155257708002722,0,0,0.0905641158318875
|coexpression_dpi_cluster_scores_median=0.00579066519177055,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.266814200011828,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.113790818113665,0.18440492317299,0.213207239280454,0,0,0,0,0,0,0,0.210087710822348,0.147681830935052,0.152487072037699,0.152691370679199,0.262674241751994,0.28100227991434,0.258650118633401,0.429020773604989,0.322458878535173,0.245883191824323,0.297785784051744,0.101668926708099,0.135434985107224,0.0910522389263605,0.14980107127196,0.193893011938994,0.314696953870186,0.306607492965986,0.250815731227818,0.165254141453003,0.0158508717912236,0,0,0,0,0,0,0,0.0570741246689917,0,0,0,0.014052381161376,0,0,0,0,0,0,0.0234784353458152,0,0,0.0347388317801137,0,0,0.03048532897689,0.0482820047261801,0,0,0,0,0,0,0,0,0.111524892460631,0.151949772756791,0,0,0,0,0.324592939768638,0.375206552143423,0.537202817762492,0.706216536279587,0.776638123061556,0.44157679082602,0.554027361714163,0.0210591418683525,0,0,0.0414719663749819,0,0,0.0359524366705627,0.0876889746819101,0.0680361098787663,0.0523528812100954,0.074598306112166,0.181102009199648,0,0,0,0,0.0532734549622995,0.06488556341682,0.0812688455295622,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.817687151067068,0.708393610862107,0,0,0,0,0,0,0,0,0,0,0,0,0.0386774267005042,0,0,0,0,0.046982063026719,0,0,0,0.0147194505648231,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.193086408031806,0.165589315855097,0,0,0,0,0,0,0,0,0,0,0,1.22355844695475,0.0576433181427177,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0421696201982708,0.0709019855629759,0.0712812415377886,0.0948573962131381,0.057716207064756,0,0,0,0,0.0325029563895826,0.0254340553719351,0,0,0,0.136990127740213,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0332484050430722,0,0.0328560430895791,0,0.0285045896907187,0,0.0216534965544966,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.06728585421298,0.996062446524854,1.08522246183987,1.01825496464043,0.677208372863442,0.559218288128925,0.640989224902194,0.69652905559521,0.66512481471733,0.731971704573404,0,0,0.0980190734489225,0.17208118264908,0.152051658298929,0.163373524380168,0.159715578577694,0.115608096853184,0.168103334988355,0.137748206855213,0.171868938041193,0.0750453505157095,0.138165606837579,0.170215474877392,0.128597245627104,0.169172763866184,0.0905291472420136,0.141706336142815,0,0.130353389977647,0.128033729919821,0.131923786075207,0.131108301552488,0.218131378243292,0.219785036720782,0.190168443418861,0.135404897539632,0.18359421108913,0.241945346991933,0,0.16724639360867,0.0766218792953725,0.204343226098226,0.187614366711608,0.0766064454112358,0.271881217361352,0.166685587652774,0.155257708002722,0,0,0.0905641158318875
|gostat_on_MCL_coexpression=GO:0008599;protein phosphatase type 1 regulator activity;0.0403056258892532;74100!GO:0001784;phosphotyrosine binding;0.0403056258892532;26417!GO:0045309;protein phosphorylated amino acid binding;0.0403056258892532;26417!GO:0043330;response to exogenous dsRNA;0.0403056258892532;26417!GO:0031663;lipopolysaccharide-mediated signaling pathway;0.0403056258892532;26417!GO:0032496;response to lipopolysaccharide;0.0403056258892532;26417!GO:0051219;phosphoprotein binding;0.0403056258892532;26417!GO:0004707;MAP kinase activity;0.0403056258892532;26417!GO:0043331;response to dsRNA;0.0403056258892532;26417!GO:0002237;response to molecule of bacterial origin;0.0474158328063201;26417!
|gostat_on_MCL_coexpression=GO:0008599;protein phosphatase type 1 regulator activity;0.0403056258892532;74100!GO:0001784;phosphotyrosine binding;0.0403056258892532;26417!GO:0045309;protein phosphorylated amino acid binding;0.0403056258892532;26417!GO:0043330;response to exogenous dsRNA;0.0403056258892532;26417!GO:0031663;lipopolysaccharide-mediated signaling pathway;0.0403056258892532;26417!GO:0032496;response to lipopolysaccharide;0.0403056258892532;26417!GO:0051219;phosphoprotein binding;0.0403056258892532;26417!GO:0004707;MAP kinase activity;0.0403056258892532;26417!GO:0043331;response to dsRNA;0.0403056258892532;26417!GO:0002237;response to molecule of bacterial origin;0.0474158328063201;26417!
|ontology_enrichment_celltype=CL:0000117!1.77e-16!23;CL:0000337!1.77e-16!23;CL:0000540!9.96e-10!33;CL:0000047!9.96e-10!33;CL:0000031!9.96e-10!33;CL:0000404!9.96e-10!33;CL:0000393!4.52e-07!39;CL:0000211!4.52e-07!39
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!1.59e-29!54;UBERON:0001049!2.00e-27!52;UBERON:0005068!2.00e-27!52;UBERON:0006241!2.00e-27!52;UBERON:0007135!2.00e-27!52;UBERON:0002346!1.80e-26!64;UBERON:0003075!1.80e-26!64;UBERON:0007284!1.80e-26!64;UBERON:0002020!1.12e-24!34;UBERON:0010371!2.98e-24!73;UBERON:0000955!4.61e-24!47;UBERON:0006238!4.61e-24!47;UBERON:0001017!5.87e-24!73;UBERON:0001016!1.23e-23!75;UBERON:0003056!2.42e-23!49;UBERON:0002616!5.07e-23!46;UBERON:0004121!2.07e-22!95;UBERON:0000924!2.07e-22!95;UBERON:0006601!2.07e-22!95;UBERON:0003080!2.62e-22!40;UBERON:0002780!2.03e-21!39;UBERON:0001890!2.03e-21!39;UBERON:0006240!2.03e-21!39;UBERON:0003528!6.33e-21!29;UBERON:0002791!6.33e-21!29;UBERON:0001893!6.33e-21!29;UBERON:0010314!5.30e-16!92;UBERON:0000956!9.50e-16!21;UBERON:0001869!9.50e-16!21;UBERON:0000203!9.50e-16!21;UBERON:0002619!5.05e-13!17;UBERON:0002021!3.45e-11!10;UBERON:0000411!3.45e-11!10;UBERON:0001950!3.45e-11!10
}}
}}

Revision as of 20:59, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr17:17539647..17539735,+p1@Lix1
Mm9::chr1:136763197..136763205,-p@chr1:136763197..136763205
-
Mm9::chr2:26998050..26998076,-p3@Fam163b
Mm9::chr3:117278186..117278200,+p6@4833424O15Rik
Mm9::chr6:5736930..5736933,+p@chr6:5736930..5736933
+
Mm9::chr6:5739540..5739543,+p@chr6:5739540..5739543
+
Mm9::chr7:133906383..133906396,+p7@Mapk3
Mm9::chr7:133906398..133906414,+p8@Mapk3
Mm9::chr7:151424595..151424610,+p@chr7:151424595..151424610
+
Mm9::chr7:151424623..151424635,+p@chr7:151424623..151424635
+
Mm9::chr9:104471931..104471961,+p3@Cpne4
Mm9::chr9:112138015..112138040,-p11@Arpp21


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:0008599protein phosphatase type 1 regulator activity0.0403056258892532
GO:0001784phosphotyrosine binding0.0403056258892532
GO:0045309protein phosphorylated amino acid binding0.0403056258892532
GO:0043330response to exogenous dsRNA0.0403056258892532
GO:0031663lipopolysaccharide-mediated signaling pathway0.0403056258892532
GO:0032496response to lipopolysaccharide0.0403056258892532
GO:0051219phosphoprotein binding0.0403056258892532
GO:0004707MAP kinase activity0.0403056258892532
GO:0043331response to dsRNA0.0403056258892532
GO:0002237response to molecule of bacterial origin0.0474158328063201



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)1.77e-1623
neuroblast (sensu Vertebrata)1.77e-1623
neuron9.96e-1033
neuronal stem cell9.96e-1033
neuroblast9.96e-1033
electrically signaling cell9.96e-1033
electrically responsive cell4.52e-0739
electrically active cell4.52e-0739

Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.59e-2954
neural tube2.00e-2752
neural rod2.00e-2752
future spinal cord2.00e-2752
neural keel2.00e-2752
neurectoderm1.80e-2664
neural plate1.80e-2664
presumptive neural plate1.80e-2664
gray matter1.12e-2434
ecto-epithelium2.98e-2473
brain4.61e-2447
future brain4.61e-2447
central nervous system5.87e-2473
nervous system1.23e-2375
pre-chordal neural plate2.42e-2349
regional part of brain5.07e-2346
ectoderm-derived structure2.07e-2295
ectoderm2.07e-2295
presumptive ectoderm2.07e-2295
anterior neural tube2.62e-2240
regional part of forebrain2.03e-2139
forebrain2.03e-2139
future forebrain2.03e-2139
brain grey matter6.33e-2129
regional part of telencephalon6.33e-2129
telencephalon6.33e-2129
structure with developmental contribution from neural crest5.30e-1692
cerebral cortex9.50e-1621
cerebral hemisphere9.50e-1621
pallium9.50e-1621
regional part of cerebral cortex5.05e-1317
occipital lobe3.45e-1110
visual cortex3.45e-1110
neocortex3.45e-1110


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}}}