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MCL coexpression mm9:1095: Difference between revisions

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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0354470656487682,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.139151649173176,0.115321149766792,0.322484032940483,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.268800900821362,0.158886068781892,0,0,0,0,0,0,0,0,0,0,0,0,0.112145192034931,0.108816382318513,0.241944181742968,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0851089148667383,0,0,0,0,0.112901225419538,0.129358133846345,0.115432590314795,0,0.06097065795378,0.131222718281153,0.138933868974914,0,0.0586534975690397,0,0,0,0,0,0,0,0.098801861608942,0,0,0,0,0,0,0,0,0,0,0.148404418111199,0,0,0,0,0,0,0,0,0,0,0,0,0.179333151877562,0,0,0,0,0,0.145528461145601,0,0,0,0,0.231362068833672,0,0.168347036942697,0,0.0623063220167371,0,0,0,0,0,0,0,0,0,0,0,0,0.101901855392646,0.432376901078102,0.379018921433599,0.359584052295502,0.302854023491376,0.276349694709285,0.290285790444849,0,0.219792932025556,0.0973736644748266,0.145480126286698,0.142992358284344,0.278483662180697,0,0,0.24518475135791,0.163457778354187,0,0.0805006992779881,0.0769870445726752,0.130552179598174,0.0743999836187831,0,0,0,0,0.0670132089181356,0.0779341159210384,0,0,0,0,0,0,0,0,0,0,0,0,0,0.284152233790825,0.923770504753492,0.876136925937556,0.675264203601739,0.554076199977568,0.399250695581751,0.290518649700687,0.250550415371553,0.565823914093939,0.507133276069325,0.509520632217209,0.17364944681578,0.181287491017976,0.198271062479628,0,0,0,0,0.358773048807313,0.458696302711342,0,0,1.04517674252757,0.904601813235722,1.13703683601399,0,0,0.108252561213616,0.58361528276474,0.653894331637568,0.65873525369059,0,0,0.0711694759496908,0.122469471105573,0.123832128606708,0,0.345158624232579,0.114718896326828,0.0750375819757342,0.112371000179637,0.208137646145581,0.0998284739419172,0,0.06712266862589,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.000987229959331148,0,0.0254340553719351,0.0489745727197172,0.0660055475634404,0.111087966368681,0.361345699164688,0,0,0,0,0,0,0,0,0,0,0.747168714182299,0.346336698424137,0.244533757727956,0.310787058879506,0.272642165925968,0.317836684998134,0.220429149935824,0.100975358632432,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0801664161057822,0.0158427924510955,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.655980247516075,0.622441888716962,0.40425240789028,0.237875402198471,0.264452449061451,0.239393094866555,0.0871588832444397,0.149856261570464,0.292866674034965,0.245041507634362,0.098117166361508,0.194758206527804,0.107523539997041,0.179609583883942,0.180962454233317,0.29061047861444,0.0905291472420136,0.141706336142815,0.14986111676545,0.0596387295197733,0.226790206858766,0.131923786075207,0.092873634605593,0.110822898586572,0.0748964051866952,0.178311376624504,0.135404897539632,0.18359421108913,0.148421355017489,0.193442483447008,0.0924644954689594,0.112441925220423,0.148982201447044,0.165781451382873,0.141704700595215,0.0968441960560167,0,0.216063761676531,0.196967476487388,0,0
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0354470656487682,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.139151649173176,0.115321149766792,0.322484032940483,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.268800900821362,0.158886068781892,0,0,0,0,0,0,0,0,0,0,0,0,0.112145192034931,0.108816382318513,0.241944181742968,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0851089148667383,0,0,0,0,0.112901225419538,0.129358133846345,0.115432590314795,0,0.06097065795378,0.131222718281153,0.138933868974914,0,0.0586534975690397,0,0,0,0,0,0,0,0.098801861608942,0,0,0,0,0,0,0,0,0,0,0.148404418111199,0,0,0,0,0,0,0,0,0,0,0,0,0.179333151877562,0,0,0,0,0,0.145528461145601,0,0,0,0,0.231362068833672,0,0.168347036942697,0,0.0623063220167371,0,0,0,0,0,0,0,0,0,0,0,0,0.101901855392646,0.432376901078102,0.379018921433599,0.359584052295502,0.302854023491376,0.276349694709285,0.290285790444849,0,0.219792932025556,0.0973736644748266,0.145480126286698,0.142992358284344,0.278483662180697,0,0,0.24518475135791,0.163457778354187,0,0.0805006992779881,0.0769870445726752,0.130552179598174,0.0743999836187831,0,0,0,0,0.0670132089181356,0.0779341159210384,0,0,0,0,0,0,0,0,0,0,0,0,0,0.284152233790825,0.923770504753492,0.876136925937556,0.675264203601739,0.554076199977568,0.399250695581751,0.290518649700687,0.250550415371553,0.565823914093939,0.507133276069325,0.509520632217209,0.17364944681578,0.181287491017976,0.198271062479628,0,0,0,0,0.358773048807313,0.458696302711342,0,0,1.04517674252757,0.904601813235722,1.13703683601399,0,0,0.108252561213616,0.58361528276474,0.653894331637568,0.65873525369059,0,0,0.0711694759496908,0.122469471105573,0.123832128606708,0,0.345158624232579,0.114718896326828,0.0750375819757342,0.112371000179637,0.208137646145581,0.0998284739419172,0,0.06712266862589,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.000987229959331148,0,0.0254340553719351,0.0489745727197172,0.0660055475634404,0.111087966368681,0.361345699164688,0,0,0,0,0,0,0,0,0,0,0.747168714182299,0.346336698424137,0.244533757727956,0.310787058879506,0.272642165925968,0.317836684998134,0.220429149935824,0.100975358632432,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0801664161057822,0.0158427924510955,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.655980247516075,0.622441888716962,0.40425240789028,0.237875402198471,0.264452449061451,0.239393094866555,0.0871588832444397,0.149856261570464,0.292866674034965,0.245041507634362,0.098117166361508,0.194758206527804,0.107523539997041,0.179609583883942,0.180962454233317,0.29061047861444,0.0905291472420136,0.141706336142815,0.14986111676545,0.0596387295197733,0.226790206858766,0.131923786075207,0.092873634605593,0.110822898586572,0.0748964051866952,0.178311376624504,0.135404897539632,0.18359421108913,0.148421355017489,0.193442483447008,0.0924644954689594,0.112441925220423,0.148982201447044,0.165781451382873,0.141704700595215,0.0968441960560167,0,0.216063761676531,0.196967476487388,0,0
|gostat_on_MCL_coexpression=GO:0007389;pattern specification process;0.00704628605978155;15399,15413!GO:0048703;embryonic viscerocranium morphogenesis;0.00704628605978155;15399!GO:0005667;transcription factor complex;0.00704628605978155;15399,15413!GO:0043565;sequence-specific DNA binding;0.00704628605978155;15399,15413!GO:0048701;embryonic cranial skeleton morphogenesis;0.00704628605978155;15399!GO:0042474;middle ear morphogenesis;0.00704628605978155;15399!GO:0009887;organ morphogenesis;0.00704628605978155;15399,15413!GO:0044451;nucleoplasm part;0.00704628605978155;15399,15413!GO:0005654;nucleoplasm;0.00704628605978155;15399,15413!GO:0045446;endothelial cell differentiation;0.00746882169324845;15413!GO:0048704;embryonic skeletal morphogenesis;0.00746882169324845;15399!GO:0031981;nuclear lumen;0.00746882169324845;15399,15413!GO:0031974;membrane-enclosed lumen;0.00814543077564118;15399,15413!GO:0043233;organelle lumen;0.00814543077564118;15399,15413!GO:0048706;embryonic skeletal development;0.00829476945773949;15399!GO:0003700;transcription factor activity;0.00859934249097884;15399,15413!GO:0048705;skeletal morphogenesis;0.0103661885975155;15399!GO:0001709;cell fate determination;0.0103661885975155;15399!GO:0044428;nuclear part;0.010608137469431;15399,15413!GO:0009653;anatomical structure morphogenesis;0.013093475674337;15399,15413!GO:0048513;organ development;0.0177494802129741;15399,15413!GO:0042471;ear morphogenesis;0.0211826435861262;15399!GO:0043234;protein complex;0.0221767273126586;15399,15413!GO:0048731;system development;0.0221767273126586;15399,15413!GO:0043583;ear development;0.0221767273126586;15399!GO:0048869;cellular developmental process;0.0221767273126586;15399,15413!GO:0030154;cell differentiation;0.0221767273126586;15399,15413!GO:0006355;regulation of transcription, DNA-dependent;0.0221767273126586;15399,15413!GO:0006351;transcription, DNA-dependent;0.0221767273126586;15399,15413!GO:0032774;RNA biosynthetic process;0.0221767273126586;15399,15413!GO:0003677;DNA binding;0.0221767273126586;15399,15413!GO:0045449;regulation of transcription;0.0221767273126586;15399,15413!GO:0048856;anatomical structure development;0.0221767273126586;15399,15413!GO:0045165;cell fate commitment;0.0221767273126586;15399!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0221767273126586;15399,15413!GO:0006350;transcription;0.0221767273126586;15399,15413!GO:0032991;macromolecular complex;0.0221835585063547;15399,15413!GO:0010468;regulation of gene expression;0.022444354649964;15399,15413!GO:0031323;regulation of cellular metabolic process;0.0236983998555817;15399,15413!GO:0007275;multicellular organismal development;0.0241833631015704;15399,15413!GO:0019222;regulation of metabolic process;0.0242401984828042;15399,15413!GO:0016070;RNA metabolic process;0.0249287093220019;15399,15413!GO:0044446;intracellular organelle part;0.0254998168855322;15399,15413!GO:0044422;organelle part;0.0254998168855322;15399,15413!GO:0001501;skeletal development;0.0309655821500028;15399!GO:0007423;sensory organ development;0.031296994214026;15399!GO:0010467;gene expression;0.031902634374277;15399,15413!GO:0048598;embryonic morphogenesis;0.0320949688724849;15399!GO:0003676;nucleic acid binding;0.0320949688724849;15399,15413!GO:0032502;developmental process;0.0333071565541416;15399,15413!GO:0043009;chordate embryonic development;0.0333071565541416;15399!GO:0009792;embryonic development ending in birth or egg hatching;0.0333071565541416;15399!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0344612923443434;15399,15413!GO:0050794;regulation of cellular process;0.0388992151408601;15399,15413!GO:0050789;regulation of biological process;0.0473715943392161;15399,15413!
|gostat_on_MCL_coexpression=GO:0007389;pattern specification process;0.00704628605978155;15399,15413!GO:0048703;embryonic viscerocranium morphogenesis;0.00704628605978155;15399!GO:0005667;transcription factor complex;0.00704628605978155;15399,15413!GO:0043565;sequence-specific DNA binding;0.00704628605978155;15399,15413!GO:0048701;embryonic cranial skeleton morphogenesis;0.00704628605978155;15399!GO:0042474;middle ear morphogenesis;0.00704628605978155;15399!GO:0009887;organ morphogenesis;0.00704628605978155;15399,15413!GO:0044451;nucleoplasm part;0.00704628605978155;15399,15413!GO:0005654;nucleoplasm;0.00704628605978155;15399,15413!GO:0045446;endothelial cell differentiation;0.00746882169324845;15413!GO:0048704;embryonic skeletal morphogenesis;0.00746882169324845;15399!GO:0031981;nuclear lumen;0.00746882169324845;15399,15413!GO:0031974;membrane-enclosed lumen;0.00814543077564118;15399,15413!GO:0043233;organelle lumen;0.00814543077564118;15399,15413!GO:0048706;embryonic skeletal development;0.00829476945773949;15399!GO:0003700;transcription factor activity;0.00859934249097884;15399,15413!GO:0048705;skeletal morphogenesis;0.0103661885975155;15399!GO:0001709;cell fate determination;0.0103661885975155;15399!GO:0044428;nuclear part;0.010608137469431;15399,15413!GO:0009653;anatomical structure morphogenesis;0.013093475674337;15399,15413!GO:0048513;organ development;0.0177494802129741;15399,15413!GO:0042471;ear morphogenesis;0.0211826435861262;15399!GO:0043234;protein complex;0.0221767273126586;15399,15413!GO:0048731;system development;0.0221767273126586;15399,15413!GO:0043583;ear development;0.0221767273126586;15399!GO:0048869;cellular developmental process;0.0221767273126586;15399,15413!GO:0030154;cell differentiation;0.0221767273126586;15399,15413!GO:0006355;regulation of transcription, DNA-dependent;0.0221767273126586;15399,15413!GO:0006351;transcription, DNA-dependent;0.0221767273126586;15399,15413!GO:0032774;RNA biosynthetic process;0.0221767273126586;15399,15413!GO:0003677;DNA binding;0.0221767273126586;15399,15413!GO:0045449;regulation of transcription;0.0221767273126586;15399,15413!GO:0048856;anatomical structure development;0.0221767273126586;15399,15413!GO:0045165;cell fate commitment;0.0221767273126586;15399!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0221767273126586;15399,15413!GO:0006350;transcription;0.0221767273126586;15399,15413!GO:0032991;macromolecular complex;0.0221835585063547;15399,15413!GO:0010468;regulation of gene expression;0.022444354649964;15399,15413!GO:0031323;regulation of cellular metabolic process;0.0236983998555817;15399,15413!GO:0007275;multicellular organismal development;0.0241833631015704;15399,15413!GO:0019222;regulation of metabolic process;0.0242401984828042;15399,15413!GO:0016070;RNA metabolic process;0.0249287093220019;15399,15413!GO:0044446;intracellular organelle part;0.0254998168855322;15399,15413!GO:0044422;organelle part;0.0254998168855322;15399,15413!GO:0001501;skeletal development;0.0309655821500028;15399!GO:0007423;sensory organ development;0.031296994214026;15399!GO:0010467;gene expression;0.031902634374277;15399,15413!GO:0048598;embryonic morphogenesis;0.0320949688724849;15399!GO:0003676;nucleic acid binding;0.0320949688724849;15399,15413!GO:0032502;developmental process;0.0333071565541416;15399,15413!GO:0043009;chordate embryonic development;0.0333071565541416;15399!GO:0009792;embryonic development ending in birth or egg hatching;0.0333071565541416;15399!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0344612923443434;15399,15413!GO:0050794;regulation of cellular process;0.0388992151408601;15399,15413!GO:0050789;regulation of biological process;0.0473715943392161;15399,15413!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002048!6.83e-12!14;UBERON:0000117!6.83e-12!14;UBERON:0000171!6.83e-12!14;UBERON:0000170!6.83e-12!14;UBERON:0005597!6.83e-12!14;UBERON:0000118!6.83e-12!14;UBERON:0005157!1.70e-11!20;UBERON:0005178!7.83e-10!17;UBERON:0005181!7.83e-10!17;UBERON:0002224!7.83e-10!17;UBERON:0000915!7.83e-10!17;UBERON:0008947!7.83e-10!17;UBERON:0003258!7.83e-10!17;UBERON:0005153!8.23e-09!17
}}
}}

Revision as of 16:19, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr11:96164887..96164894,+p4@Hoxb5
Mm9::chr11:96164905..96164919,+p2@Hoxb5
Mm9::chr11:96164928..96164947,+p@chr11:96164928..96164947
+
Mm9::chr11:96164964..96165032,+p@chr11:96164964..96165032
+
Mm9::chr11:96165039..96165073,+p@chr11:96165039..96165073
+
Mm9::chr6:52114447..52114463,-p@chr6:52114447..52114463
-
Mm9::chr6:52114472..52114489,-p@chr6:52114472..52114489
-


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:0007389pattern specification process0.00704628605978155
GO:0048703embryonic viscerocranium morphogenesis0.00704628605978155
GO:0005667transcription factor complex0.00704628605978155
GO:0043565sequence-specific DNA binding0.00704628605978155
GO:0048701embryonic cranial skeleton morphogenesis0.00704628605978155
GO:0042474middle ear morphogenesis0.00704628605978155
GO:0009887organ morphogenesis0.00704628605978155
GO:0044451nucleoplasm part0.00704628605978155
GO:0005654nucleoplasm0.00704628605978155
GO:0045446endothelial cell differentiation0.00746882169324845
GO:0048704embryonic skeletal morphogenesis0.00746882169324845
GO:0031981nuclear lumen0.00746882169324845
GO:0031974membrane-enclosed lumen0.00814543077564118
GO:0043233organelle lumen0.00814543077564118
GO:0048706embryonic skeletal development0.00829476945773949
GO:0003700transcription factor activity0.00859934249097884
GO:0048705skeletal morphogenesis0.0103661885975155
GO:0001709cell fate determination0.0103661885975155
GO:0044428nuclear part0.010608137469431
GO:0009653anatomical structure morphogenesis0.013093475674337
GO:0048513organ development0.0177494802129741
GO:0042471ear morphogenesis0.0211826435861262
GO:0043234protein complex0.0221767273126586
GO:0048731system development0.0221767273126586
GO:0043583ear development0.0221767273126586
GO:0048869cellular developmental process0.0221767273126586
GO:0030154cell differentiation0.0221767273126586
GO:0006355regulation of transcription, DNA-dependent0.0221767273126586
GO:0006351transcription, DNA-dependent0.0221767273126586
GO:0032774RNA biosynthetic process0.0221767273126586
GO:0003677DNA binding0.0221767273126586
GO:0045449regulation of transcription0.0221767273126586
GO:0048856anatomical structure development0.0221767273126586
GO:0045165cell fate commitment0.0221767273126586
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0221767273126586
GO:0006350transcription0.0221767273126586
GO:0032991macromolecular complex0.0221835585063547
GO:0010468regulation of gene expression0.022444354649964
GO:0031323regulation of cellular metabolic process0.0236983998555817
GO:0007275multicellular organismal development0.0241833631015704
GO:0019222regulation of metabolic process0.0242401984828042
GO:0016070RNA metabolic process0.0249287093220019
GO:0044446intracellular organelle part0.0254998168855322
GO:0044422organelle part0.0254998168855322
GO:0001501skeletal development0.0309655821500028
GO:0007423sensory organ development0.031296994214026
GO:0010467gene expression0.031902634374277
GO:0048598embryonic morphogenesis0.0320949688724849
GO:0003676nucleic acid binding0.0320949688724849
GO:0032502developmental process0.0333071565541416
GO:0043009chordate embryonic development0.0333071565541416
GO:0009792embryonic development ending in birth or egg hatching0.0333071565541416
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0344612923443434
GO:0050794regulation of cellular process0.0388992151408601
GO:0050789regulation of biological process0.0473715943392161



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
lung6.83e-1214
respiratory tube6.83e-1214
respiration organ6.83e-1214
pair of lungs6.83e-1214
lung primordium6.83e-1214
lung bud6.83e-1214
epithelial fold1.70e-1120
thoracic cavity element7.83e-1017
thoracic segment organ7.83e-1017
thoracic cavity7.83e-1017
thoracic segment of trunk7.83e-1017
respiratory primordium7.83e-1017
endoderm of foregut7.83e-1017
epithelial bud8.23e-0917


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)

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