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MCL coexpression mm9:267: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000065!1.44e-19!41;UBERON:0001004!6.22e-19!42;UBERON:0002370!2.06e-18!23;UBERON:0000974!2.06e-18!23;UBERON:0004807!2.06e-18!23;UBERON:0005058!2.06e-18!23;UBERON:0003351!2.06e-18!23;UBERON:0009113!2.06e-18!23;UBERON:0003295!2.06e-18!23;UBERON:0009722!2.06e-18!23;UBERON:0005562!2.06e-18!23;UBERON:0007690!2.06e-18!23;UBERON:0006562!1.94e-17!24;UBERON:0003408!1.94e-17!24;UBERON:0001557!1.94e-17!24;UBERON:0001042!1.94e-17!24;UBERON:0008814!1.94e-17!24;UBERON:0009145!1.94e-17!24;UBERON:0002193!4.97e-17!48;UBERON:0002405!4.97e-17!48;UBERON:0002390!5.22e-17!45;UBERON:0003061!5.22e-17!45;UBERON:0004177!1.10e-16!29;UBERON:0005057!1.10e-16!29;UBERON:0000072!5.87e-15!27;UBERON:0000077!1.58e-14!35;UBERON:0007811!3.92e-11!36;UBERON:0000063!1.86e-10!35;UBERON:0005911!7.80e-10!69;UBERON:0001041!9.47e-10!80;UBERON:0002384!1.02e-08!46;UBERON:0000153!1.52e-08!43;UBERON:0003081!1.50e-07!87;UBERON:0000490!1.72e-07!66
|ontology_enrichment_uberon=UBERON:0000065!1.44e-19!41;UBERON:0001004!6.22e-19!42;UBERON:0002370!2.06e-18!23;UBERON:0000974!2.06e-18!23;UBERON:0004807!2.06e-18!23;UBERON:0005058!2.06e-18!23;UBERON:0003351!2.06e-18!23;UBERON:0009113!2.06e-18!23;UBERON:0003295!2.06e-18!23;UBERON:0009722!2.06e-18!23;UBERON:0005562!2.06e-18!23;UBERON:0007690!2.06e-18!23;UBERON:0006562!1.94e-17!24;UBERON:0003408!1.94e-17!24;UBERON:0001557!1.94e-17!24;UBERON:0001042!1.94e-17!24;UBERON:0008814!1.94e-17!24;UBERON:0009145!1.94e-17!24;UBERON:0002193!4.97e-17!48;UBERON:0002405!4.97e-17!48;UBERON:0002390!5.22e-17!45;UBERON:0003061!5.22e-17!45;UBERON:0004177!1.10e-16!29;UBERON:0005057!1.10e-16!29;UBERON:0000072!5.87e-15!27;UBERON:0000077!1.58e-14!35;UBERON:0007811!3.92e-11!36;UBERON:0000063!1.86e-10!35;UBERON:0005911!7.80e-10!69;UBERON:0001041!9.47e-10!80;UBERON:0002384!1.02e-08!46;UBERON:0000153!1.52e-08!43;UBERON:0003081!1.50e-07!87;UBERON:0000490!1.72e-07!66
|tfbs_overrepresentation_for_novel_motifs=0.487079,1.63438,0.432388,0.0803981,0.0895641,0.293623,1.34037,0.577188,0.618787,1.65458,0.355895,0.400509,0.839352,0.857752,0.252098,0,0.740836,0.0186281,0.320534,0.318509,0.359144,1.00854,0.140634,0.0883885,1.19118,1.48234,0.29651,1.61783,0.302369,0.185929,0.627721,0.345924,0.402091,0.243363,0.103182,0.0777,0.933467,0.125378,0.546738,1.71548,0.684118,0.639618,0.511863,0.255497,0.58441,0.261432,0.6098,0.105003,0.100392,0.30772,0.711629,0.174075,0.294051,0.462148,0.477006,0.875514,0.324148,0.767045,0.271373,0.443095,0.330215,0.531848,0.119176,0.692928,0.462592,0.760654,0.596353,0.920398,0.871514,0.781435,1.07824,0.21646,0.844989,0.505848,0.626532,0.569165,0.0550687,0.204903,0.316915,0.0414786,0.218909,0.28165,0.179134,0.192046,0.408287,3.64643,0.758515,0.18626,1.81307,1.07627,0.659258,0.412394,0.356069,0.0215347,1.13529,0.133345,0.031133,0.358304,1.14813,0.139752,0.0164145,0.345703,0.44741,0.25656,0.710864,0.638602,0.299999,0.10296,0.165666,1.01049,0.817447,1.13982,0.0418408,1.75978,0.665677,0.0851703,1.91944,0.587754,0.743023,0.61238,1.2719,1.22681,0.158574,0.204297,0.715313,0.319766,0.138785,0.35069,0.594996,0.239081,0.433157,0.953835,1.3952,0.153414,0.685415,0.0991348,0.234265,0.311081,0.640623,1.43657,1.04548,0.600569,0.16595,0.354213,0.25114,0.0929729,0.214675,1.39749,0.237053,1.04011,1.59631,1.12209,0.46348,0.752137,0.464961,0.533955,0.174709,1.17873,0.0615652,2.38821,0.649247,0.407582,0.32011,1.23127,0.694619,0.148453,0.192381,0.126498,2.45114
}}
}}

Revision as of 18:04, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:18724766..18724782,-p@chr10:18724766..18724782
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Mm9::chr10:18735010..18735015,-p6@Tnfaip3
Mm9::chr10:18735109..18735123,-p2@Tnfaip3
Mm9::chr10:18735153..18735185,-p1@Tnfaip3
Mm9::chr10:5958538..5958568,+p1@Zbtb2
Mm9::chr10:92628684..92628719,-p@chr10:92628684..92628719
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Mm9::chr11:120435018..120435029,-p7@P4hb
Mm9::chr12:114099097..114099178,-p1@Gpr132
Mm9::chr12:60320433..60320481,-p1@Fbxo33
Mm9::chr14:32149981..32149992,+p3@Capn7
Mm9::chr15:101084397..101084429,-p@chr15:101084397..101084429
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Mm9::chr16:78576894..78576911,-p1@D16Ertd472e
Mm9::chr16:78576927..78576941,-p3@D16Ertd472e
Mm9::chr17:71825231..71825243,-p@chr17:71825231..71825243
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Mm9::chr17:71948007..71948018,-p2@ENSMUST00000137830
Mm9::chr19:30105105..30105124,+p2@Uhrf2
Mm9::chr19:30105132..30105143,+p3@Uhrf2
Mm9::chr1:162836606..162836631,+p2@Rc3h1
Mm9::chr2:126501847..126501876,-p5@Gabpb1
Mm9::chr3:152059025..152059046,+p4@Gm8261
p4@Zzz3
Mm9::chr4:102242999..102243006,+p17@Pde4b
Mm9::chr4:48058102..48058110,+p5@Nr4a3
Mm9::chr4:8738493..8738504,+p@chr4:8738493..8738504
+
Mm9::chr4:8738510..8738524,+p@chr4:8738510..8738524
+
Mm9::chr5:52581099..52581110,+p@chr5:52581099..52581110
+
Mm9::chr7:148042601..148042621,-p2@Bet1l
Mm9::chr7:150812280..150812293,+p@chr7:150812280..150812293
+
Mm9::chr7:51053393..51053466,+p1@Klk8
Mm9::chr7:71083729..71083742,-p4@Klf13
Mm9::chr8:87501773..87501787,-p@chr8:87501773..87501787
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Mm9::chr9:45983558..45983575,-p@chr9:45983558..45983575
-


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

no results for this coexpression

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
lymphoid lineage restricted progenitor cell6.15e-1512
mature alpha-beta T cell2.55e-149
alpha-beta T cell2.55e-149
immature T cell2.55e-149
mature T cell2.55e-149
immature alpha-beta T cell2.55e-149
lymphocyte1.41e-1313
common lymphoid progenitor1.41e-1313
T cell1.47e-1311
pro-T cell1.47e-1311
hematopoietic cell4.35e-1332
hematopoietic oligopotent progenitor cell4.35e-1332
hematopoietic stem cell4.35e-1332
angioblastic mesenchymal cell4.35e-1332
hematopoietic multipotent progenitor cell4.35e-1332
CD4-positive, alpha-beta T cell8.40e-138
thymocyte7.20e-106
double negative thymocyte7.20e-106
naive T cell7.20e-106
double-positive, alpha-beta thymocyte7.20e-106
CD4-positive, alpha-beta thymocyte7.20e-106
naive thymus-derived CD4-positive, alpha-beta T cell7.20e-106
DN4 thymocyte7.20e-106
DN1 thymic pro-T cell7.20e-106
DN2 thymocyte7.20e-106
DN3 thymocyte7.20e-106
immature single positive thymocyte7.20e-106
early T lineage precursor7.20e-106
mature CD4 single-positive thymocyte7.20e-106
resting double-positive thymocyte7.20e-106
double-positive blast7.20e-106
CD69-positive double-positive thymocyte7.20e-106
CD69-positive, CD4-positive single-positive thymocyte7.20e-106
CD4-positive, CD8-intermediate double-positive thymocyte7.20e-106
CD24-positive, CD4 single-positive thymocyte7.20e-106
leukocyte9.45e-1017
nongranular leukocyte9.45e-1017
connective tissue cell1.02e-0846
mesenchymal cell1.02e-0846
nucleate cell1.14e-0716
hematopoietic lineage restricted progenitor cell1.92e-0725

Uber Anatomy
Ontology termp-valuen
respiratory tract1.44e-1941
respiratory system6.22e-1942
thymus2.06e-1823
neck2.06e-1823
respiratory system epithelium2.06e-1823
hemolymphoid system gland2.06e-1823
pharyngeal epithelium2.06e-1823
thymic region2.06e-1823
pharyngeal gland2.06e-1823
entire pharyngeal arch endoderm2.06e-1823
thymus primordium2.06e-1823
early pharyngeal endoderm2.06e-1823
pharynx1.94e-1724
gland of gut1.94e-1724
upper respiratory tract1.94e-1724
chordate pharynx1.94e-1724
pharyngeal arch system1.94e-1724
pharyngeal region of foregut1.94e-1724
hemolymphoid system4.97e-1748
immune system4.97e-1748
hematopoietic system5.22e-1745
blood island5.22e-1745
hemopoietic organ1.10e-1629
immune organ1.10e-1629
segment of respiratory tract5.87e-1527
mixed endoderm/mesoderm-derived structure1.58e-1435
craniocervical region3.92e-1136
organ segment1.86e-1035
endo-epithelium7.80e-1069
foregut9.47e-1080
connective tissue1.02e-0846
anterior region of body1.52e-0843
lateral plate mesoderm1.50e-0787
unilaminar epithelium1.72e-0766


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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