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MCL coexpression mm9:570: Difference between revisions

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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0.0527413783866199,0.920176229317415,0.166764232955903,0.662340078653825,0.120273978885459,0.572780051507714,0.0699790221274244,0,0,0,0.119078361648301,0.0558041721483835,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.389294454188438,0.428210788219066,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.181236227563129,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0149427454282617,0,0,0,0,0.0894734883806707,0,0.056886356216389,0.0562185712770556,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.119259559192106,0,0,0,0,0,0.0492938041367021,0.0598244186619439,0.0531754751244564,0.031895734489288,0.0797788474440915,0.111388092060353,0.170572420628752,0.286684384770788,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0.0527413783866199,0.920176229317415,0.166764232955903,0.662340078653825,0.120273978885459,0.572780051507714,0.0699790221274244,0,0,0,0.119078361648301,0.0558041721483835,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.389294454188438,0.428210788219066,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.181236227563129,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0149427454282617,0,0,0,0,0.0894734883806707,0,0.056886356216389,0.0562185712770556,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.119259559192106,0,0,0,0,0,0.0492938041367021,0.0598244186619439,0.0531754751244564,0.031895734489288,0.0797788474440915,0.111388092060353,0.170572420628752,0.286684384770788,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=
|gostat_on_MCL_coexpression=
|ontology_enrichment_celltype=CL:0000791!8.21e-33!9;CL:0000789!8.21e-33!9;CL:0002420!8.21e-33!9;CL:0002419!8.21e-33!9;CL:0000790!8.21e-33!9;CL:0000624!3.64e-29!8;CL:0000084!1.37e-26!11;CL:0000827!1.37e-26!11;CL:0000838!2.97e-24!12;CL:0000893!1.30e-22!6;CL:0002489!1.30e-22!6;CL:0000898!1.30e-22!6;CL:0000809!1.30e-22!6;CL:0000810!1.30e-22!6;CL:0000895!1.30e-22!6;CL:0000808!1.30e-22!6;CL:0000894!1.30e-22!6;CL:0000806!1.30e-22!6;CL:0000807!1.30e-22!6;CL:0000805!1.30e-22!6;CL:0002425!1.30e-22!6;CL:0002436!1.30e-22!6;CL:0002427!1.30e-22!6;CL:0002428!1.30e-22!6;CL:0002429!1.30e-22!6;CL:0002433!1.30e-22!6;CL:0002431!1.30e-22!6;CL:0002432!1.30e-22!6;CL:0000542!2.82e-22!13;CL:0000051!2.82e-22!13;CL:0002242!7.96e-18!16;CL:0000738!1.09e-16!17;CL:0002087!1.09e-16!17;CL:0002031!3.51e-16!25;CL:0000988!3.33e-12!32;CL:0002032!3.33e-12!32;CL:0000037!3.33e-12!32;CL:0000566!3.33e-12!32;CL:0000837!3.33e-12!32;CL:0002320!6.96e-08!46;CL:0000134!6.96e-08!46
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004177!5.89e-33!29;UBERON:0005057!5.89e-33!29;UBERON:0002370!5.99e-33!23;UBERON:0000974!5.99e-33!23;UBERON:0004807!5.99e-33!23;UBERON:0005058!5.99e-33!23;UBERON:0003351!5.99e-33!23;UBERON:0009113!5.99e-33!23;UBERON:0003295!5.99e-33!23;UBERON:0009722!5.99e-33!23;UBERON:0005562!5.99e-33!23;UBERON:0007690!5.99e-33!23;UBERON:0006562!1.85e-31!24;UBERON:0003408!1.85e-31!24;UBERON:0001557!1.85e-31!24;UBERON:0001042!1.85e-31!24;UBERON:0008814!1.85e-31!24;UBERON:0009145!1.85e-31!24;UBERON:0000072!1.19e-27!27;UBERON:0000077!9.12e-27!35;UBERON:0002193!1.20e-26!48;UBERON:0002405!1.20e-26!48;UBERON:0002390!1.53e-25!45;UBERON:0003061!1.53e-25!45;UBERON:0000063!1.10e-20!35;UBERON:0007811!4.97e-20!36;UBERON:0000065!3.07e-17!41;UBERON:0001004!9.25e-17!42;UBERON:0000153!2.65e-16!43;UBERON:0003929!4.04e-12!55;UBERON:0003081!1.67e-11!87;UBERON:0002368!7.19e-11!60;UBERON:0001041!6.79e-10!80;UBERON:0002530!8.20e-10!65;UBERON:0000490!1.28e-09!66;UBERON:0005911!4.46e-09!69;UBERON:0000949!1.40e-08!72;UBERON:0000064!1.57e-08!99;UBERON:0002384!6.96e-08!46;UBERON:0000926!2.39e-07!120;UBERON:0004120!2.39e-07!120;UBERON:0006603!2.39e-07!120
}}
}}

Revision as of 20:54, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr12:29320098..29320105,-p@chr12:29320098..29320105
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Mm9::chr14:53989688..53989700,+p1@uc007trz.1
p1@uc007tsa.1
Mm9::chr14:54382812..54382860,+p1@ENSMUST00000103669
Mm9::chr14:54827851..54827895,+p@chr14:54827851..54827895
+
Mm9::chr14:54843708..54843722,+p@chr14:54843708..54843722
+
Mm9::chr15:66277121..66277159,+p@chr15:66277121..66277159
+
Mm9::chr17:19096061..19096064,-p@chr17:19096061..19096064
-
Mm9::chr17:19105945..19105962,-p1@uc008apx.1
Mm9::chr17:19105991..19106024,-p2@uc008apx.1
Mm9::chr17:29567158..29567162,-p@chr17:29567158..29567162
-
Mm9::chr4:32252125..32252136,+p@chr4:32252125..32252136
+
Mm9::chr4:32378680..32378685,+p@chr4:32378680..32378685
+
Mm9::chr7:89077761..89077781,+p@chr7:89077761..89077781
+


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
mature alpha-beta T cell8.21e-339
alpha-beta T cell8.21e-339
immature T cell8.21e-339
mature T cell8.21e-339
immature alpha-beta T cell8.21e-339
CD4-positive, alpha-beta T cell3.64e-298
T cell1.37e-2611
pro-T cell1.37e-2611
lymphoid lineage restricted progenitor cell2.97e-2412
thymocyte1.30e-226
double negative thymocyte1.30e-226
naive T cell1.30e-226
double-positive, alpha-beta thymocyte1.30e-226
CD4-positive, alpha-beta thymocyte1.30e-226
naive thymus-derived CD4-positive, alpha-beta T cell1.30e-226
DN4 thymocyte1.30e-226
DN1 thymic pro-T cell1.30e-226
DN2 thymocyte1.30e-226
DN3 thymocyte1.30e-226
immature single positive thymocyte1.30e-226
early T lineage precursor1.30e-226
mature CD4 single-positive thymocyte1.30e-226
resting double-positive thymocyte1.30e-226
double-positive blast1.30e-226
CD69-positive double-positive thymocyte1.30e-226
CD69-positive, CD4-positive single-positive thymocyte1.30e-226
CD4-positive, CD8-intermediate double-positive thymocyte1.30e-226
CD24-positive, CD4 single-positive thymocyte1.30e-226
lymphocyte2.82e-2213
common lymphoid progenitor2.82e-2213
nucleate cell7.96e-1816
leukocyte1.09e-1617
nongranular leukocyte1.09e-1617
hematopoietic lineage restricted progenitor cell3.51e-1625
hematopoietic cell3.33e-1232
hematopoietic oligopotent progenitor cell3.33e-1232
hematopoietic stem cell3.33e-1232
angioblastic mesenchymal cell3.33e-1232
hematopoietic multipotent progenitor cell3.33e-1232
connective tissue cell6.96e-0846
mesenchymal cell6.96e-0846

Uber Anatomy
Ontology termp-valuen
hemopoietic organ5.89e-3329
immune organ5.89e-3329
thymus5.99e-3323
neck5.99e-3323
respiratory system epithelium5.99e-3323
hemolymphoid system gland5.99e-3323
pharyngeal epithelium5.99e-3323
thymic region5.99e-3323
pharyngeal gland5.99e-3323
entire pharyngeal arch endoderm5.99e-3323
thymus primordium5.99e-3323
early pharyngeal endoderm5.99e-3323
pharynx1.85e-3124
gland of gut1.85e-3124
upper respiratory tract1.85e-3124
chordate pharynx1.85e-3124
pharyngeal arch system1.85e-3124
pharyngeal region of foregut1.85e-3124
segment of respiratory tract1.19e-2727
mixed endoderm/mesoderm-derived structure9.12e-2735
hemolymphoid system1.20e-2648
immune system1.20e-2648
hematopoietic system1.53e-2545
blood island1.53e-2545
organ segment1.10e-2035
craniocervical region4.97e-2036
respiratory tract3.07e-1741
respiratory system9.25e-1742
anterior region of body2.65e-1643
gut epithelium4.04e-1255
lateral plate mesoderm1.67e-1187
endocrine gland7.19e-1160
foregut6.79e-1080
gland8.20e-1065
unilaminar epithelium1.28e-0966
endo-epithelium4.46e-0969
endocrine system1.40e-0872
organ part1.57e-0899
connective tissue6.96e-0846
mesoderm2.39e-07120
mesoderm-derived structure2.39e-07120
presumptive mesoderm2.39e-07120


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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