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MCL coexpression mm9:639: Difference between revisions

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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0.413854914439209,0.881787943371597,0.835792834727366,0.180026585552633,0.273578499709972,0.342107724764957,0.230286214243433,0,0,0,0.119078361648301,0.0558041721483835,0,0,0.0411126530948397,0,0.0644551523736777,0,0,0,0,0,0,0.0839793170280262,0,0,0,0,0,0,0.86455965894399,0.615459892883158,0.490533640609026,1.19605970885837,0.762026887945864,0.643311751835009,0.0514985917256918,0.0419359757688424,0.073185417993707,0,0,0,0,0,0,0.22705576246071,0.389294454188438,0.125836948423969,0,0.033995335178371,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0317017435824471,0,0.68815506582299,0,0,0,0,0,0.0397519380874063,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.427715163864743,0.300173318036138,0.423559264412865,0,0,0,0,0,0,0,0.00508484160320079,0.0509235292940968,0,0,0,0,0,0,0.0285860945550467,0,0,0,0,0,0,0,0,0,0,0,0.231013950740173,0.307365864513145,0.383962049647022,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0774164737207147,0,0,0,0,0.0691813633419548,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.120939615821127,0,0,0,0.0564111250741226,0,0,0,0,0,0,0,0,0.0254340553719351,0,0,0,0,0,0,0,0,0,0,0.431329067459534,0.428040377850264,0.424620276916781,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0417740847988257,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
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|gostat_on_MCL_coexpression=GO:0008538;proteasome activator activity;0.00542317164695645;19188!GO:0008537;proteasome activator complex;0.00542317164695645;19188!GO:0019884;antigen processing and presentation of exogenous antigen;0.0276880692576502;19188!
|gostat_on_MCL_coexpression=GO:0008538;proteasome activator activity;0.00542317164695645;19188!GO:0008537;proteasome activator complex;0.00542317164695645;19188!GO:0019884;antigen processing and presentation of exogenous antigen;0.0276880692576502;19188!
|ontology_enrichment_celltype=CL:0000838!3.62e-19!12;CL:0000988!4.32e-19!32;CL:0002032!4.32e-19!32;CL:0000037!4.32e-19!32;CL:0000566!4.32e-19!32;CL:0000837!4.32e-19!32;CL:0000791!4.65e-18!9;CL:0000789!4.65e-18!9;CL:0002420!4.65e-18!9;CL:0002419!4.65e-18!9;CL:0000790!4.65e-18!9;CL:0000542!1.71e-17!13;CL:0000051!1.71e-17!13;CL:0000084!1.82e-17!11;CL:0000827!1.82e-17!11;CL:0000624!2.09e-16!8;CL:0002242!9.82e-14!16;CL:0002320!1.97e-13!46;CL:0000134!1.97e-13!46;CL:0000738!8.89e-13!17;CL:0002087!8.89e-13!17;CL:0000893!1.07e-12!6;CL:0002489!1.07e-12!6;CL:0000898!1.07e-12!6;CL:0000809!1.07e-12!6;CL:0000810!1.07e-12!6;CL:0000895!1.07e-12!6;CL:0000808!1.07e-12!6;CL:0000894!1.07e-12!6;CL:0000806!1.07e-12!6;CL:0000807!1.07e-12!6;CL:0000805!1.07e-12!6;CL:0002425!1.07e-12!6;CL:0002436!1.07e-12!6;CL:0002427!1.07e-12!6;CL:0002428!1.07e-12!6;CL:0002429!1.07e-12!6;CL:0002433!1.07e-12!6;CL:0002431!1.07e-12!6;CL:0002432!1.07e-12!6;CL:0000034!2.34e-12!97;CL:0000219!7.03e-12!54;CL:0002031!4.08e-11!25;CL:0000355!3.65e-10!9;CL:0000723!3.83e-10!91;CL:0000048!3.83e-10!91;CL:0002371!5.18e-07!118
|ontology_enrichment_disease=DOID:0060100!1.06e-07!3;DOID:4045!1.06e-07!3
|ontology_enrichment_uberon=UBERON:0002384!1.97e-13!46;UBERON:0001134!3.65e-10!9;UBERON:0002036!3.65e-10!9;UBERON:0002385!3.65e-10!9;UBERON:0000486!3.65e-10!9;UBERON:0007503!3.65e-10!9;UBERON:0001015!3.65e-10!9;UBERON:0002329!3.65e-10!9;UBERON:0003082!3.65e-10!9;UBERON:0003059!3.65e-10!9;UBERON:0007282!3.65e-10!9;UBERON:0004290!3.65e-10!9;UBERON:0009618!3.65e-10!9;UBERON:0000383!4.90e-09!10;UBERON:0007524!4.10e-08!11;UBERON:0003077!4.10e-08!11;UBERON:0007285!4.10e-08!11
}}
}}

Revision as of 21:01, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:61969312..61969341,+p@chr10:61969312..61969341
+
Mm9::chr10:89208517..89208523,-p@chr10:89208517..89208523
-
Mm9::chr10:89208554..89208568,-p@chr10:89208554..89208568
-
Mm9::chr11:103558635..103558654,+p2@ENSMUST00000129780
p2@ENSMUST00000154471
p2@uc007lvp.1
p2@uc011yfx.1
Mm9::chr11:78059245..78059323,+p2@Sdf2
Mm9::chr14:56210316..56210343,-p6@Psme2
Mm9::chr1:58769066..58769089,-p@chr1:58769066..58769089
-
Mm9::chr1:58769240..58769278,+p@chr1:58769240..58769278
+
Mm9::chr1:58783936..58783956,-p@chr1:58783936..58783956
-
Mm9::chr2:160472300..160472306,-p@chr2:160472300..160472306
-
Mm9::chr7:148127785..148127855,+p2@Athl1


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:0008538proteasome activator activity0.00542317164695645
GO:0008537proteasome activator complex0.00542317164695645
GO:0019884antigen processing and presentation of exogenous antigen0.0276880692576502



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>disease_data<br>

Cell Type
Ontology termp-valuen
lymphoid lineage restricted progenitor cell3.62e-1912
hematopoietic cell4.32e-1932
hematopoietic oligopotent progenitor cell4.32e-1932
hematopoietic stem cell4.32e-1932
angioblastic mesenchymal cell4.32e-1932
hematopoietic multipotent progenitor cell4.32e-1932
mature alpha-beta T cell4.65e-189
alpha-beta T cell4.65e-189
immature T cell4.65e-189
mature T cell4.65e-189
immature alpha-beta T cell4.65e-189
lymphocyte1.71e-1713
common lymphoid progenitor1.71e-1713
T cell1.82e-1711
pro-T cell1.82e-1711
CD4-positive, alpha-beta T cell2.09e-168
nucleate cell9.82e-1416
connective tissue cell1.97e-1346
mesenchymal cell1.97e-1346
leukocyte8.89e-1317
nongranular leukocyte8.89e-1317
thymocyte1.07e-126
double negative thymocyte1.07e-126
naive T cell1.07e-126
double-positive, alpha-beta thymocyte1.07e-126
CD4-positive, alpha-beta thymocyte1.07e-126
naive thymus-derived CD4-positive, alpha-beta T cell1.07e-126
DN4 thymocyte1.07e-126
DN1 thymic pro-T cell1.07e-126
DN2 thymocyte1.07e-126
DN3 thymocyte1.07e-126
immature single positive thymocyte1.07e-126
early T lineage precursor1.07e-126
mature CD4 single-positive thymocyte1.07e-126
resting double-positive thymocyte1.07e-126
double-positive blast1.07e-126
CD69-positive double-positive thymocyte1.07e-126
CD69-positive, CD4-positive single-positive thymocyte1.07e-126
CD4-positive, CD8-intermediate double-positive thymocyte1.07e-126
CD24-positive, CD4 single-positive thymocyte1.07e-126
stem cell2.34e-1297
motile cell7.03e-1254
hematopoietic lineage restricted progenitor cell4.08e-1125
multi-potent skeletal muscle stem cell3.65e-109
somatic stem cell3.83e-1091
multi fate stem cell3.83e-1091
somatic cell5.18e-07118

Disease
Ontology termp-valuen
musculoskeletal system cancer1.06e-073
muscle cancer1.06e-073


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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