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MCL coexpression mm9:1148: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!6.67e-21!48;UBERON:0002405!6.67e-21!48;UBERON:0002390!9.26e-19!45;UBERON:0003061!9.26e-19!45;UBERON:0004177!2.03e-18!29;UBERON:0005057!2.03e-18!29;UBERON:0000077!3.56e-16!35;UBERON:0002370!1.16e-15!23;UBERON:0000974!1.16e-15!23;UBERON:0004807!1.16e-15!23;UBERON:0005058!1.16e-15!23;UBERON:0003351!1.16e-15!23;UBERON:0009113!1.16e-15!23;UBERON:0003295!1.16e-15!23;UBERON:0009722!1.16e-15!23;UBERON:0005562!1.16e-15!23;UBERON:0007690!1.16e-15!23;UBERON:0006562!1.06e-14!24;UBERON:0003408!1.06e-14!24;UBERON:0001557!1.06e-14!24;UBERON:0001042!1.06e-14!24;UBERON:0008814!1.06e-14!24;UBERON:0009145!1.06e-14!24;UBERON:0000072!2.95e-12!27;UBERON:0000065!1.86e-11!41;UBERON:0001004!5.65e-11!42;UBERON:0001041!9.46e-11!80;UBERON:0005911!6.93e-10!69;UBERON:0003081!1.12e-09!87;UBERON:0003929!2.75e-09!55;UBERON:0002384!3.28e-09!46;UBERON:0004119!6.11e-09!118;UBERON:0000925!6.11e-09!118;UBERON:0006595!6.11e-09!118;UBERON:0001007!9.29e-09!116;UBERON:0001555!9.29e-09!116;UBERON:0007026!9.29e-09!116;UBERON:0000063!1.03e-08!35;UBERON:0004921!6.27e-08!114;UBERON:0002368!9.39e-08!60;UBERON:0000490!1.16e-07!66;UBERON:0007811!1.64e-07!36;UBERON:0002530!3.95e-07!65
|ontology_enrichment_uberon=UBERON:0002193!6.67e-21!48;UBERON:0002405!6.67e-21!48;UBERON:0002390!9.26e-19!45;UBERON:0003061!9.26e-19!45;UBERON:0004177!2.03e-18!29;UBERON:0005057!2.03e-18!29;UBERON:0000077!3.56e-16!35;UBERON:0002370!1.16e-15!23;UBERON:0000974!1.16e-15!23;UBERON:0004807!1.16e-15!23;UBERON:0005058!1.16e-15!23;UBERON:0003351!1.16e-15!23;UBERON:0009113!1.16e-15!23;UBERON:0003295!1.16e-15!23;UBERON:0009722!1.16e-15!23;UBERON:0005562!1.16e-15!23;UBERON:0007690!1.16e-15!23;UBERON:0006562!1.06e-14!24;UBERON:0003408!1.06e-14!24;UBERON:0001557!1.06e-14!24;UBERON:0001042!1.06e-14!24;UBERON:0008814!1.06e-14!24;UBERON:0009145!1.06e-14!24;UBERON:0000072!2.95e-12!27;UBERON:0000065!1.86e-11!41;UBERON:0001004!5.65e-11!42;UBERON:0001041!9.46e-11!80;UBERON:0005911!6.93e-10!69;UBERON:0003081!1.12e-09!87;UBERON:0003929!2.75e-09!55;UBERON:0002384!3.28e-09!46;UBERON:0004119!6.11e-09!118;UBERON:0000925!6.11e-09!118;UBERON:0006595!6.11e-09!118;UBERON:0001007!9.29e-09!116;UBERON:0001555!9.29e-09!116;UBERON:0007026!9.29e-09!116;UBERON:0000063!1.03e-08!35;UBERON:0004921!6.27e-08!114;UBERON:0002368!9.39e-08!60;UBERON:0000490!1.16e-07!66;UBERON:0007811!1.64e-07!36;UBERON:0002530!3.95e-07!65
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.369498,0.411716,1.20801,0.810002,0.495263,0.587291,0.206208,0.616096,0.219671,0.542749,0.575086,0.206435,0.599731,0.315771,0,0.795315,0.291368,0.561256,0.361892,0.374752,0.27937,0.598814,0.29769,1.07577,0.62766,0.542568,0.516511,0.911169,0.145661,0.50223,0.897561,0.78719,0.498917,0.316253,0.0235321,0.279977,0.57142,0.258564,0.230656,0.295233,0.507468,0.258106,0.317766,1.19315,0.469348,0.714592,0.532496,0.219744,0.917701,0.777641,0.654933,1.3744,1.04034,1.0579,0.606984,0.356236,0.56214,0.522357,0.604914,0.877332,0.664501,0.642748,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.21183,0.611537,1.09164,0.17012,0.482617,0.166511,0.703064,0.859987,0.98764,0.212973,0.812889,0.663039,0.200155,0.975495,0.339494,0.374181,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.668513,0.203879,0.913319,0.71485,0.399703,1.40122,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,0.430942,1.02459,2.63898,0.547992,1.27206,0.293461,0.187586,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.0806013,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.452587,1.38961,1.04192,0.243291,0.619892,1.12411,0.655955,0.327731,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,1.3969,0.573477,0.433127
}}
}}

Revision as of 19:28, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr16:49855630..49855685,-p@chr16:49855630..49855685
-
Mm9::chr18:32557234..32557249,+p@chr18:32557234..32557249
+
Mm9::chr19:4154620..4154629,+p2@Ptprcap
Mm9::chr19:4154640..4154668,+p1@Ptprcap
Mm9::chr19:4156100..4156111,+p@chr19:4156100..4156111
+
Mm9::chr19:46114855..46114867,-p@chr19:46114855..46114867
-
Mm9::chr2:79095076..79095083,+p12@Itga4


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:0001968fibronectin binding0.0131481633363305
GO:0007159leukocyte adhesion0.0289101108018125
GO:0001974blood vessel remodeling0.0289101108018125
GO:0007185transmembrane receptor protein tyrosine phosphatase signaling pathway0.0289101108018125
GO:0007157heterophilic cell adhesion0.0289101108018125
GO:0008305integrin complex0.0372204718592457



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
hematopoietic cell8.25e-1632
hematopoietic oligopotent progenitor cell8.25e-1632
hematopoietic stem cell8.25e-1632
angioblastic mesenchymal cell8.25e-1632
hematopoietic multipotent progenitor cell8.25e-1632
lymphoid lineage restricted progenitor cell5.58e-1412
T cell6.49e-1311
pro-T cell6.49e-1311
lymphocyte1.50e-1213
common lymphoid progenitor1.50e-1213
hematopoietic lineage restricted progenitor cell5.03e-1225
nucleate cell6.92e-1116
mature alpha-beta T cell8.56e-119
alpha-beta T cell8.56e-119
immature T cell8.56e-119
mature T cell8.56e-119
immature alpha-beta T cell8.56e-119
CD4-positive, alpha-beta T cell9.01e-108
connective tissue cell3.28e-0946
mesenchymal cell3.28e-0946
leukocyte1.43e-0817
nongranular leukocyte1.43e-0817
thymocyte1.51e-076
double negative thymocyte1.51e-076
naive T cell1.51e-076
double-positive, alpha-beta thymocyte1.51e-076
CD4-positive, alpha-beta thymocyte1.51e-076
naive thymus-derived CD4-positive, alpha-beta T cell1.51e-076
DN4 thymocyte1.51e-076
DN1 thymic pro-T cell1.51e-076
DN2 thymocyte1.51e-076
DN3 thymocyte1.51e-076
immature single positive thymocyte1.51e-076
early T lineage precursor1.51e-076
mature CD4 single-positive thymocyte1.51e-076
resting double-positive thymocyte1.51e-076
double-positive blast1.51e-076
CD69-positive double-positive thymocyte1.51e-076
CD69-positive, CD4-positive single-positive thymocyte1.51e-076
CD4-positive, CD8-intermediate double-positive thymocyte1.51e-076
CD24-positive, CD4 single-positive thymocyte1.51e-076
motile cell3.31e-0754

Uber Anatomy
Ontology termp-valuen
hemolymphoid system6.67e-2148
immune system6.67e-2148
hematopoietic system9.26e-1945
blood island9.26e-1945
hemopoietic organ2.03e-1829
immune organ2.03e-1829
mixed endoderm/mesoderm-derived structure3.56e-1635
thymus1.16e-1523
neck1.16e-1523
respiratory system epithelium1.16e-1523
hemolymphoid system gland1.16e-1523
pharyngeal epithelium1.16e-1523
thymic region1.16e-1523
pharyngeal gland1.16e-1523
entire pharyngeal arch endoderm1.16e-1523
thymus primordium1.16e-1523
early pharyngeal endoderm1.16e-1523
pharynx1.06e-1424
gland of gut1.06e-1424
upper respiratory tract1.06e-1424
chordate pharynx1.06e-1424
pharyngeal arch system1.06e-1424
pharyngeal region of foregut1.06e-1424
segment of respiratory tract2.95e-1227
respiratory tract1.86e-1141
respiratory system5.65e-1142
foregut9.46e-1180
endo-epithelium6.93e-1069
lateral plate mesoderm1.12e-0987
gut epithelium2.75e-0955
connective tissue3.28e-0946
endoderm-derived structure6.11e-09118
endoderm6.11e-09118
presumptive endoderm6.11e-09118
digestive system9.29e-09116
digestive tract9.29e-09116
primitive gut9.29e-09116
organ segment1.03e-0835
subdivision of digestive tract6.27e-08114
endocrine gland9.39e-0860
unilaminar epithelium1.16e-0766
craniocervical region1.64e-0736
gland3.95e-0765


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}}}