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MCL coexpression mm9:433: Difference between revisions

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|ontology_enrichment_disease=DOID:0060100!1.34e-08!3;DOID:4045!1.34e-08!3
|ontology_enrichment_disease=DOID:0060100!1.34e-08!3;DOID:4045!1.34e-08!3
|ontology_enrichment_uberon=UBERON:0002384!8.89e-22!46
|ontology_enrichment_uberon=UBERON:0002384!8.89e-22!46
|tfbs_overrepresentation_for_novel_motifs=1.00028,0.0322544,0.476315,0.205657,0.0882392,0.216369,0.286882,0.165361,0.177198,0.896006,0.252112,0.760086,0.165655,0.296787,0.322172,0,0.46143,0.596872,0.147449,0.53564,0.415519,1.15861,0.296055,1.02912,0.16256,0.319311,0.13779,0.232181,0.366819,0.230852,0.630968,0.552579,0.281806,0.279585,0.322914,0.144175,0.268195,0.753507,0.0668978,0.0536011,0.290922,0.640129,0.528785,0.325245,0.434967,0.197508,0.391673,0.244272,0.64057,0.37148,0.445973,0.341665,0.217128,0.683824,0.700221,0.302599,0.385691,0.26711,0.554816,0.300938,0.534331,0.349585,0.427506,0.43605,0.311703,0.471894,0.829699,1.16897,0.530087,1.02503,0.444898,0.390307,0.623456,0.731855,0.531778,0.263994,0.027847,0.994033,1.28944,0.422405,0.696815,0.476893,0.920052,1.00736,0.623727,0.572181,0.288683,0.0927017,0.395899,1.32869,0.896685,0.62835,2.37195,0.0914951,1.29816,0.207461,0.370414,0.56686,0.391893,0.614116,0.959508,0.552324,0.667487,0.446498,0.445567,0.639347,0.498793,0.241171,0.848883,0.134388,0.50853,0.669156,0.136675,0.711663,0.903482,0.085085,0.529599,0.208431,0.462587,0.944825,0.736964,0.4177,0.320815,0.381122,0.955823,0.522111,0.293459,0.558086,0.828246,0.093155,0.651613,0.200314,0.799981,0.313768,0.92434,0.204108,0.181334,1.20107,0.876916,1.69384,1.29725,0.834212,1.58373,0.562149,1.12026,0.225756,0.394362,1.65442,0.183006,0.299565,0.447655,0.767951,0.685297,0.215456,0.313008,0.762455,0.342508,1.68492,0.993295,0.181136,0.886073,0.622933,1.29742,0.168927,1.11397,1.49864,0.0772819,0.275979,0.478093
}}
}}

Revision as of 18:21, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:120416369..120416378,-p@chr10:120416369..120416378
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Mm9::chr12:4925036..4925055,-p@chr12:4925036..4925055
-
Mm9::chr16:17722647..17722693,+p@chr16:17722647..17722693
+
Mm9::chr17:17511579..17511588,+p@chr17:17511579..17511588
+
Mm9::chr17:29626018..29626030,-p@chr17:29626018..29626030
-
Mm9::chr17:29626283..29626293,+p@chr17:29626283..29626293
+
Mm9::chr19:36423777..36423809,-p@chr19:36423777..36423809
-
Mm9::chr2:56976467..56976482,-p4@Nr4a2
Mm9::chr4:102244812..102244831,-p@chr4:102244812..102244831
-
Mm9::chr4:102244969..102244982,+p@chr4:102244969..102244982
+
Mm9::chr7:25155202..25155218,+p8@Kcnn4
Mm9::chr7:26465861..26465880,+p2@B9d2
Mm9::chr7:87546167..87546184,+p@chr7:87546167..87546184
+
Mm9::chr9:75255861..75255886,+p@chr9:75255861..75255886
+
Mm9::chr9:75255893..75255906,+p@chr9:75255893..75255906
+
Mm9::chr9:75256131..75256135,+p@chr9:75256131..75256135
+
Mm9::chrX:101176473..101176487,-p3@Rlim


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:0046541saliva secretion0.0456920771900011
GO:0050714positive regulation of protein secretion0.0456920771900011
GO:0042069regulation of catecholamine metabolic process0.0456920771900011
GO:0042053regulation of dopamine metabolic process0.0456920771900011
GO:0051047positive regulation of secretion0.0456920771900011
GO:0007589fluid secretion0.0456920771900011
GO:0015269calcium-activated potassium channel activity0.0456920771900011
GO:0022600digestive system process0.0456920771900011
GO:0022839ion gated channel activity0.0456920771900011
GO:0005227calcium activated cation channel activity0.0456920771900011
GO:0050708regulation of protein secretion0.0456920771900011



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
hematopoietic cell5.50e-3032
hematopoietic oligopotent progenitor cell5.50e-3032
hematopoietic stem cell5.50e-3032
angioblastic mesenchymal cell5.50e-3032
hematopoietic multipotent progenitor cell5.50e-3032
lymphoid lineage restricted progenitor cell5.82e-3012
lymphocyte1.83e-2713
common lymphoid progenitor1.83e-2713
T cell1.86e-2711
pro-T cell1.86e-2711
mature alpha-beta T cell3.91e-239
alpha-beta T cell3.91e-239
immature T cell3.91e-239
mature T cell3.91e-239
immature alpha-beta T cell3.91e-239
nucleate cell7.68e-2216
connective tissue cell8.89e-2246
mesenchymal cell8.89e-2246
motile cell1.18e-2154
CD4-positive, alpha-beta T cell9.72e-218
leukocyte2.08e-2017
nongranular leukocyte2.08e-2017
hematopoietic lineage restricted progenitor cell7.06e-1825
stem cell1.21e-1697
thymocyte6.40e-166
double negative thymocyte6.40e-166
naive T cell6.40e-166
double-positive, alpha-beta thymocyte6.40e-166
CD4-positive, alpha-beta thymocyte6.40e-166
naive thymus-derived CD4-positive, alpha-beta T cell6.40e-166
DN4 thymocyte6.40e-166
DN1 thymic pro-T cell6.40e-166
DN2 thymocyte6.40e-166
DN3 thymocyte6.40e-166
immature single positive thymocyte6.40e-166
early T lineage precursor6.40e-166
mature CD4 single-positive thymocyte6.40e-166
resting double-positive thymocyte6.40e-166
double-positive blast6.40e-166
CD69-positive double-positive thymocyte6.40e-166
CD69-positive, CD4-positive single-positive thymocyte6.40e-166
CD4-positive, CD8-intermediate double-positive thymocyte6.40e-166
CD24-positive, CD4 single-positive thymocyte6.40e-166
somatic stem cell2.14e-1391
multi fate stem cell2.14e-1391
somatic cell3.66e-12118
animal cell2.69e-09115
eukaryotic cell2.69e-09115
common myeloid progenitor2.95e-0819
barrier cell4.38e-083

Uber Anatomy
Ontology termp-valuen
connective tissue8.89e-2246

Disease
Ontology termp-valuen
musculoskeletal system cancer1.34e-083
muscle cancer1.34e-083


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}}}