Personal tools

MCL coexpression mm9:878: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 6: Line 6:
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002384!3.95e-15!46;UBERON:0000344!1.60e-10!15;UBERON:0000485!7.17e-09!11;UBERON:0001242!8.86e-09!13;UBERON:0000060!8.86e-09!13;UBERON:0001262!8.86e-09!13;UBERON:0004786!8.86e-09!13;UBERON:0003350!1.24e-07!9;UBERON:0004808!1.24e-07!9;UBERON:0001277!1.24e-07!9;UBERON:0002193!4.92e-07!48;UBERON:0002405!4.92e-07!48
|ontology_enrichment_uberon=UBERON:0002384!3.95e-15!46;UBERON:0000344!1.60e-10!15;UBERON:0000485!7.17e-09!11;UBERON:0001242!8.86e-09!13;UBERON:0000060!8.86e-09!13;UBERON:0001262!8.86e-09!13;UBERON:0004786!8.86e-09!13;UBERON:0003350!1.24e-07!9;UBERON:0004808!1.24e-07!9;UBERON:0001277!1.24e-07!9;UBERON:0002193!4.92e-07!48;UBERON:0002405!4.92e-07!48
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.121181,0.96259,0.434198,0.720982,0.448401,0.538088,0.515265,0.181564,0.0447303,0.494602,0.526159,0.173454,0.550255,0.275867,0,0.742571,0.252772,0.160384,0.620214,0.332107,0.223663,1.35437,0.717658,0.374936,0.577606,0.153291,0.469052,0.818708,0.376624,0.455168,0.843667,0.699026,0.136998,0.757987,0.363049,0.242032,0.522578,0.221921,0.195877,0.256422,0.460258,0.450632,0.27776,0.0824666,0.423266,0.662995,0.484612,0.170971,0.825035,0.725127,0.604356,0.362495,0.985264,1.00271,1.37128,0.314394,0.513517,0.145699,0.555328,0.823643,0.613749,0.560836,0.713876,1.39465,0.754324,1.139,1.48833,0.818971,1.34113,0.922232,0.178433,0.0665967,1.03623,0.433216,0.131016,0.42492,0.651651,0.806481,0.892913,0.530481,0.759925,0.612313,0.501608,0.920903,0.491838,0.0299392,0.118251,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,0.202284,0.510015,0.859272,1.59353,0.101559,1.26039,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,1.20804,0.340849,0.333829,0.386136,0.96962,0.337254,0.499714,1.21576,0.254749,0.143112,1.11602,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,1.34763,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,1.25705,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.724779,0.120154,0.0553085,0.986833,0.207643,0.569994,1.06851,0.605358,0.782826,0.39061,0.400939,1.1977,0.920047,0.810622,0.998505,1.70092,0.562634,0.676555,0.524587,0.166768
}}
}}

Revision as of 19:03, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:80289414..80289438,+p1@Oaz1
Mm9::chr17:80333927..80333940,-p@chr17:80333927..80333940
-
Mm9::chr2:121854322..121854334,+p2@Gm9781
Mm9::chr2:157727184..157727213,+p1@ENSMUST00000121302
Mm9::chr2:170110460..170110480,+p1@ENSMUST00000118388
Mm9::chr3:95231497..95231510,+p1@Gm4349
Mm9::chr3:96433842..96433878,+p1@Rbm8a
Mm9::chr7:144562355..144562367,+p@chr7:144562355..144562367
+


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:0008073ornithine decarboxylase inhibitor activity0.016159955885354
GO:0042979ornithine decarboxylase regulator activity0.016159955885354
GO:0006595polyamine metabolic process0.02584813721866
GO:0000184mRNA catabolic process, nonsense-mediated decay0.02584813721866
GO:0006402mRNA catabolic process0.0273101551622031
GO:0003729mRNA binding0.0273101551622031
GO:0006401RNA catabolic process0.0273101551622031
GO:0051028mRNA transport0.0273101551622031
GO:0050658RNA transport0.0273101551622031
GO:0051236establishment of RNA localization0.0273101551622031
GO:0050657nucleic acid transport0.0273101551622031
GO:0006403RNA localization0.0273101551622031
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.0273101551622031
GO:0006576biogenic amine metabolic process0.0331823158039291
GO:0006575amino acid derivative metabolic process0.0374068710784698



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
somatic cell1.09e-17118
hematopoietic cell4.92e-1732
hematopoietic oligopotent progenitor cell4.92e-1732
hematopoietic stem cell4.92e-1732
angioblastic mesenchymal cell4.92e-1732
hematopoietic multipotent progenitor cell4.92e-1732
animal cell5.79e-16115
eukaryotic cell5.79e-16115
connective tissue cell3.95e-1546
mesenchymal cell3.95e-1546
hematopoietic lineage restricted progenitor cell7.93e-1525
epithelial cell3.13e-1425
endo-epithelial cell4.27e-1415
motile cell1.04e-1354
lymphoid lineage restricted progenitor cell4.62e-1212
mature alpha-beta T cell4.22e-119
alpha-beta T cell4.22e-119
immature T cell4.22e-119
mature T cell4.22e-119
immature alpha-beta T cell4.22e-119
endodermal cell4.99e-1120
leukocyte6.64e-1117
nongranular leukocyte6.64e-1117
T cell6.91e-1111
pro-T cell6.91e-1111
lymphocyte7.56e-1113
common lymphoid progenitor7.56e-1113
CD4-positive, alpha-beta T cell7.05e-108
stem cell8.15e-1097
nucleate cell9.68e-1016
common myeloid progenitor7.71e-0819
thymocyte8.09e-086
double negative thymocyte8.09e-086
naive T cell8.09e-086
double-positive, alpha-beta thymocyte8.09e-086
CD4-positive, alpha-beta thymocyte8.09e-086
naive thymus-derived CD4-positive, alpha-beta T cell8.09e-086
DN4 thymocyte8.09e-086
DN1 thymic pro-T cell8.09e-086
DN2 thymocyte8.09e-086
DN3 thymocyte8.09e-086
immature single positive thymocyte8.09e-086
early T lineage precursor8.09e-086
mature CD4 single-positive thymocyte8.09e-086
resting double-positive thymocyte8.09e-086
double-positive blast8.09e-086
CD69-positive double-positive thymocyte8.09e-086
CD69-positive, CD4-positive single-positive thymocyte8.09e-086
CD4-positive, CD8-intermediate double-positive thymocyte8.09e-086
CD24-positive, CD4 single-positive thymocyte8.09e-086
intestinal epithelial cell1.24e-079
epithelial cell of alimentary canal1.24e-079
somatic stem cell8.18e-0791
multi fate stem cell8.18e-0791


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}}}

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:878&oldid=2562098"