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MCL coexpression mm9:1129: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002384!7.19e-20!46;UBERON:0000344!2.61e-11!15;UBERON:0001242!7.57e-09!13;UBERON:0000060!7.57e-09!13;UBERON:0001262!7.57e-09!13;UBERON:0004786!7.57e-09!13;UBERON:0000485!4.94e-08!11
|ontology_enrichment_uberon=UBERON:0002384!7.19e-20!46;UBERON:0000344!2.61e-11!15;UBERON:0001242!7.57e-09!13;UBERON:0000060!7.57e-09!13;UBERON:0001262!7.57e-09!13;UBERON:0004786!7.57e-09!13;UBERON:0000485!4.94e-08!11
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.161863,0.411716,0.480627,0.299217,0.495263,0.587291,0.206208,0.215218,0.219671,0.542749,0.575086,0.206435,0.599731,0.315771,0,0.795315,0.291368,0.561256,0.361892,0.374752,0.08187,0.598814,0.29769,0.419327,0.62766,0.184473,0.516511,0.344372,0.145661,0.50223,0.897561,0.289148,0.498917,0.848378,0.468714,0.279977,0.57142,1.32199,0.230656,0.800988,0.507468,0.258106,0.317766,0.277561,0.469348,0.714592,0.532496,0.219744,0.347313,0.777641,0.654933,0.139618,1.04034,1.0579,0.606984,0.356236,0.56214,0.176152,0.604914,0.877332,0.664501,0.226529,0.766235,1.49952,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.21183,0.293368,1.09164,0.17012,0.159969,0.498755,0.703064,0.859987,0.378988,0.212973,0.812889,0.663039,0.580284,0.975495,0.0369809,0.164297,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.237542,0.589174,0.913319,0.71485,0.399703,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,0.430942,1.02459,0.380122,0.547992,1.27206,0.293461,0.418498,1.21618,0.796633,0.757997,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.829907,1.00568,0.473246,1.16374,0.620831,1.29374,0.0806013,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.147909,0.0736236,1.04192,0.243291,0.619892,1.12411,0.655955,0.327731,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.278874,0.573477,0.227149
}}
}}

Revision as of 19:26, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr14:122230170..122230176,+p@chr14:122230170..122230176
+
Mm9::chr14:48189081..48189085,+p1@Gm6616
Mm9::chr18:75160143..75160153,+p4@Gm10294
p4@Rpl17
Mm9::chr19:37858699..37858749,+p@chr19:37858699..37858749
+
Mm9::chr1:39424719..39424730,+p3@Gm10191
p3@Gm13004
p3@Gm7689
p3@Gm8759
p3@LOC100505081
p3@LOC638399
p3@Rpl31
Mm9::chr7:58713316..58713326,+p1@ENSMUST00000077381
Mm9::chr9:57181873..57181884,+p1@Gm5121


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:0003735structural constituent of ribosome0.00114928015399592
GO:0005840ribosome0.00114928015399592
GO:0006412translation0.00426107607803767
GO:0030529ribonucleoprotein complex0.00426107607803767
GO:0009059macromolecule biosynthetic process0.00711973963157119
GO:0044249cellular biosynthetic process0.010248901411155
GO:0015934large ribosomal subunit0.0140788124567925
GO:0009058biosynthetic process0.0140788124567925
GO:0043228non-membrane-bound organelle0.0178799545036496
GO:0043232intracellular non-membrane-bound organelle0.0178799545036496
GO:0033279ribosomal subunit0.0178799545036496
GO:0032991macromolecular complex0.0279377444569467
GO:0044267cellular protein metabolic process0.0400583390841314
GO:0044260cellular macromolecule metabolic process0.0400583390841314
GO:0010467gene expression0.0400583390841314
GO:0019538protein metabolic process0.0400583390841314
GO:0044444cytoplasmic part0.0478671182542338



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 cell1.61e-2232
hematopoietic oligopotent progenitor cell1.61e-2232
hematopoietic stem cell1.61e-2232
angioblastic mesenchymal cell1.61e-2232
hematopoietic multipotent progenitor cell1.61e-2232
somatic cell2.54e-21118
motile cell3.14e-2054
connective tissue cell7.19e-2046
mesenchymal cell7.19e-2046
animal cell7.71e-20115
eukaryotic cell7.71e-20115
hematopoietic lineage restricted progenitor cell6.30e-1825
stem cell2.49e-1597
lymphoid lineage restricted progenitor cell3.18e-1312
leukocyte1.94e-1217
nongranular leukocyte1.94e-1217
mature alpha-beta T cell3.07e-129
alpha-beta T cell3.07e-129
immature T cell3.07e-129
mature T cell3.07e-129
immature alpha-beta T cell3.07e-129
T cell3.50e-1211
pro-T cell3.50e-1211
lymphocyte5.37e-1213
common lymphoid progenitor5.37e-1213
common myeloid progenitor1.13e-1119
nucleate cell3.07e-1116
CD4-positive, alpha-beta T cell3.37e-118
somatic stem cell1.10e-1091
multi fate stem cell1.10e-1091
epithelial cell2.73e-0925
thymocyte3.82e-096
double negative thymocyte3.82e-096
naive T cell3.82e-096
double-positive, alpha-beta thymocyte3.82e-096
CD4-positive, alpha-beta thymocyte3.82e-096
naive thymus-derived CD4-positive, alpha-beta T cell3.82e-096
DN4 thymocyte3.82e-096
DN1 thymic pro-T cell3.82e-096
DN2 thymocyte3.82e-096
DN3 thymocyte3.82e-096
immature single positive thymocyte3.82e-096
early T lineage precursor3.82e-096
mature CD4 single-positive thymocyte3.82e-096
resting double-positive thymocyte3.82e-096
double-positive blast3.82e-096
CD69-positive double-positive thymocyte3.82e-096
CD69-positive, CD4-positive single-positive thymocyte3.82e-096
CD4-positive, CD8-intermediate double-positive thymocyte3.82e-096
CD24-positive, CD4 single-positive thymocyte3.82e-096
myeloid cell3.08e-0816
endo-epithelial cell6.35e-0815

Uber Anatomy
Ontology termp-valuen
connective tissue7.19e-2046
mucosa2.61e-1115
intestinal mucosa7.57e-0913
anatomical wall7.57e-0913
wall of intestine7.57e-0913
gastrointestinal system mucosa7.57e-0913
simple columnar epithelium4.94e-0811


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}}}