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MCL coexpression mm9:308: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002384!6.79e-18!46;UBERON:0000344!6.87e-14!15;UBERON:0001242!2.57e-11!13;UBERON:0000060!2.57e-11!13;UBERON:0001262!2.57e-11!13;UBERON:0004786!2.57e-11!13;UBERON:0000485!3.80e-11!11;UBERON:0003350!1.61e-09!9;UBERON:0004808!1.61e-09!9;UBERON:0001277!1.61e-09!9;UBERON:0004923!2.43e-07!24;UBERON:0002193!6.25e-07!48;UBERON:0002405!6.25e-07!48
|ontology_enrichment_uberon=UBERON:0002384!6.79e-18!46;UBERON:0000344!6.87e-14!15;UBERON:0001242!2.57e-11!13;UBERON:0000060!2.57e-11!13;UBERON:0001262!2.57e-11!13;UBERON:0004786!2.57e-11!13;UBERON:0000485!3.80e-11!11;UBERON:0003350!1.61e-09!9;UBERON:0004808!1.61e-09!9;UBERON:0001277!1.61e-09!9;UBERON:0004923!2.43e-07!24;UBERON:0002193!6.25e-07!48;UBERON:0002405!6.25e-07!48
|tfbs_overrepresentation_for_novel_motifs=0.621914,0.734167,0.264934,0.357342,0.13626,0.378043,0.173296,0.802044,0.169209,0.201274,0.44746,0.165604,0.52939,0.181267,0.633867,0,0.321317,0.882528,1.03294,0.980393,1.25234,0.195815,1.61733,0.316587,0.0801894,0.199623,0.444085,0.811999,0.0490134,0.0736806,0.388015,0.403236,0.0308777,0.377102,0.153647,0.069489,0.28244,0.95082,1.08815,0.626782,0.132316,0.395563,1.04718,0.640187,0.0101868,0.696406,0.260475,0.139809,0.639076,0.187406,0.307679,0.218134,0.680586,0.524674,0.540069,0.546195,0.197567,0.927074,0.235144,0.184626,0.386651,0.638588,0.187517,0.80944,1.07232,0.880487,0.662968,0.992392,0.382806,0.851665,0.517607,0.550805,0.057172,0.569888,0.0357104,1.11649,0.098925,0.702334,1.73008,0.22435,0.165658,0.890404,0.636199,0.295929,0.468641,0.00212005,0.00317853,0.164918,0.729995,1.14963,0.72731,0.472928,0.41392,0.600223,0.021752,0.20598,0.151563,0.416272,0.722077,1.45087,0.0283065,0.403003,0.509378,0.308141,0.828295,0.394918,0.354606,0.137427,0.497774,0.831712,0.0856504,0.510939,0.225717,0.149001,0.733862,0.564124,0.0814819,0.732983,0.322341,1.18719,0.574718,1.41182,0.20086,0.251444,0.784453,0.375593,0.178582,0.408257,0.661578,0.337079,0.494561,0.106861,0.634573,0.195077,0.753996,0.0177816,0.310556,0.126256,0.708276,1.51166,1.11861,0.667289,0.209097,0.411967,0.302305,0.125712,0.726958,1.47245,0.0944245,0.0343953,0.076247,0.0140779,1.30495,1.38393,0.566627,0.598868,0.624647,0.165822,0.0878751,0.0931012,0.717087,0.467905,0.375957,0.0845658,0.811218,0.1895,0.280354,0.494051,0.0956157
}}
}}

Revision as of 18:09, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:28749875..28749924,+p@chr10:28749875..28749924
+
Mm9::chr10:43243886..43243899,+p2@ENSMUST00000057649
Mm9::chr12:24587988..24588001,+p@chr12:24587988..24588001
+
Mm9::chr12:70223961..70223973,+p@chr12:70223961..70223973
+
Mm9::chr13:118018159..118018169,+p@chr13:118018159..118018169
+
Mm9::chr14:28023521..28023536,+p@chr14:28023521..28023536
+
Mm9::chr15:81296769..81296795,+p1@Gm9840
p1@Rbx1
Mm9::chr17:47547801..47547833,+p@chr17:47547801..47547833
+
Mm9::chr18:38873969..38873988,+p@chr18:38873969..38873988
+
Mm9::chr19:25107619..25107626,+p@chr19:25107619..25107626
+
Mm9::chr19:28838027..28838030,-p1@Gm6788
Mm9::chr1:13426571..13426575,+p@chr1:13426571..13426575
+
Mm9::chr1:15057084..15057123,+p@chr1:15057084..15057123
+
Mm9::chr2:150131486..150131493,+p1@ENSMUST00000120921
Mm9::chr2:36244522..36244568,+p1@ENSMUST00000121366
Mm9::chr2:52475255..52475266,+p2@Bloc1s2
p2@Gm13540
Mm9::chr2:80479001..80479013,+p3@Nup35
Mm9::chr4:116821517..116821519,+p1@ENSMUST00000118674
Mm9::chr4:34432983..34433015,+p2@ENSMUST00000117487
Mm9::chr7:144629334..144629355,+p1@Gm12669
Mm9::chr7:3181067..3181081,+p@chr7:3181067..3181081
+
Mm9::chr7:54087766..54087785,+p2@Gm5331
Mm9::chr7:54087805..54087833,+p1@Gm5331
Mm9::chr9:120293968..120293975,+p1@ENSMUST00000118890
Mm9::chr9:48258428..48258437,+p5@Gm5616
p5@LOC100045968
p5@LOC100505330
p5@Nhp2l1
Mm9::chrX:101543820..101543838,-p1@ENSMUST00000120233


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:0009055electron carrier activity0.0235749622765852
GO:0015035protein disulfide oxidoreductase activity0.030000362435492
GO:0006118electron transport0.030000362435492
GO:0031975envelope0.030000362435492
GO:0031967organelle envelope0.030000362435492
GO:0015036disulfide oxidoreductase activity0.030000362435492
GO:0006091generation of precursor metabolites and energy0.030000362435492
GO:0031090organelle membrane0.0382432531186327
GO:0045454cell redox homeostasis0.0382432531186327
GO:0016491oxidoreductase activity0.0382432531186327
GO:0008137NADH dehydrogenase (ubiquinone) activity0.0382432531186327
GO:0003954NADH dehydrogenase activity0.0382432531186327
GO:0050136NADH dehydrogenase (quinone) activity0.0382432531186327
GO:0051028mRNA transport0.0382432531186327
GO:0016655oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor0.0382432531186327
GO:0050658RNA transport0.0382432531186327
GO:0051236establishment of RNA localization0.0382432531186327
GO:0050657nucleic acid transport0.0382432531186327
GO:0006403RNA localization0.0382432531186327
GO:0005643nuclear pore0.0382432531186327
GO:0065002intracellular protein transport across a membrane0.0382432531186327
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.0382432531186327
GO:0046930pore complex0.0382432531186327
GO:0044453nuclear membrane part0.0395589900222561
GO:0031965nuclear membrane0.0395589900222561
GO:0016651oxidoreductase activity, acting on NADH or NADPH0.0398389700056067



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 cell4.06e-24118
animal cell6.87e-22115
eukaryotic cell6.87e-22115
hematopoietic cell5.21e-2032
hematopoietic oligopotent progenitor cell5.21e-2032
hematopoietic stem cell5.21e-2032
angioblastic mesenchymal cell5.21e-2032
hematopoietic multipotent progenitor cell5.21e-2032
connective tissue cell6.79e-1846
mesenchymal cell6.79e-1846
motile cell6.78e-1754
hematopoietic lineage restricted progenitor cell1.03e-1625
epithelial cell4.03e-1625
endo-epithelial cell1.32e-1415
stem cell3.94e-1497
lymphoid lineage restricted progenitor cell3.33e-1212
endodermal cell7.66e-1220
leukocyte1.05e-1117
nongranular leukocyte1.05e-1117
T cell4.41e-1111
pro-T cell4.41e-1111
lymphocyte4.84e-1113
common lymphoid progenitor4.84e-1113
mature alpha-beta T cell5.42e-119
alpha-beta T cell5.42e-119
immature T cell5.42e-119
mature T cell5.42e-119
immature alpha-beta T cell5.42e-119
somatic stem cell3.08e-1091
multi fate stem cell3.08e-1091
common myeloid progenitor3.16e-1019
nucleate cell3.78e-1016
CD4-positive, alpha-beta T cell4.81e-108
intestinal epithelial cell1.61e-099
epithelial cell of alimentary canal1.61e-099
thymocyte5.16e-086
double negative thymocyte5.16e-086
naive T cell5.16e-086
double-positive, alpha-beta thymocyte5.16e-086
CD4-positive, alpha-beta thymocyte5.16e-086
naive thymus-derived CD4-positive, alpha-beta T cell5.16e-086
DN4 thymocyte5.16e-086
DN1 thymic pro-T cell5.16e-086
DN2 thymocyte5.16e-086
DN3 thymocyte5.16e-086
immature single positive thymocyte5.16e-086
early T lineage precursor5.16e-086
mature CD4 single-positive thymocyte5.16e-086
resting double-positive thymocyte5.16e-086
double-positive blast5.16e-086
CD69-positive double-positive thymocyte5.16e-086
CD69-positive, CD4-positive single-positive thymocyte5.16e-086
CD4-positive, CD8-intermediate double-positive thymocyte5.16e-086
CD24-positive, CD4 single-positive thymocyte5.16e-086
columnar/cuboidal epithelial cell9.20e-087
myeloid cell1.43e-0716
brush border epithelial cell6.22e-076
gut absorptive cell6.22e-076
absorptive cell6.22e-076
enterocyte6.22e-076


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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