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MCL coexpression mm9:415: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000344!1.22e-16!15;UBERON:0002384!1.84e-16!46;UBERON:0001242!1.06e-13!13;UBERON:0000060!1.06e-13!13;UBERON:0001262!1.06e-13!13;UBERON:0004786!1.06e-13!13;UBERON:0000485!2.42e-13!11;UBERON:0003350!1.34e-11!9;UBERON:0004808!1.34e-11!9;UBERON:0001277!1.34e-11!9;UBERON:0004923!5.93e-09!24
|ontology_enrichment_uberon=UBERON:0000344!1.22e-16!15;UBERON:0002384!1.84e-16!46;UBERON:0001242!1.06e-13!13;UBERON:0000060!1.06e-13!13;UBERON:0001262!1.06e-13!13;UBERON:0004786!1.06e-13!13;UBERON:0000485!2.42e-13!11;UBERON:0003350!1.34e-11!9;UBERON:0004808!1.34e-11!9;UBERON:0001277!1.34e-11!9;UBERON:0004923!5.93e-09!24
|tfbs_overrepresentation_for_novel_motifs=0.162057,0.134766,0.444727,0.191238,0.572598,0.583749,0.270195,0.340454,0.040605,0.0489646,0.236307,0.722367,0.0372188,0.27987,0.295744,0,0.44163,0.0750368,0.307533,0.136088,0.121654,0.0810878,0.279154,0.26934,0.149704,0.301898,0.0293349,0.216938,0.103721,0.203444,0.206597,0.531719,0.257084,0.101305,0.296456,0.00193047,0.0693463,0.257981,0.0591424,0.0468666,0.265799,0.210373,0.0688446,0.298695,0.00273825,0.183361,0.372907,0.6478,0.0489995,0.343195,0.426383,0.323798,0.190678,0.661847,0.67813,0.28555,0.110603,0.25091,0.27058,0.283926,0.513661,0.331566,0.045155,1.06984,0.294453,0.451957,0.806865,1.14503,0.509463,1.00145,0.414221,0.353861,0.0300638,0.709559,0.105151,0.234413,0.0235315,0.363297,1.24575,0.392419,0.640048,0.456892,0.879999,0.139579,0.602212,0.053467,0.00700265,0.203713,0.377064,1.30447,0.873554,0.606796,0.543309,0.587829,0.057338,0.416353,0.0362583,0.545856,0.373124,0.328581,0.244202,0.531465,0.645628,0.4269,0.425983,0.21005,0.478524,0.225669,0.127231,0.388577,0.157325,0.647285,0.124928,0.240232,0.880323,0.0761019,0.0863406,0.565346,0.442771,0.0675617,0.714636,0.398522,0.303371,0.362534,0.932468,0.501574,0.276618,0.53717,0.805419,0.284377,0.629874,0.186072,0.777296,0.296474,0.9011,0.0259009,0.501821,0.607069,0.853868,1.66928,1.27308,0.811357,0.313144,0.541193,0.420352,0.210705,0.375553,1.62988,0.169369,0.0799646,0.0181622,0.00366709,0.66331,0.0522757,0.29573,0.739975,0.324625,0.0943424,0.160402,0.167568,0.862985,0.601424,0.501973,0.15582,0.417485,0.289792,0.242542,0.259556,0.00651025
}}
}}

Revision as of 18:19, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:42069681..42069682,+p@chr10:42069681..42069682
+
Mm9::chr11:54012860..54012868,+p1@ENSMUST00000081565
Mm9::chr13:74543835..74543844,+p4@Ftl1
Mm9::chr17:7183242..7183261,+p1@Rnaset2a
p1@Rnaset2b
Mm9::chr17:87477595..87477607,+p1@ENSMUST00000090731
Mm9::chr2:175868413..175868426,+p1@Gm6710
p2@Gm14391
Mm9::chr2:35195857..35195886,+p1@ENSMUST00000120770
Mm9::chr2:90213339..90213368,+p@chr2:90213339..90213368
+
Mm9::chr3:155177407..155177427,+p@chr3:155177407..155177427
+
Mm9::chr4:32138685..32138706,+p1@ENSMUST00000118472
Mm9::chr5:123516216..123516243,+p1@ENSMUST00000119611
Mm9::chrM:5319..5333,+p1@COX1
Mm9::chrM:5722..5731,+p6@uc009vey.1
Mm9::chrM:6239..6248,+p@chrM:6239..6248
+
Mm9::chrM:7024..7052,+p1@uc009vez.1
Mm9::chrM:8600..8616,+p1@COX3
Mm9::chrM:8618..8619,+p@chrM:8618..8619
+
Mm9::chrM:8962..8969,+p@chrM:8962..8969
+


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:0004666prostaglandin-endoperoxide synthase activity3.89009571904692e-06
GO:0046457prostanoid biosynthetic process3.62916469088e-05
GO:0001516prostaglandin biosynthetic process3.62916469088e-05
GO:0006693prostaglandin metabolic process6.06367358332774e-05
GO:0006692prostanoid metabolic process6.06367358332774e-05
GO:0030216keratinocyte differentiation0.000153134506745507
GO:0046456icosanoid biosynthetic process0.000153134506745507
GO:0006690icosanoid metabolic process0.000186301976999254
GO:0005506iron ion binding0.000186301976999254
GO:0004601peroxidase activity0.000186301976999254
GO:0016684oxidoreductase activity, acting on peroxide as acceptor0.000186301976999254
GO:0008217regulation of blood pressure0.000252154800350663
GO:0006979response to oxidative stress0.000295315933460486
GO:0051213dioxygenase activity0.000428520525538543
GO:0016702oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen0.000428520525538543
GO:0016701oxidoreductase activity, acting on single donors with incorporation of molecular oxygen0.000428520525538543
GO:0006633fatty acid biosynthetic process0.000534209130421097
GO:0016053organic acid biosynthetic process0.000535274786417597
GO:0046394carboxylic acid biosynthetic process0.000535274786417597
GO:0065008regulation of biological quality0.000782351827223182
GO:0008015blood circulation0.000784158683003003
GO:0003013circulatory system process0.000784158683003003
GO:0020037heme binding0.000981680819807866
GO:0046906tetrapyrrole binding0.000981680819807866
GO:0016705oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen0.00119512058405546
GO:0005792microsome0.00172063762134358
GO:0042598vesicular fraction0.0017444587094867
GO:0006631fatty acid metabolic process0.00174688220475826
GO:0032787monocarboxylic acid metabolic process0.00298215665127091
GO:0008610lipid biosynthetic process0.00353457034005823
GO:0006118electron transport0.00602689689208029
GO:0042640anagen0.00716661879967187
GO:0008199ferric iron binding0.00716661879967187
GO:0048820hair follicle maturation0.00900010873064759
GO:0006091generation of precursor metabolites and energy0.00900010873064759
GO:0042221response to chemical stimulus0.00935044996864805
GO:0005624membrane fraction0.00966493200881029
GO:0019752carboxylic acid metabolic process0.00966493200881029
GO:0006082organic acid metabolic process0.00966493200881029
GO:0000267cell fraction0.0115122084135358
GO:0044255cellular lipid metabolic process0.0116806601661614
GO:0055072iron ion homeostasis0.0131847305268283
GO:0006879cellular iron ion homeostasis0.0131847305268283
GO:0006629lipid metabolic process0.0141700903658431
GO:0006826iron ion transport0.0141700903658431
GO:0046914transition metal ion binding0.0164872840486589
GO:0005783endoplasmic reticulum0.0180704133387437
GO:0022404molting cycle process0.0188732725824415
GO:0001942hair follicle development0.0188732725824415
GO:0022405hair cycle process0.0188732725824415
GO:0006950response to stress0.0191356268445424
GO:0042633hair cycle0.0191356268445424
GO:0042303molting cycle0.0191356268445424
GO:0016491oxidoreductase activity0.0194942515739056
GO:0048589developmental growth0.0205754867926271
GO:0044249cellular biosynthetic process0.0230587317209953
GO:0000041transition metal ion transport0.0239699767016792
GO:0044444cytoplasmic part0.0306017770355671
GO:0043169cation binding0.0329474628057774
GO:0021700developmental maturation0.0356308322922689
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.0361361919428277
GO:0008544epidermis development0.0361361919428277
GO:0055066di-, tri-valent inorganic cation homeostasis0.0361361919428277
GO:0009058biosynthetic process0.0361361919428277
GO:0007398ectoderm development0.036474269846928
GO:0030003cellular cation homeostasis0.0366419168396595
GO:0046872metal ion binding0.0366419168396595
GO:0055080cation homeostasis0.0369180792714478
GO:0043167ion binding0.0377095642421444
GO:0015674di-, tri-valent inorganic cation transport0.0444824625843817
GO:0055082cellular chemical homeostasis0.0468260302002133
GO:0006873cellular ion homeostasis0.0468260302002133
GO:0065007biological regulation0.0468260302002133



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 cell1.71e-22118
animal cell3.08e-20115
eukaryotic cell3.08e-20115
hematopoietic cell3.78e-1832
hematopoietic oligopotent progenitor cell3.78e-1832
hematopoietic stem cell3.78e-1832
angioblastic mesenchymal cell3.78e-1832
hematopoietic multipotent progenitor cell3.78e-1832
hematopoietic lineage restricted progenitor cell4.03e-1725
epithelial cell1.36e-1625
connective tissue cell1.84e-1646
mesenchymal cell1.84e-1646
motile cell1.83e-1554
endo-epithelial cell2.20e-1415
stem cell6.65e-1397
lymphoid lineage restricted progenitor cell1.05e-1212
leukocyte3.74e-1217
nongranular leukocyte3.74e-1217
endodermal cell8.11e-1220
intestinal epithelial cell1.34e-119
epithelial cell of alimentary canal1.34e-119
T cell1.40e-1111
pro-T cell1.40e-1111
mature alpha-beta T cell1.52e-119
alpha-beta T cell1.52e-119
immature T cell1.52e-119
mature T cell1.52e-119
immature alpha-beta T cell1.52e-119
lymphocyte1.64e-1113
common lymphoid progenitor1.64e-1113
nucleate cell1.85e-1016
CD4-positive, alpha-beta T cell2.85e-108
columnar/cuboidal epithelial cell8.73e-107
somatic stem cell4.19e-0991
multi fate stem cell4.19e-0991
brush border epithelial cell6.90e-096
gut absorptive cell6.90e-096
absorptive cell6.90e-096
enterocyte6.90e-096
common myeloid progenitor2.70e-0819
thymocyte4.45e-086
double negative thymocyte4.45e-086
naive T cell4.45e-086
double-positive, alpha-beta thymocyte4.45e-086
CD4-positive, alpha-beta thymocyte4.45e-086
naive thymus-derived CD4-positive, alpha-beta T cell4.45e-086
DN4 thymocyte4.45e-086
DN1 thymic pro-T cell4.45e-086
DN2 thymocyte4.45e-086
DN3 thymocyte4.45e-086
immature single positive thymocyte4.45e-086
early T lineage precursor4.45e-086
mature CD4 single-positive thymocyte4.45e-086
resting double-positive thymocyte4.45e-086
double-positive blast4.45e-086
CD69-positive double-positive thymocyte4.45e-086
CD69-positive, CD4-positive single-positive thymocyte4.45e-086
CD4-positive, CD8-intermediate double-positive thymocyte4.45e-086
CD24-positive, CD4 single-positive thymocyte4.45e-086


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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