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MCL coexpression mm9:231: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003350!2.10e-13!9;UBERON:0004808!2.10e-13!9;UBERON:0001277!2.10e-13!9;UBERON:0000485!4.49e-13!11;UBERON:0002384!4.52e-12!46;UBERON:0000490!5.72e-12!66;UBERON:0003929!7.31e-11!55;UBERON:0005911!6.07e-10!69;UBERON:0000072!1.11e-09!27;UBERON:0002370!6.66e-09!23;UBERON:0000974!6.66e-09!23;UBERON:0004807!6.66e-09!23;UBERON:0005058!6.66e-09!23;UBERON:0003351!6.66e-09!23;UBERON:0009113!6.66e-09!23;UBERON:0003295!6.66e-09!23;UBERON:0009722!6.66e-09!23;UBERON:0005562!6.66e-09!23;UBERON:0007690!6.66e-09!23;UBERON:0001242!1.11e-08!13;UBERON:0000060!1.11e-08!13;UBERON:0001262!1.11e-08!13;UBERON:0004786!1.11e-08!13;UBERON:0006562!2.10e-08!24;UBERON:0003408!2.10e-08!24;UBERON:0001557!2.10e-08!24;UBERON:0001042!2.10e-08!24;UBERON:0008814!2.10e-08!24;UBERON:0009145!2.10e-08!24;UBERON:0000065!8.07e-08!41;UBERON:0001004!1.56e-07!42;UBERON:0002193!1.72e-07!48;UBERON:0002405!1.72e-07!48;UBERON:0002390!2.80e-07!45;UBERON:0003061!2.80e-07!45;UBERON:0000344!2.83e-07!15;UBERON:0000064!6.40e-07!99
|ontology_enrichment_uberon=UBERON:0003350!2.10e-13!9;UBERON:0004808!2.10e-13!9;UBERON:0001277!2.10e-13!9;UBERON:0000485!4.49e-13!11;UBERON:0002384!4.52e-12!46;UBERON:0000490!5.72e-12!66;UBERON:0003929!7.31e-11!55;UBERON:0005911!6.07e-10!69;UBERON:0000072!1.11e-09!27;UBERON:0002370!6.66e-09!23;UBERON:0000974!6.66e-09!23;UBERON:0004807!6.66e-09!23;UBERON:0005058!6.66e-09!23;UBERON:0003351!6.66e-09!23;UBERON:0009113!6.66e-09!23;UBERON:0003295!6.66e-09!23;UBERON:0009722!6.66e-09!23;UBERON:0005562!6.66e-09!23;UBERON:0007690!6.66e-09!23;UBERON:0001242!1.11e-08!13;UBERON:0000060!1.11e-08!13;UBERON:0001262!1.11e-08!13;UBERON:0004786!1.11e-08!13;UBERON:0006562!2.10e-08!24;UBERON:0003408!2.10e-08!24;UBERON:0001557!2.10e-08!24;UBERON:0001042!2.10e-08!24;UBERON:0008814!2.10e-08!24;UBERON:0009145!2.10e-08!24;UBERON:0000065!8.07e-08!41;UBERON:0001004!1.56e-07!42;UBERON:0002193!1.72e-07!48;UBERON:0002405!1.72e-07!48;UBERON:0002390!2.80e-07!45;UBERON:0003061!2.80e-07!45;UBERON:0000344!2.83e-07!15;UBERON:0000064!6.40e-07!99
|tfbs_overrepresentation_for_novel_motifs=0.683155,1.12894,0.607382,0.213815,0.158125,0.497287,0.69671,0.0576812,0.450182,0.960429,0.597753,0.669176,0.252344,0.358132,0.355805,0,0.64442,0.0544716,0.362059,0.113976,0.27166,0.521483,0.356921,0.313575,0.982186,1.28609,0.333756,0.541549,0.695759,0.493616,0.511671,0.811158,0.50224,0.271358,3.66178,0.721318,0.724885,0.660965,0.229127,1.36561,0.152868,0.243838,0.134931,0.183623,0.862895,0.776173,0.520226,0.575595,0.144973,0.227531,0.616607,0.433626,1.72834,1.05744,0.425236,0.367773,0.0976851,0.64031,0.304202,0.113689,0.284859,0.877348,0.167995,1.1295,0.767927,0.235321,0.541105,0.859836,0.769624,0.722621,0.877924,0.142659,0.187406,0.453125,0.64162,0.395283,0.425755,0.168288,0.272308,0.278742,0.144565,0.239205,0.144928,0.235899,0.943925,0.98559,0.251875,0.331576,0.178324,1.01435,0.602595,0.363085,0.309353,0.06252,1.56508,0.086074,0.245602,0.837645,0.520611,2.21349,0.0482794,0.299519,1.02647,0.617549,0.215126,0.892076,0.712239,0.566847,0.530148,0.815818,0.662434,0.398154,0.28065,1.02234,0.608883,0.516703,0.590825,0.475191,0.646506,0.459994,0.457657,0.194256,0.126502,0.167736,0.657577,0.754951,0.108979,0.304247,0.539782,0.170045,0.383004,0.787977,0.514133,0.121912,0.628232,0.509039,2.0515,0.24548,0.584355,1.37293,0.983786,0.545219,0.415128,0.30759,0.605645,0.244366,0.524947,1.33397,1.1012,0.54213,0.945337,0.773589,0.412186,0.356655,0.12142,0.480377,0.140946,0.384749,0.0435255,0.399953,0.592794,0.358477,0.27532,0.0413831,1.13213,0.117512,0.468292,0.32399,0.759646
}}
}}

Revision as of 18:01, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:13684655..13684681,+p@chr10:13684655..13684681
+
Mm9::chr10:13684820..13684849,+p@chr10:13684820..13684849
+
Mm9::chr10:13685450..13685456,-p@chr10:13685450..13685456
-
Mm9::chr10:13685468..13685481,-p@chr10:13685468..13685481
-
Mm9::chr11:69224446..69224477,+p@chr11:69224446..69224477
+
Mm9::chr11:69224603..69224618,+p@chr11:69224603..69224618
+
Mm9::chr11:69225467..69225488,+p@chr11:69225467..69225488
+
Mm9::chr11:69572358..69572371,+p@chr11:69572358..69572371
+
Mm9::chr12:25336286..25336297,+p2@Klf11
Mm9::chr12:74692849..74692855,+p@chr12:74692849..74692855
+
Mm9::chr13:42148162..42148173,-p@chr13:42148162..42148173
-
Mm9::chr14:62299800..62299832,+p@chr14:62299800..62299832
+
Mm9::chr14:76234648..76234679,-p@chr14:76234648..76234679
-
Mm9::chr18:14941747..14941768,+p1@Taf4b
Mm9::chr18:4353243..4353254,-p3@Map3k8
Mm9::chr18:5591389..5591406,+p3@Zeb1
Mm9::chr18:80911813..80911827,+p@chr18:80911813..80911827
+
Mm9::chr19:36423891..36423907,-p@chr19:36423891..36423907
-
Mm9::chr19:46380054..46380065,-p2@uc008hss.1
Mm9::chr1:34491937..34491951,+p@chr1:34491937..34491951
+
Mm9::chr2:14971056..14971074,+p3@Arl5b
Mm9::chr2:34726609..34726633,+p@chr2:34726609..34726633
+
Mm9::chr3:108247192..108247215,+p@chr3:108247192..108247215
+
Mm9::chr3:145587837..145587859,-p@chr3:145587837..145587859
-
Mm9::chr5:134789543..134789566,+p@chr5:134789543..134789566
+
Mm9::chr5:53981417..53981431,-p@chr5:53981417..53981431
-
Mm9::chr6:48658128..48658158,-p3@Gimap6
Mm9::chr6:86422158..86422169,-p@chr6:86422158..86422169
-
Mm9::chr7:20214327..20214347,+p@chr7:20214327..20214347
+
Mm9::chr7:26474119..26474128,-p@chr7:26474119..26474128
-
Mm9::chr7:29164244..29164254,-p2@Zfp36
Mm9::chr8:87500597..87500641,+p@chr8:87500597..87500641
+
Mm9::chr8:87501892..87501899,-p@chr8:87501892..87501899
-
Mm9::chr9:107198554..107198566,+p4@Cish
Mm9::chr9:56266642..56266653,-p@chr9:56266642..56266653
-
Mm9::chr9:75255922..75255931,+p@chr9:75255922..75255931
+


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:0043283biopolymer metabolic process0.0460031566354788
GO:0045892negative regulation of transcription, DNA-dependent0.0460031566354788
GO:0050794regulation of cellular process0.0460031566354788
GO:0006351transcription, DNA-dependent0.0460031566354788
GO:0032774RNA biosynthetic process0.0460031566354788
GO:0048523negative regulation of cellular process0.0460031566354788
GO:0043170macromolecule metabolic process0.0460031566354788
GO:0048519negative regulation of biological process0.0460031566354788
GO:0006350transcription0.0460031566354788
GO:0016481negative regulation of transcription0.0460031566354788
GO:0050789regulation of biological process0.0460031566354788
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0460031566354788
GO:0016251general RNA polymerase II transcription factor activity0.0460031566354788
GO:0007205protein kinase C activation0.0465929420968227
GO:0031324negative regulation of cellular metabolic process0.0480820316684421
GO:0016070RNA metabolic process0.0485965440168064
GO:0065007biological regulation0.0485965440168064
GO:0009892negative regulation of metabolic process0.0485965440168064
GO:0004709MAP kinase kinase kinase activity0.0485965440168064



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
lymphoid lineage restricted progenitor cell3.58e-1712
mature alpha-beta T cell2.32e-169
alpha-beta T cell2.32e-169
immature T cell2.32e-169
mature T cell2.32e-169
immature alpha-beta T cell2.32e-169
hematopoietic cell4.40e-1632
hematopoietic oligopotent progenitor cell4.40e-1632
hematopoietic stem cell4.40e-1632
angioblastic mesenchymal cell4.40e-1632
hematopoietic multipotent progenitor cell4.40e-1632
T cell1.13e-1511
pro-T cell1.13e-1511
lymphocyte1.29e-1513
common lymphoid progenitor1.29e-1513
CD4-positive, alpha-beta T cell8.70e-158
intestinal epithelial cell2.10e-139
epithelial cell of alimentary canal2.10e-139
nucleate cell3.96e-1216
connective tissue cell4.52e-1246
mesenchymal cell4.52e-1246
somatic cell1.74e-11118
thymocyte2.15e-116
double negative thymocyte2.15e-116
naive T cell2.15e-116
double-positive, alpha-beta thymocyte2.15e-116
CD4-positive, alpha-beta thymocyte2.15e-116
naive thymus-derived CD4-positive, alpha-beta T cell2.15e-116
DN4 thymocyte2.15e-116
DN1 thymic pro-T cell2.15e-116
DN2 thymocyte2.15e-116
DN3 thymocyte2.15e-116
immature single positive thymocyte2.15e-116
early T lineage precursor2.15e-116
mature CD4 single-positive thymocyte2.15e-116
resting double-positive thymocyte2.15e-116
double-positive blast2.15e-116
CD69-positive double-positive thymocyte2.15e-116
CD69-positive, CD4-positive single-positive thymocyte2.15e-116
CD4-positive, CD8-intermediate double-positive thymocyte2.15e-116
CD24-positive, CD4 single-positive thymocyte2.15e-116
leukocyte3.05e-1117
nongranular leukocyte3.05e-1117
animal cell4.20e-11115
eukaryotic cell4.20e-11115
endo-epithelial cell9.18e-1115
motile cell1.91e-1054
stem cell1.38e-0997
epithelial cell1.48e-0925
hematopoietic lineage restricted progenitor cell1.94e-0925
brush border epithelial cell2.14e-096
gut absorptive cell2.14e-096
absorptive cell2.14e-096
enterocyte2.14e-096
endodermal cell3.10e-0920
columnar/cuboidal epithelial cell6.26e-087
somatic stem cell7.02e-0891
multi fate stem cell7.02e-0891

Uber Anatomy
Ontology termp-valuen
epithelium of mucosa2.10e-139
gastrointestinal system epithelium2.10e-139
intestinal epithelium2.10e-139
simple columnar epithelium4.49e-1311
connective tissue4.52e-1246
unilaminar epithelium5.72e-1266
gut epithelium7.31e-1155
endo-epithelium6.07e-1069
segment of respiratory tract1.11e-0927
thymus6.66e-0923
neck6.66e-0923
respiratory system epithelium6.66e-0923
hemolymphoid system gland6.66e-0923
pharyngeal epithelium6.66e-0923
thymic region6.66e-0923
pharyngeal gland6.66e-0923
entire pharyngeal arch endoderm6.66e-0923
thymus primordium6.66e-0923
early pharyngeal endoderm6.66e-0923
intestinal mucosa1.11e-0813
anatomical wall1.11e-0813
wall of intestine1.11e-0813
gastrointestinal system mucosa1.11e-0813
pharynx2.10e-0824
gland of gut2.10e-0824
upper respiratory tract2.10e-0824
chordate pharynx2.10e-0824
pharyngeal arch system2.10e-0824
pharyngeal region of foregut2.10e-0824
respiratory tract8.07e-0841
respiratory system1.56e-0742
hemolymphoid system1.72e-0748
immune system1.72e-0748
hematopoietic system2.80e-0745
blood island2.80e-0745
mucosa2.83e-0715
organ part6.40e-0799


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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