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MCL coexpression mm9:241: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002384!3.66e-11!46;UBERON:0004177!5.09e-10!29;UBERON:0005057!5.09e-10!29;UBERON:0002390!6.61e-10!45;UBERON:0003061!6.61e-10!45;UBERON:0002193!5.29e-09!48;UBERON:0002405!5.29e-09!48;UBERON:0000077!5.70e-09!35;UBERON:0003929!2.97e-07!55;UBERON:0002370!6.14e-07!23;UBERON:0000974!6.14e-07!23;UBERON:0004807!6.14e-07!23;UBERON:0005058!6.14e-07!23;UBERON:0003351!6.14e-07!23;UBERON:0009113!6.14e-07!23;UBERON:0003295!6.14e-07!23;UBERON:0009722!6.14e-07!23;UBERON:0005562!6.14e-07!23;UBERON:0007690!6.14e-07!23
|ontology_enrichment_uberon=UBERON:0002384!3.66e-11!46;UBERON:0004177!5.09e-10!29;UBERON:0005057!5.09e-10!29;UBERON:0002390!6.61e-10!45;UBERON:0003061!6.61e-10!45;UBERON:0002193!5.29e-09!48;UBERON:0002405!5.29e-09!48;UBERON:0000077!5.70e-09!35;UBERON:0003929!2.97e-07!55;UBERON:0002370!6.14e-07!23;UBERON:0000974!6.14e-07!23;UBERON:0004807!6.14e-07!23;UBERON:0005058!6.14e-07!23;UBERON:0003351!6.14e-07!23;UBERON:0009113!6.14e-07!23;UBERON:0003295!6.14e-07!23;UBERON:0009722!6.14e-07!23;UBERON:0005562!6.14e-07!23;UBERON:0007690!6.14e-07!23
|tfbs_overrepresentation_for_novel_motifs=0.179293,0.0752559,0.353019,0.224784,0.169613,0.88676,0.355593,0.0637648,0.296659,0.648525,0.298295,0.339541,0.271958,1.22758,0.930644,0,0.234849,0.059344,0.233646,0.675985,0.120003,0.412111,0.37098,0.333169,0.36717,0.131253,0.359043,0.266282,0.7287,0.223466,0.24944,0.830362,0.80476,0.457471,0.625698,0.0994184,0.762338,0.33477,0.428683,0.0868443,0.16413,0.543836,1.05941,0.0762499,0.196692,0.0584129,1.02705,0.597765,0.491779,0.456879,0.63414,0.880283,0.112722,1.07812,0.434849,0.382021,0.480429,0.663481,0.193018,0.761483,0.796396,0.462675,0.329551,0.215255,0.126192,1.26392,0.551407,0.871196,0.289732,0.733632,0.318591,0.0219808,0.317273,0.462927,0.474893,0.618838,0.170117,0.174925,0.280507,0.294464,0.290274,1.97878,0.151098,0.419379,0.963995,0.877886,0.838608,0.223872,0.544194,1.02598,1.48882,0.372211,0.317967,0.0678504,0.112877,0.093986,0.434111,0.320112,1.0277,0.0895173,0.499565,0.308028,1.047,0.635092,0.222555,0.255044,0.264397,0.082328,0.879616,0.535364,0.389135,0.407566,0.86501,0.304852,0.619492,0.545356,0.494916,0.0641298,0.235751,0.0101565,0.467488,0.583146,0.81937,0.174363,0.668374,0.773729,0.114301,0.312808,0.550077,0.893686,0.392297,0.472633,0.524295,0.40098,0.638919,0.0571551,0.737039,0.0739723,0.59486,1.3849,0.995371,0.555542,0.430144,0.316186,0.218168,0.073569,0.184016,1.34592,0.0511204,0.172038,0.230707,1.28657,0.421705,0.865536,0.399685,0.490348,0.14703,0.406532,0.176772,0.418776,0.603336,0.367562,0.283555,0.683845,0.215941,0.778934,1.07117,0.337444,0.0767843
}}
}}

Revision as of 18:02, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr11:104171122..104171127,+p@chr11:104171122..104171127
+
Mm9::chr11:52174441..52174457,-p@chr11:52174441..52174457
-
Mm9::chr11:68886926..68886931,+p1@ENSMUST00000082965
Mm9::chr11:95720195..95720215,+p1@ENSMUST00000146868
p1@uc007law.1
Mm9::chr13:22133226..22133232,-p5@Hist1h4c
p5@Hist1h4d
p5@Hist1h4f
p5@Hist1h4h
p5@Hist1h4i
p5@Hist1h4j
p5@Hist1h4k
p5@Hist1h4m
p5@Hist1h4n
p6@Hist1h4a
p6@Hist1h4b
p6@Hist2h4
p6@Hist4h4
Mm9::chr16:17148308..17148320,-p@chr16:17148308..17148320
-
Mm9::chr16:17554899..17554907,-p2@4930451C15Rik
Mm9::chr17:39982953..39982969,-p@chr17:39982953..39982969
-
Mm9::chr17:69766631..69766643,-p@chr17:69766631..69766643
-
Mm9::chr18:85018335..85018342,+p@chr18:85018335..85018342
+
Mm9::chr19:7093818..7093829,-p3@Fermt3
Mm9::chr2:12901236..12901237,-p1@ENSMUST00000158941
Mm9::chr2:156853529..156853540,-p7@9830001H06Rik
Mm9::chr2:31095001..31095006,-p@chr2:31095001..31095006
-
Mm9::chr2:92274608..92274611,-p2@Cry2
Mm9::chr3:106525050..106525057,+p@chr3:106525050..106525057
+
Mm9::chr3:88100320..88100332,-p@chr3:88100320..88100332
-
Mm9::chr3:96023781..96023796,+p2@Hist2h2ab
Mm9::chr4:107475970..107475974,-p@chr4:107475970..107475974
-
Mm9::chr4:107476279..107476302,-p@chr4:107476279..107476302
-
Mm9::chr4:134409768..134409794,-p@chr4:134409768..134409794
-
Mm9::chr4:135734188..135734201,+p@chr4:135734188..135734201
+
Mm9::chr4:154975381..154975386,+p7@Slc35e2
Mm9::chr6:47738177..47738187,-p2@ENSMUST00000083767
Mm9::chr7:134339697..134339710,+p@chr7:134339697..134339710
+
Mm9::chr7:148744394..148744397,+p@chr7:148744394..148744397
+
Mm9::chr7:152024495..152024519,+p1@Fgf3
Mm9::chr7:152082369..152082376,+p2@Fgf15
Mm9::chr7:29595220..29595257,-p@chr7:29595220..29595257
-
Mm9::chr7:4740532..4740555,+p@chr7:4740532..4740555
+
Mm9::chr8:129468876..129468878,-p1@ENSMUST00000083703
Mm9::chr8:26610056..26610057,-p@chr8:26610056..26610057
-
Mm9::chr9:20837766..20837781,-p@chr9:20837766..20837781
-
Mm9::chrX:11582947..11582949,+p@chrX:11582947..11582949
+
Mm9::chrX:133654667..133654672,-p1@Esx1


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:0005104fibroblast growth factor receptor binding0.00313765220463548
GO:0006334nucleosome assembly0.0213505593954297
GO:0000786nucleosome0.0213505593954297
GO:0031497chromatin assembly0.0213505593954297
GO:0003913DNA photolyase activity0.0213505593954297
GO:0065004protein-DNA complex assembly0.0213505593954297
GO:0006333chromatin assembly or disassembly0.0213505593954297
GO:0006259DNA metabolic process0.0213505593954297
GO:0008083growth factor activity0.0219511109229636
GO:0000785chromatin0.032931276727162
GO:0005125cytokine activity0.0366841803551525
GO:0048538thymus development0.0372475257366139
GO:0009881photoreceptor activity0.0372475257366139
GO:0018298protein-chromophore linkage0.0372475257366139
GO:0006325establishment and/or maintenance of chromatin architecture0.0372475257366139
GO:0006323DNA packaging0.0372475257366139
GO:0010092specification of organ identity0.0372475257366139
GO:0001759induction of an organ0.0372475257366139
GO:0044427chromosomal part0.0372475257366139
GO:0031128induction0.0372475257366139
GO:0045168cell-cell signaling during cell fate commitment0.0372475257366139
GO:0065003macromolecular complex assembly0.0390702222401256
GO:0005634nucleus0.0416675625033155
GO:0005694chromosome0.0451706917797152
GO:0022607cellular component assembly0.0470825267985147
GO:0051276chromosome organization and biogenesis0.0470825267985147
GO:0001755neural crest cell migration0.0475237234237468



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 cell2.48e-1632
hematopoietic oligopotent progenitor cell2.48e-1632
hematopoietic stem cell2.48e-1632
angioblastic mesenchymal cell2.48e-1632
hematopoietic multipotent progenitor cell2.48e-1632
nucleate cell1.12e-1216
lymphoid lineage restricted progenitor cell2.88e-1112
connective tissue cell3.66e-1146
mesenchymal cell3.66e-1146
hematopoietic lineage restricted progenitor cell1.93e-1025
lymphocyte2.94e-1013
common lymphoid progenitor2.94e-1013
T cell1.18e-0911
pro-T cell1.18e-0911
motile cell8.76e-0954
stem cell3.45e-0897
common myeloid progenitor1.14e-0719
CD4-positive, alpha-beta T cell1.34e-078
leukocyte2.03e-0717
nongranular leukocyte2.03e-0717
thymocyte2.29e-076
double negative thymocyte2.29e-076
naive T cell2.29e-076
double-positive, alpha-beta thymocyte2.29e-076
CD4-positive, alpha-beta thymocyte2.29e-076
naive thymus-derived CD4-positive, alpha-beta T cell2.29e-076
DN4 thymocyte2.29e-076
DN1 thymic pro-T cell2.29e-076
DN2 thymocyte2.29e-076
DN3 thymocyte2.29e-076
immature single positive thymocyte2.29e-076
early T lineage precursor2.29e-076
mature CD4 single-positive thymocyte2.29e-076
resting double-positive thymocyte2.29e-076
double-positive blast2.29e-076
CD69-positive double-positive thymocyte2.29e-076
CD69-positive, CD4-positive single-positive thymocyte2.29e-076
CD4-positive, CD8-intermediate double-positive thymocyte2.29e-076
CD24-positive, CD4 single-positive thymocyte2.29e-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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