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MCL coexpression mm9:614: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001048!1.49e-09!134;UBERON:0001004!4.34e-09!42;UBERON:0000153!6.05e-09!43;UBERON:0000065!9.27e-09!41;UBERON:0007811!4.82e-08!36;UBERON:0004177!7.37e-08!29;UBERON:0005057!7.37e-08!29;UBERON:0000077!1.16e-07!35;UBERON:0003408!5.22e-07!24;UBERON:0000475!9.79e-07!150
|ontology_enrichment_uberon=UBERON:0001048!1.49e-09!134;UBERON:0001004!4.34e-09!42;UBERON:0000153!6.05e-09!43;UBERON:0000065!9.27e-09!41;UBERON:0007811!4.82e-08!36;UBERON:0004177!7.37e-08!29;UBERON:0005057!7.37e-08!29;UBERON:0000077!1.16e-07!35;UBERON:0003408!5.22e-07!24;UBERON:0000475!9.79e-07!150
|tfbs_overrepresentation_for_novel_motifs=0.737036,0.409645,0.686572,0.303186,0.1565,0.315748,1.02601,0.303924,0.0967611,0.336879,0.939294,0.385627,0.0909495,1.05028,0.504927,0,0.587245,0.150639,0.0817508,0.33293,0.215242,0.447169,1.84784,0.471175,1.29598,0.432737,0.265362,0.334131,0.191143,0.0536593,0.321757,0.683831,0.891038,0.0658632,0.975762,0.0172637,0.438297,0.382372,0.126724,0.347926,0.153518,0.870859,0.0834993,0.508662,0.283915,0.293566,0.512146,0.34807,0.169751,0.19345,0.570705,1.15826,0.419161,0.82076,0.837732,1.06445,0.200484,0.977003,0.0716833,0.412262,0.664611,2.04847,0.104381,0.560059,0.424276,0.598412,0.970969,1.3158,0.660133,1.17005,0.650349,0.647992,1.98355,0.870406,0.51601,0.222652,0.0658238,0.50152,0.648171,0.624196,0.0952669,0.60374,0.464847,0.0868537,0.758319,0.842691,0.0395547,0.198381,0.516731,1.47691,1.03946,0.763136,0.696137,0.16091,0.782777,0.360425,0.622881,0.698838,0.512384,0.0434558,0.438441,0.683562,0.803823,0.571268,0.57027,1.56637,0.627019,0.344504,0.63348,0.216685,0.261228,0.805555,0.626352,0.361667,1.04639,0.463309,0.479057,0.306448,1.43693,0.139554,0.875675,0.540309,0.434408,0.500675,1.09972,0.651709,0.403884,1.64843,2.22387,0.163147,0.787341,0.296885,0.940498,0.426575,1.06766,0.092963,0.274293,0.873625,1.01927,1.84381,1.44523,0.975592,0.445463,0.693891,0.564145,0.326684,0.515065,1.80426,0.276297,0.927992,0.445509,2.768,0.822286,0.747142,0.425729,0.901933,0.458393,0.178202,0.265096,0.274055,1.02862,0.757491,0.652135,0.25933,0.561023,0.418964,0.141416,0.384198,0.788879
}}
}}

Revision as of 18:38, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr12:66137306..66137345,+p1@Prpf39
Mm9::chr15:6658372..6658396,+p1@Rictor
Mm9::chr18:84758883..84758919,-p1@Zfp407
Mm9::chr19:3575708..3575756,-p1@Ppp6r3
Mm9::chr1:129765361..129765384,+p1@Rab3gap1
Mm9::chr2:119722948..119723028,+p1@Mga
Mm9::chr2:180436702..180436751,-p1@Dido1
Mm9::chr2:53050248..53050294,-p1@Prpf40a
Mm9::chr2:59963708..59963832,-p1@Baz2b
Mm9::chr5:33196834..33196897,-p1@C330019G07Rik
Mm9::chr7:117205217..117205246,+p1@Zfp143
Mm9::chrX:39265054..39265089,-p1@Thoc2


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:0006359regulation of transcription from RNA polymerase III promoter0.013477236618638
GO:0003709RNA polymerase III transcription factor activity0.013477236618638
GO:0031932TORC 2 complex0.013477236618638
GO:0006383transcription from RNA polymerase III promoter0.0303104929307956
GO:0051896regulation of protein kinase B signaling cascade0.0372893614573972
GO:0003704specific RNA polymerase II transcription factor activity0.0372893614573972
GO:0008380RNA splicing0.0372893614573972
GO:0006397mRNA processing0.0493083604530968
GO:0043491protein kinase B signaling cascade0.0493083604530968



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
lymphocyte4.03e-0713
common lymphoid progenitor4.03e-0713
lymphoid lineage restricted progenitor cell4.69e-0712

Uber Anatomy
Ontology termp-valuen
primordium1.49e-09134
respiratory system4.34e-0942
anterior region of body6.05e-0943
respiratory tract9.27e-0941
craniocervical region4.82e-0836
hemopoietic organ7.37e-0829
immune organ7.37e-0829
mixed endoderm/mesoderm-derived structure1.16e-0735
gland of gut5.22e-0724
organism subdivision9.79e-07150


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}}}