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MCL coexpression mm9:3443: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004921!1.86e-16!114;UBERON:0004119!2.19e-16!118;UBERON:0000925!2.19e-16!118;UBERON:0006595!2.19e-16!118;UBERON:0001007!4.01e-16!116;UBERON:0001555!4.01e-16!116;UBERON:0007026!4.01e-16!116;UBERON:0001041!3.82e-12!80;UBERON:0005911!9.94e-12!69;UBERON:0003929!7.87e-11!55;UBERON:0004177!4.60e-10!29;UBERON:0005057!4.60e-10!29;UBERON:0000490!5.03e-10!66;UBERON:0000077!7.80e-10!35;UBERON:0002193!1.16e-07!48;UBERON:0002405!1.16e-07!48;UBERON:0002390!1.18e-07!45;UBERON:0003061!1.18e-07!45;UBERON:0003408!1.85e-07!24;UBERON:0002370!2.56e-07!23;UBERON:0000974!2.56e-07!23;UBERON:0004807!2.56e-07!23;UBERON:0005058!2.56e-07!23;UBERON:0003351!2.56e-07!23;UBERON:0009113!2.56e-07!23;UBERON:0003295!2.56e-07!23;UBERON:0009722!2.56e-07!23;UBERON:0005562!2.56e-07!23;UBERON:0007690!2.56e-07!23;UBERON:0006562!4.11e-07!24;UBERON:0001557!4.11e-07!24;UBERON:0001042!4.11e-07!24;UBERON:0008814!4.11e-07!24;UBERON:0009145!4.11e-07!24;UBERON:0001048!4.37e-07!134;UBERON:0001004!5.38e-07!42;UBERON:0000065!7.82e-07!41
|ontology_enrichment_uberon=UBERON:0004921!1.86e-16!114;UBERON:0004119!2.19e-16!118;UBERON:0000925!2.19e-16!118;UBERON:0006595!2.19e-16!118;UBERON:0001007!4.01e-16!116;UBERON:0001555!4.01e-16!116;UBERON:0007026!4.01e-16!116;UBERON:0001041!3.82e-12!80;UBERON:0005911!9.94e-12!69;UBERON:0003929!7.87e-11!55;UBERON:0004177!4.60e-10!29;UBERON:0005057!4.60e-10!29;UBERON:0000490!5.03e-10!66;UBERON:0000077!7.80e-10!35;UBERON:0002193!1.16e-07!48;UBERON:0002405!1.16e-07!48;UBERON:0002390!1.18e-07!45;UBERON:0003061!1.18e-07!45;UBERON:0003408!1.85e-07!24;UBERON:0002370!2.56e-07!23;UBERON:0000974!2.56e-07!23;UBERON:0004807!2.56e-07!23;UBERON:0005058!2.56e-07!23;UBERON:0003351!2.56e-07!23;UBERON:0009113!2.56e-07!23;UBERON:0003295!2.56e-07!23;UBERON:0009722!2.56e-07!23;UBERON:0005562!2.56e-07!23;UBERON:0007690!2.56e-07!23;UBERON:0006562!4.11e-07!24;UBERON:0001557!4.11e-07!24;UBERON:0001042!4.11e-07!24;UBERON:0008814!4.11e-07!24;UBERON:0009145!4.11e-07!24;UBERON:0001048!4.37e-07!134;UBERON:0001004!5.38e-07!42;UBERON:0000065!7.82e-07!41
|tfbs_overrepresentation_for_novel_motifs=0.752782,0.193418,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,1.91723,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,1.98772,0.328717,0.679146,0.275782,0.932027,0.585919,0.731217,0.963352,1.1146,0.841386,0.64294,0.99159,0.825437,1.24901,0.575271,0.411696,1.47967,0.144706,0.563758,0.902078,0.536514,1.24975,0.582863,0.831295,0.261619,0.610669,0.922882,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,2.29231,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,1.6706,1.19585,5.97285,1.44925,1.07031,1.03818,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,1.16164,2.95371,3.0674,0.195254,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,3.3325,0.509215,0.464141,1.26539,1.05692,1.65883,1.38502,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,1.63106,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,1.79445,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,1.44008,0.999018,11.4,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,0.421338
}}
}}

Revision as of 22:55, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr4:102791976..102792008,+p2@Mier1
Mm9::chr4:102792009..102792021,+p6@Mier1
Mm9::chr8:108583462..108583523,+p1@Nfatc3


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:0045333cellular respiration0.0487770845455421
GO:0015980energy derivation by oxidation of organic compounds0.0487770845455421
GO:0006355regulation of transcription, DNA-dependent0.0487770845455421
GO:0006351transcription, DNA-dependent0.0487770845455421
GO:0032774RNA biosynthetic process0.0487770845455421
GO:0003677DNA binding0.0487770845455421
GO:0045449regulation of transcription0.0487770845455421
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0487770845455421
GO:0006350transcription0.0487770845455421
GO:0010468regulation of gene expression0.0487770845455421
GO:0031323regulation of cellular metabolic process0.0487770845455421
GO:0019222regulation of metabolic process0.0487770845455421
GO:0016070RNA metabolic process0.0487770845455421



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
subdivision of digestive tract1.86e-16114
endoderm-derived structure2.19e-16118
endoderm2.19e-16118
presumptive endoderm2.19e-16118
digestive system4.01e-16116
digestive tract4.01e-16116
primitive gut4.01e-16116
foregut3.82e-1280
endo-epithelium9.94e-1269
gut epithelium7.87e-1155
hemopoietic organ4.60e-1029
immune organ4.60e-1029
unilaminar epithelium5.03e-1066
mixed endoderm/mesoderm-derived structure7.80e-1035
hemolymphoid system1.16e-0748
immune system1.16e-0748
hematopoietic system1.18e-0745
blood island1.18e-0745
gland of gut1.85e-0724
thymus2.56e-0723
neck2.56e-0723
respiratory system epithelium2.56e-0723
hemolymphoid system gland2.56e-0723
pharyngeal epithelium2.56e-0723
thymic region2.56e-0723
pharyngeal gland2.56e-0723
entire pharyngeal arch endoderm2.56e-0723
thymus primordium2.56e-0723
early pharyngeal endoderm2.56e-0723
pharynx4.11e-0724
upper respiratory tract4.11e-0724
chordate pharynx4.11e-0724
pharyngeal arch system4.11e-0724
pharyngeal region of foregut4.11e-0724
primordium4.37e-07134
respiratory system5.38e-0742
respiratory tract7.82e-0741


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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