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MCL coexpression mm9:1271: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!3.50e-18!48;UBERON:0002405!3.50e-18!48;UBERON:0004177!8.68e-18!29;UBERON:0005057!8.68e-18!29;UBERON:0002390!4.93e-16!45;UBERON:0003061!4.93e-16!45;UBERON:0000077!3.66e-14!35;UBERON:0003408!5.91e-14!24;UBERON:0006562!6.01e-14!24;UBERON:0001557!6.01e-14!24;UBERON:0001042!6.01e-14!24;UBERON:0008814!6.01e-14!24;UBERON:0009145!6.01e-14!24;UBERON:0002370!2.05e-13!23;UBERON:0000974!2.05e-13!23;UBERON:0004807!2.05e-13!23;UBERON:0005058!2.05e-13!23;UBERON:0003351!2.05e-13!23;UBERON:0009113!2.05e-13!23;UBERON:0003295!2.05e-13!23;UBERON:0009722!2.05e-13!23;UBERON:0005562!2.05e-13!23;UBERON:0007690!2.05e-13!23;UBERON:0001004!9.14e-12!42;UBERON:0000072!1.80e-11!27;UBERON:0000065!2.91e-11!41;UBERON:0001041!1.22e-09!80;UBERON:0007811!7.68e-09!36;UBERON:0001007!3.26e-08!116;UBERON:0001555!3.26e-08!116;UBERON:0007026!3.26e-08!116;UBERON:0000063!5.19e-08!35;UBERON:0004119!8.48e-08!118;UBERON:0000925!8.48e-08!118;UBERON:0006595!8.48e-08!118;UBERON:0003081!9.42e-08!87;UBERON:0004921!1.92e-07!114
|ontology_enrichment_uberon=UBERON:0002193!3.50e-18!48;UBERON:0002405!3.50e-18!48;UBERON:0004177!8.68e-18!29;UBERON:0005057!8.68e-18!29;UBERON:0002390!4.93e-16!45;UBERON:0003061!4.93e-16!45;UBERON:0000077!3.66e-14!35;UBERON:0003408!5.91e-14!24;UBERON:0006562!6.01e-14!24;UBERON:0001557!6.01e-14!24;UBERON:0001042!6.01e-14!24;UBERON:0008814!6.01e-14!24;UBERON:0009145!6.01e-14!24;UBERON:0002370!2.05e-13!23;UBERON:0000974!2.05e-13!23;UBERON:0004807!2.05e-13!23;UBERON:0005058!2.05e-13!23;UBERON:0003351!2.05e-13!23;UBERON:0009113!2.05e-13!23;UBERON:0003295!2.05e-13!23;UBERON:0009722!2.05e-13!23;UBERON:0005562!2.05e-13!23;UBERON:0007690!2.05e-13!23;UBERON:0001004!9.14e-12!42;UBERON:0000072!1.80e-11!27;UBERON:0000065!2.91e-11!41;UBERON:0001041!1.22e-09!80;UBERON:0007811!7.68e-09!36;UBERON:0001007!3.26e-08!116;UBERON:0001555!3.26e-08!116;UBERON:0007026!3.26e-08!116;UBERON:0000063!5.19e-08!35;UBERON:0004119!8.48e-08!118;UBERON:0000925!8.48e-08!118;UBERON:0006595!8.48e-08!118;UBERON:0003081!9.42e-08!87;UBERON:0004921!1.92e-07!114
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.819928,0.464605,0.535892,0.916672,0.550971,0.645383,0.247459,0.257202,0.594834,0.599767,0.632897,0.692139,0.6581,0.364314,0,0.856992,0.338549,0.656199,0.86893,0.426133,0.35122,0.657163,0.345236,0.472505,0.686615,0.63639,0.572827,0.394364,0.534301,0.558142,0.960397,0.336199,0.589948,0.364821,0.144368,0.326478,0.629145,0.303703,0.752287,0.342638,0.56353,0.0995018,0.366415,0.161543,0.524258,0.77511,0.589246,0.284064,0.397446,0.839084,0.714419,0.995874,1.10437,1.12205,0.66551,0.406788,0.619643,0.614918,0.663395,0.939962,0.724164,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.70565,0.11437,1.156,0.208101,0.19692,0.589776,0.763395,0.922432,0.430551,0.254777,0.874787,0.722675,0.676326,1.03903,0.439832,0.827903,0.181203,0.780154,1.77427,1.33021,1.04409,0.973447,0.9304,0.2995,0.769162,0.244935,0.976308,0.775372,0.160254,0.871473,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,0.428007,1.21641,1.0885,0.431734,0.605144,1.33732,0.340765,0.0704207,0.53982,0.858327,0.862623,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.937314,1.06946,0.52828,1.2285,0.679647,1.35909,1.1648,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.348692,1.03315,0.325363,1.10596,0.287383,0.678689,1.18867,0.71546,0.376898,0.48935,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.86867,0.63125,0.0323861
}}
}}

Revision as of 19:39, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr11:109294025..109294044,+p8@Amz2
Mm9::chr12:85559762..85559778,-p5@C130039O16Rik
Mm9::chr18:56629179..56629195,+p@chr18:56629179..56629195
+
Mm9::chr19:12873114..12873126,+p2@Lpxn
Mm9::chr2:122252168..122252197,+p1@Slc28a2
Mm9::chr9:103391679..103391706,-p@chr9:103391679..103391706
-


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:0015211purine nucleoside transmembrane transporter activity0.00451955733015958
GO:0005415nucleoside:sodium symporter activity0.00451955733015958
GO:0001882nucleoside binding0.00451955733015958
GO:0015860purine nucleoside transport0.00451955733015958
GO:0015858nucleoside transport0.00723049934476794
GO:0005337nucleoside transmembrane transporter activity0.009036638597603
GO:0015932nucleobase, nucleoside, nucleotide and nucleic acid transmembrane transporter activity0.009036638597603
GO:0015370solute:sodium symporter activity0.0451015396334998
GO:0015294solute:cation symporter activity0.0495709027396678
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.0495709027396678



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>


Uber Anatomy
Ontology termp-valuen
hemolymphoid system3.50e-1848
immune system3.50e-1848
hemopoietic organ8.68e-1829
immune organ8.68e-1829
hematopoietic system4.93e-1645
blood island4.93e-1645
mixed endoderm/mesoderm-derived structure3.66e-1435
gland of gut5.91e-1424
pharynx6.01e-1424
upper respiratory tract6.01e-1424
chordate pharynx6.01e-1424
pharyngeal arch system6.01e-1424
pharyngeal region of foregut6.01e-1424
thymus2.05e-1323
neck2.05e-1323
respiratory system epithelium2.05e-1323
hemolymphoid system gland2.05e-1323
pharyngeal epithelium2.05e-1323
thymic region2.05e-1323
pharyngeal gland2.05e-1323
entire pharyngeal arch endoderm2.05e-1323
thymus primordium2.05e-1323
early pharyngeal endoderm2.05e-1323
respiratory system9.14e-1242
segment of respiratory tract1.80e-1127
respiratory tract2.91e-1141
foregut1.22e-0980
craniocervical region7.68e-0936
digestive system3.26e-08116
digestive tract3.26e-08116
primitive gut3.26e-08116
organ segment5.19e-0835
endoderm-derived structure8.48e-08118
endoderm8.48e-08118
presumptive endoderm8.48e-08118
lateral plate mesoderm9.42e-0887
subdivision of digestive tract1.92e-07114


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}}}