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MCL coexpression mm9:1330: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!2.75e-37!73;UBERON:0001016!3.55e-37!75;UBERON:0004121!9.72e-34!95;UBERON:0000924!9.72e-34!95;UBERON:0006601!9.72e-34!95;UBERON:0002346!6.73e-30!64;UBERON:0003075!6.73e-30!64;UBERON:0007284!6.73e-30!64;UBERON:0000073!3.79e-28!54;UBERON:0010371!6.74e-27!73;UBERON:0001049!7.53e-27!52;UBERON:0005068!7.53e-27!52;UBERON:0006241!7.53e-27!52;UBERON:0007135!7.53e-27!52;UBERON:0000955!8.75e-24!47;UBERON:0006238!8.75e-24!47;UBERON:0002616!3.67e-23!46;UBERON:0003056!4.71e-21!49;UBERON:0010314!1.39e-19!92;UBERON:0002020!1.92e-19!34;UBERON:0003080!6.14e-19!40;UBERON:0002780!2.34e-18!39;UBERON:0001890!2.34e-18!39;UBERON:0006240!2.34e-18!39;UBERON:0003528!9.07e-17!29;UBERON:0002791!9.07e-17!29;UBERON:0001893!9.07e-17!29;UBERON:0000956!1.51e-12!21;UBERON:0001869!1.51e-12!21;UBERON:0000203!1.51e-12!21;UBERON:0002619!1.14e-10!17;UBERON:0003076!1.83e-08!12;UBERON:0003057!1.83e-08!12;UBERON:0002021!3.60e-07!10;UBERON:0000411!3.60e-07!10;UBERON:0001950!3.60e-07!10
|ontology_enrichment_uberon=UBERON:0001017!2.75e-37!73;UBERON:0001016!3.55e-37!75;UBERON:0004121!9.72e-34!95;UBERON:0000924!9.72e-34!95;UBERON:0006601!9.72e-34!95;UBERON:0002346!6.73e-30!64;UBERON:0003075!6.73e-30!64;UBERON:0007284!6.73e-30!64;UBERON:0000073!3.79e-28!54;UBERON:0010371!6.74e-27!73;UBERON:0001049!7.53e-27!52;UBERON:0005068!7.53e-27!52;UBERON:0006241!7.53e-27!52;UBERON:0007135!7.53e-27!52;UBERON:0000955!8.75e-24!47;UBERON:0006238!8.75e-24!47;UBERON:0002616!3.67e-23!46;UBERON:0003056!4.71e-21!49;UBERON:0010314!1.39e-19!92;UBERON:0002020!1.92e-19!34;UBERON:0003080!6.14e-19!40;UBERON:0002780!2.34e-18!39;UBERON:0001890!2.34e-18!39;UBERON:0006240!2.34e-18!39;UBERON:0003528!9.07e-17!29;UBERON:0002791!9.07e-17!29;UBERON:0001893!9.07e-17!29;UBERON:0000956!1.51e-12!21;UBERON:0001869!1.51e-12!21;UBERON:0000203!1.51e-12!21;UBERON:0002619!1.14e-10!17;UBERON:0003076!1.83e-08!12;UBERON:0003057!1.83e-08!12;UBERON:0002021!3.60e-07!10;UBERON:0000411!3.60e-07!10;UBERON:0001950!3.60e-07!10
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.473747,0.464605,1.32583,0.916672,0.550971,0.645383,0.247459,0.257202,0.0835344,0.599767,0.632897,0.692139,0.6581,0.364314,0,0.856992,0.338549,0.232269,0.442204,0.426133,1.72037,1.58083,0.345236,1.19059,0.686615,0.63639,0.572827,0.394364,0.181062,0.558142,0.960397,0.336199,0.204204,0.364821,2.34972,0.326478,0.629145,0.303703,1.37841,0.907317,0.56353,0.0995018,0.366415,0.161543,0.524258,0.77511,0.589246,0.594982,1.02809,0.839084,0.714419,3.00063,1.10437,1.12205,0.66551,0.406788,0.619643,0.614918,0.663395,0.939962,0.724164,1.36208,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.253541,0.11437,1.156,0.208101,0.19692,0.589776,1.80128,0.922432,0.430551,0.254777,0.874787,0.722675,0.676326,1.03903,0.0539203,0.220054,1.02367,0.780154,1.77427,1.33021,1.04409,0.973447,0.9304,0.2995,1.40549,0.244935,0.976308,0.775372,0.160254,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,1.09461,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,0.902522,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.347287,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,1.67199,0.971067,0.831964,0.564002,1.83209,2.10357,0.503174,0.348692,0.540361,0.0987301,1.10596,1.42796,0.678689,1.18867,1.70209,0.376898,0.48935,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.86867,0.63125,0.30995
}}
}}

Revision as of 19:44, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr12:73509649..73509660,-p5@Rtn1
Mm9::chr15:88809388..88809422,-p4@Mlc1
Mm9::chr7:31076790..31076798,+p5@Clip3
Mm9::chr7:31076822..31076826,+p7@Clip3
Mm9::chr7:31076935..31076958,+p2@Clip3
Mm9::chr7:31076960..31076987,+p4@Clip3


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:0000299integral to membrane of membrane fraction0.0394336841875496



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
central nervous system2.75e-3773
nervous system3.55e-3775
ectoderm-derived structure9.72e-3495
ectoderm9.72e-3495
presumptive ectoderm9.72e-3495
neurectoderm6.73e-3064
neural plate6.73e-3064
presumptive neural plate6.73e-3064
regional part of nervous system3.79e-2854
ecto-epithelium6.74e-2773
neural tube7.53e-2752
neural rod7.53e-2752
future spinal cord7.53e-2752
neural keel7.53e-2752
brain8.75e-2447
future brain8.75e-2447
regional part of brain3.67e-2346
pre-chordal neural plate4.71e-2149
structure with developmental contribution from neural crest1.39e-1992
gray matter1.92e-1934
anterior neural tube6.14e-1940
regional part of forebrain2.34e-1839
forebrain2.34e-1839
future forebrain2.34e-1839
brain grey matter9.07e-1729
regional part of telencephalon9.07e-1729
telencephalon9.07e-1729
cerebral cortex1.51e-1221
cerebral hemisphere1.51e-1221
pallium1.51e-1221
regional part of cerebral cortex1.14e-1017
posterior neural tube1.83e-0812
chordal neural plate1.83e-0812
occipital lobe3.60e-0710
visual cortex3.60e-0710
neocortex3.60e-0710


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}}}