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MCL coexpression mm9:2274: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001016!1.94e-36!75;UBERON:0001017!1.31e-35!73;UBERON:0000073!6.38e-30!54;UBERON:0004121!2.78e-28!95;UBERON:0000924!2.78e-28!95;UBERON:0006601!2.78e-28!95;UBERON:0001049!3.39e-28!52;UBERON:0005068!3.39e-28!52;UBERON:0006241!3.39e-28!52;UBERON:0007135!3.39e-28!52;UBERON:0002346!4.91e-26!64;UBERON:0003075!4.91e-26!64;UBERON:0007284!4.91e-26!64;UBERON:0000955!1.15e-24!47;UBERON:0006238!1.15e-24!47;UBERON:0002616!5.54e-24!46;UBERON:0010371!2.86e-22!73;UBERON:0003080!1.92e-19!40;UBERON:0010314!8.65e-19!92;UBERON:0002780!1.17e-18!39;UBERON:0001890!1.17e-18!39;UBERON:0006240!1.17e-18!39;UBERON:0003056!1.29e-17!49;UBERON:0002020!2.05e-16!34;UBERON:0003528!2.08e-13!29;UBERON:0002791!2.08e-13!29;UBERON:0001893!2.08e-13!29;UBERON:0000956!3.18e-10!21;UBERON:0001869!3.18e-10!21;UBERON:0000203!3.18e-10!21;UBERON:0002619!1.36e-09!17;UBERON:0003076!2.62e-09!12;UBERON:0003057!2.62e-09!12;UBERON:0002021!2.01e-07!10;UBERON:0000411!2.01e-07!10;UBERON:0001950!2.01e-07!10
|ontology_enrichment_uberon=UBERON:0001016!1.94e-36!75;UBERON:0001017!1.31e-35!73;UBERON:0000073!6.38e-30!54;UBERON:0004121!2.78e-28!95;UBERON:0000924!2.78e-28!95;UBERON:0006601!2.78e-28!95;UBERON:0001049!3.39e-28!52;UBERON:0005068!3.39e-28!52;UBERON:0006241!3.39e-28!52;UBERON:0007135!3.39e-28!52;UBERON:0002346!4.91e-26!64;UBERON:0003075!4.91e-26!64;UBERON:0007284!4.91e-26!64;UBERON:0000955!1.15e-24!47;UBERON:0006238!1.15e-24!47;UBERON:0002616!5.54e-24!46;UBERON:0010371!2.86e-22!73;UBERON:0003080!1.92e-19!40;UBERON:0010314!8.65e-19!92;UBERON:0002780!1.17e-18!39;UBERON:0001890!1.17e-18!39;UBERON:0006240!1.17e-18!39;UBERON:0003056!1.29e-17!49;UBERON:0002020!2.05e-16!34;UBERON:0003528!2.08e-13!29;UBERON:0002791!2.08e-13!29;UBERON:0001893!2.08e-13!29;UBERON:0000956!3.18e-10!21;UBERON:0001869!3.18e-10!21;UBERON:0000203!3.18e-10!21;UBERON:0002619!1.36e-09!17;UBERON:0003076!2.62e-09!12;UBERON:0003057!2.62e-09!12;UBERON:0002021!2.01e-07!10;UBERON:0000411!2.01e-07!10;UBERON:0001950!2.01e-07!10
|tfbs_overrepresentation_for_novel_motifs=0.641384,1.30284,0.612053,0.688265,0.483253,0.704257,0.803568,0.96814,0.381467,0.489964,0.755749,0.790506,0.37041,0.81685,0.502646,0,2.33178,0.473993,1.65947,0.683591,1.39891,0.57409,0.815872,0.481455,0.620553,0.846564,0.342316,0.727368,0.535752,0.290745,0.711848,1.12823,1.18815,0.854272,0.503207,0.089443,0.460474,0.786577,0.434783,0.40068,0.478558,0.717547,1.04032,0.504971,1.10847,0.675898,2.16014,0.744678,0.162985,1.3327,1.0041,0.875451,0.282443,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,0.205546,1.32691,0.864765,0.310084,0.318792,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,0.377699,0.129654,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,1.4032,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,0.869142,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.569254,0.650785,1.70963,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.293812,1.03606,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,1.52606,0.993294,0.830321,0.459159,0.788782,0.280875
}}
}}

Revision as of 21:10, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr19:7015918..7016008,-p1@Gpr137
Mm9::chr4:147534740..147534761,+p3@Fbxo2
Mm9::chr4:147534765..147534789,+p2@Fbxo2
Mm9::chr9:54509651..54509662,-p4@Acsbg1


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:0031957very-long-chain-fatty-acid-CoA ligase activity0.00953267955952446
GO:0001948glycoprotein binding0.011436082012144
GO:0030433ER-associated protein catabolic process0.011436082012144
GO:0000038very-long-chain fatty acid metabolic process0.011436082012144
GO:0006515misfolded or incompletely synthesized protein catabolic process0.011436082012144
GO:0006516glycoprotein catabolic process0.0133362479456937
GO:0004467long-chain-fatty-acid-CoA ligase activity0.0133362479456937
GO:0043161proteasomal ubiquitin-dependent protein catabolic process0.0133362479456937
GO:0015645fatty-acid ligase activity0.0133362479456937
GO:0001676long-chain fatty acid metabolic process0.0133362479456937
GO:0016877ligase activity, forming carbon-sulfur bonds0.0199079506232692



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
nervous system1.94e-3675
central nervous system1.31e-3573
regional part of nervous system6.38e-3054
ectoderm-derived structure2.78e-2895
ectoderm2.78e-2895
presumptive ectoderm2.78e-2895
neural tube3.39e-2852
neural rod3.39e-2852
future spinal cord3.39e-2852
neural keel3.39e-2852
neurectoderm4.91e-2664
neural plate4.91e-2664
presumptive neural plate4.91e-2664
brain1.15e-2447
future brain1.15e-2447
regional part of brain5.54e-2446
ecto-epithelium2.86e-2273
anterior neural tube1.92e-1940
structure with developmental contribution from neural crest8.65e-1992
regional part of forebrain1.17e-1839
forebrain1.17e-1839
future forebrain1.17e-1839
pre-chordal neural plate1.29e-1749
gray matter2.05e-1634
brain grey matter2.08e-1329
regional part of telencephalon2.08e-1329
telencephalon2.08e-1329
cerebral cortex3.18e-1021
cerebral hemisphere3.18e-1021
pallium3.18e-1021
regional part of cerebral cortex1.36e-0917
posterior neural tube2.62e-0912
chordal neural plate2.62e-0912
occipital lobe2.01e-0710
visual cortex2.01e-0710
neocortex2.01e-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}}}