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MCL coexpression mm9:778: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!4.22e-25!54;UBERON:0000955!2.74e-24!47;UBERON:0006238!2.74e-24!47;UBERON:0001017!9.21e-24!73;UBERON:0001049!2.49e-23!52;UBERON:0005068!2.49e-23!52;UBERON:0006241!2.49e-23!52;UBERON:0007135!2.49e-23!52;UBERON:0002616!2.70e-23!46;UBERON:0001016!1.05e-22!75;UBERON:0002346!8.03e-20!64;UBERON:0003075!8.03e-20!64;UBERON:0007284!8.03e-20!64;UBERON:0003080!6.19e-19!40;UBERON:0004121!3.13e-18!95;UBERON:0000924!3.13e-18!95;UBERON:0006601!3.13e-18!95;UBERON:0002780!5.78e-18!39;UBERON:0001890!5.78e-18!39;UBERON:0006240!5.78e-18!39;UBERON:0010371!1.25e-17!73;UBERON:0003056!6.07e-17!49;UBERON:0010314!1.01e-15!92;UBERON:0003528!5.05e-13!29;UBERON:0002791!5.05e-13!29;UBERON:0001893!5.05e-13!29;UBERON:0002619!6.17e-13!17;UBERON:0002021!1.06e-12!10;UBERON:0000411!1.06e-12!10;UBERON:0001950!1.06e-12!10;UBERON:0002020!2.92e-12!34;UBERON:0000956!2.57e-11!21;UBERON:0001869!2.57e-11!21;UBERON:0000203!2.57e-11!21;UBERON:0000025!2.01e-08!114;UBERON:0004111!4.37e-08!122
|ontology_enrichment_uberon=UBERON:0000073!4.22e-25!54;UBERON:0000955!2.74e-24!47;UBERON:0006238!2.74e-24!47;UBERON:0001017!9.21e-24!73;UBERON:0001049!2.49e-23!52;UBERON:0005068!2.49e-23!52;UBERON:0006241!2.49e-23!52;UBERON:0007135!2.49e-23!52;UBERON:0002616!2.70e-23!46;UBERON:0001016!1.05e-22!75;UBERON:0002346!8.03e-20!64;UBERON:0003075!8.03e-20!64;UBERON:0007284!8.03e-20!64;UBERON:0003080!6.19e-19!40;UBERON:0004121!3.13e-18!95;UBERON:0000924!3.13e-18!95;UBERON:0006601!3.13e-18!95;UBERON:0002780!5.78e-18!39;UBERON:0001890!5.78e-18!39;UBERON:0006240!5.78e-18!39;UBERON:0010371!1.25e-17!73;UBERON:0003056!6.07e-17!49;UBERON:0010314!1.01e-15!92;UBERON:0003528!5.05e-13!29;UBERON:0002791!5.05e-13!29;UBERON:0001893!5.05e-13!29;UBERON:0002619!6.17e-13!17;UBERON:0002021!1.06e-12!10;UBERON:0000411!1.06e-12!10;UBERON:0001950!1.06e-12!10;UBERON:0002020!2.92e-12!34;UBERON:0000956!2.57e-11!21;UBERON:0001869!2.57e-11!21;UBERON:0000203!2.57e-11!21;UBERON:0000025!2.01e-08!114;UBERON:0004111!4.37e-08!122
|tfbs_overrepresentation_for_novel_motifs=0.354643,0.227469,0.330161,0.394491,0.227651,0.40827,0.495658,0.146465,0.468136,0.573183,0.453212,0.484001,0.146657,0.507558,0.24249,0,0.696644,0.62892,0.419123,0.528436,0.296085,0.047629,0.50668,1.20034,0.337218,2.27409,0.801525,0.428336,0.739731,1.09271,0.414842,0.796599,0.218674,0.113369,0.242923,0.482999,0.210533,0.480503,1.06548,0.500908,0.224094,0.419787,0.0422275,0.684206,0.158271,0.383899,0.618203,0.443479,0.314152,0.745859,0.679429,0.560572,0.30602,0.937018,0.954342,0.514504,0.764433,0.471658,0.770972,0.512521,0.776777,0.569793,0.163832,0.668331,0.525334,0.708248,1.08987,1.43807,0.772155,1.29123,0.31262,0.151245,0.0512949,0.987652,0.116281,0.349958,0.364033,0.607043,0.759798,0.81171,0.463363,0.713779,0.568383,0.858535,0.873141,0.0176817,4.72209,2.20227,0.623015,1.60001,1.15927,0.878077,0.809272,0.232894,0.188213,0.515495,0.871972,0.812053,0.618454,2.02396,1.13987,0.796322,0.919715,0.680015,0.678976,0.419366,0.737915,0.439611,0.30446,0.297733,0.919252,0.921485,0.301014,0.458194,1.16629,0.633313,0.496288,1.02946,0.697928,0.207304,0.993019,0.647706,1.3263,1.47408,1.22022,0.763454,0.503569,0.802564,1.08836,0.235546,0.90286,1.00644,1.05894,0.527782,1.18781,0.398576,0.362565,2.83137,1.13883,1.96797,1.5682,1.09456,0.547855,1.89109,0.672593,1.07771,0.621266,1.92834,0.364791,0.649035,0.665499,0.041769,0.938577,0.178329,1.3067,1.01974,0.561556,0.253271,0.352329,0.362302,1.1483,0.872292,0.763895,0.345891,0.669337,0.519673,0.209556,0.482466,0.12239
}}
}}

Revision as of 18:54, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr11:115641974..115642002,+p@chr11:115641974..115642002
+
Mm9::chr11:115642012..115642032,+p@chr11:115642012..115642032
+
Mm9::chr14:9129624..9129650,-p@chr14:9129624..9129650
-
Mm9::chr14:9130880..9130889,-p@chr14:9130880..9130889
-
Mm9::chr14:9132143..9132179,-p@chr14:9132143..9132179
-
Mm9::chr14:9142192..9142239,-p1@Fam107a
Mm9::chr14:9142248..9142259,-p3@Fam107a
Mm9::chr14:9142284..9142298,-p2@Fam107a
Mm9::chr15:8660734..8660760,-p2@Slc1a3


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:0017153sodium:dicarboxylate symporter activity0.00821782720648661
GO:0005310dicarboxylic acid transmembrane transporter activity0.00821782720648661
GO:0006835dicarboxylic acid transport0.00821782720648661
GO:0015296anion:cation symporter activity0.00936832301539473
GO:0005343organic acid:sodium symporter activity0.00936832301539473
GO:0015370solute:sodium symporter activity0.0123267408097299
GO:0015294solute:cation symporter activity0.0123267408097299
GO:0043025cell soma0.0123267408097299
GO:0046943carboxylic acid transmembrane transporter activity0.0123267408097299
GO:0005342organic acid transmembrane transporter activity0.0123267408097299
GO:0046942carboxylic acid transport0.0123267408097299
GO:0015849organic acid transport0.0123267408097299
GO:0008509anion transmembrane transporter activity0.0212399226259961
GO:0015293symporter activity0.0234208075384868
GO:0015291secondary active transmembrane transporter activity0.0289267517668328
GO:0006605protein targeting0.0289678409028653
GO:0022804active transmembrane transporter activity0.0456814512360579
GO:0042995cell projection0.0498548183860187
GO:0006886intracellular protein transport0.0499557390710107



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
oligodendrocyte precursor cell4.74e-078

Uber Anatomy
Ontology termp-valuen
regional part of nervous system4.22e-2554
brain2.74e-2447
future brain2.74e-2447
central nervous system9.21e-2473
neural tube2.49e-2352
neural rod2.49e-2352
future spinal cord2.49e-2352
neural keel2.49e-2352
regional part of brain2.70e-2346
nervous system1.05e-2275
neurectoderm8.03e-2064
neural plate8.03e-2064
presumptive neural plate8.03e-2064
anterior neural tube6.19e-1940
ectoderm-derived structure3.13e-1895
ectoderm3.13e-1895
presumptive ectoderm3.13e-1895
regional part of forebrain5.78e-1839
forebrain5.78e-1839
future forebrain5.78e-1839
ecto-epithelium1.25e-1773
pre-chordal neural plate6.07e-1749
structure with developmental contribution from neural crest1.01e-1592
brain grey matter5.05e-1329
regional part of telencephalon5.05e-1329
telencephalon5.05e-1329
regional part of cerebral cortex6.17e-1317
occipital lobe1.06e-1210
visual cortex1.06e-1210
neocortex1.06e-1210
gray matter2.92e-1234
cerebral cortex2.57e-1121
cerebral hemisphere2.57e-1121
pallium2.57e-1121
tube2.01e-08114
anatomical conduit4.37e-08122


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}}}