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MCL coexpression mm9:959: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001016!4.76e-23!75;UBERON:0001017!2.49e-22!73;UBERON:0004121!1.47e-21!95;UBERON:0000924!1.47e-21!95;UBERON:0006601!1.47e-21!95;UBERON:0002346!1.05e-20!64;UBERON:0003075!1.05e-20!64;UBERON:0007284!1.05e-20!64;UBERON:0010371!2.88e-18!73;UBERON:0010314!2.98e-18!92;UBERON:0000073!6.18e-18!54;UBERON:0001049!2.44e-17!52;UBERON:0005068!2.44e-17!52;UBERON:0006241!2.44e-17!52;UBERON:0007135!2.44e-17!52;UBERON:0003056!5.26e-17!49;UBERON:0002020!1.22e-15!34;UBERON:0000955!1.57e-15!47;UBERON:0006238!1.57e-15!47;UBERON:0003080!4.17e-15!40;UBERON:0002616!4.86e-15!46;UBERON:0002780!1.24e-14!39;UBERON:0001890!1.24e-14!39;UBERON:0006240!1.24e-14!39;UBERON:0003528!1.20e-13!29;UBERON:0002791!1.20e-13!29;UBERON:0001893!1.20e-13!29;UBERON:0000468!4.75e-11!333;UBERON:0000956!1.62e-10!21;UBERON:0001869!1.62e-10!21;UBERON:0000203!1.62e-10!21;UBERON:0000922!1.52e-09!320;UBERON:0002619!4.34e-08!17;UBERON:0000025!5.03e-07!114;UBERON:0002021!6.14e-07!10;UBERON:0000411!6.14e-07!10;UBERON:0001950!6.14e-07!10
|ontology_enrichment_uberon=UBERON:0001016!4.76e-23!75;UBERON:0001017!2.49e-22!73;UBERON:0004121!1.47e-21!95;UBERON:0000924!1.47e-21!95;UBERON:0006601!1.47e-21!95;UBERON:0002346!1.05e-20!64;UBERON:0003075!1.05e-20!64;UBERON:0007284!1.05e-20!64;UBERON:0010371!2.88e-18!73;UBERON:0010314!2.98e-18!92;UBERON:0000073!6.18e-18!54;UBERON:0001049!2.44e-17!52;UBERON:0005068!2.44e-17!52;UBERON:0006241!2.44e-17!52;UBERON:0007135!2.44e-17!52;UBERON:0003056!5.26e-17!49;UBERON:0002020!1.22e-15!34;UBERON:0000955!1.57e-15!47;UBERON:0006238!1.57e-15!47;UBERON:0003080!4.17e-15!40;UBERON:0002616!4.86e-15!46;UBERON:0002780!1.24e-14!39;UBERON:0001890!1.24e-14!39;UBERON:0006240!1.24e-14!39;UBERON:0003528!1.20e-13!29;UBERON:0002791!1.20e-13!29;UBERON:0001893!1.20e-13!29;UBERON:0000468!4.75e-11!333;UBERON:0000956!1.62e-10!21;UBERON:0001869!1.62e-10!21;UBERON:0000203!1.62e-10!21;UBERON:0000922!1.52e-09!320;UBERON:0002619!4.34e-08!17;UBERON:0000025!5.03e-07!114;UBERON:0002021!6.14e-07!10;UBERON:0000411!6.14e-07!10;UBERON:0001950!6.14e-07!10
|tfbs_overrepresentation_for_novel_motifs=1.01838,1.66496,0.367606,0.434198,0.260188,0.448401,0.538088,0.173246,0.535519,2.55967,1.23792,0.526159,0.515774,1.35627,0.275867,0,0.742571,0.252772,0.160384,0.620214,0.332107,0.223663,3.41212,0.258745,0.978733,0.577606,0.153291,0.469052,0.818708,0.757024,0.455168,0.843667,0.699026,0.425071,0.757987,3.12971,0.242032,0.522578,0.631914,0.195877,0.256422,0.460258,0.0558565,0.27776,1.7835,0.423266,0.662995,0.484612,0.0447507,0.305876,0.725127,0.604356,0.362495,0.985264,1.00271,1.37128,0.314394,1.27827,0.447041,0.555328,3.19733,3.69504,0.192045,0.713876,2.38538,0.754324,1.139,1.48833,0.818971,1.34113,0.922232,0.178433,1.31587,1.03623,3.4185,1.32088,0.42492,0.651651,0.806481,0.336166,0.179489,0.759925,0.612313,0.167672,0.920903,2.55025,0.123242,1.23935,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,1.82579,0.202284,0.1711,1.99856,0.663249,0.101559,0.679141,0.843387,0.967837,0.725721,0.724668,1.16334,1.84452,0.480639,0.340849,0.887702,0.386136,0.96962,0.337254,0.499714,1.21576,0.254749,1.82084,0.437894,0.743872,0.238599,1.04163,1.65536,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,1.09252,1.10792,0.570914,1.23736,0.061199,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,1.16523,0.666107,1.9792,0.403515,0.724779,0.381863,2.79776,0.986833,0.207643,0.569994,1.06851,0.605358,0.287226,0.39061,1.03572,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.240994,0.524587,0.331912
}}
}}

Revision as of 19:10, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr15:27955589..27955634,-p1@Trio
Mm9::chr15:27955649..27955679,-p2@Trio
Mm9::chr15:76701830..76701883,-p1@Zfp251
Mm9::chr1:178744201..178744264,-p1@Cep170
Mm9::chr2:124949317..124949353,-p1@Myef2
Mm9::chr2:124949354..124949384,-p2@Myef2
Mm9::chr6:92041399..92041417,+p2@Nr2c2
Mm9::chrX:13423601..13423619,-p3@Cask


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:0048136male germ-line cyst formation0.0140250917657371
GO:0048134germ-line cyst formation0.0140250917657371
GO:0048137spermatocyte division0.0140250917657371



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 system4.76e-2375
central nervous system2.49e-2273
ectoderm-derived structure1.47e-2195
ectoderm1.47e-2195
presumptive ectoderm1.47e-2195
neurectoderm1.05e-2064
neural plate1.05e-2064
presumptive neural plate1.05e-2064
ecto-epithelium2.88e-1873
structure with developmental contribution from neural crest2.98e-1892
regional part of nervous system6.18e-1854
neural tube2.44e-1752
neural rod2.44e-1752
future spinal cord2.44e-1752
neural keel2.44e-1752
pre-chordal neural plate5.26e-1749
gray matter1.22e-1534
brain1.57e-1547
future brain1.57e-1547
anterior neural tube4.17e-1540
regional part of brain4.86e-1546
regional part of forebrain1.24e-1439
forebrain1.24e-1439
future forebrain1.24e-1439
brain grey matter1.20e-1329
regional part of telencephalon1.20e-1329
telencephalon1.20e-1329
multi-cellular organism4.75e-11333
cerebral cortex1.62e-1021
cerebral hemisphere1.62e-1021
pallium1.62e-1021
embryo1.52e-09320
regional part of cerebral cortex4.34e-0817
tube5.03e-07114
occipital lobe6.14e-0710
visual cortex6.14e-0710
neocortex6.14e-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}}}