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MCL coexpression mm9:482: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!6.66e-18!54;UBERON:0002346!1.87e-17!64;UBERON:0003075!1.87e-17!64;UBERON:0007284!1.87e-17!64;UBERON:0001049!4.93e-17!52;UBERON:0005068!4.93e-17!52;UBERON:0006241!4.93e-17!52;UBERON:0007135!4.93e-17!52;UBERON:0010371!6.32e-17!73;UBERON:0001017!9.31e-17!73;UBERON:0003056!1.57e-16!49;UBERON:0001016!4.14e-16!75;UBERON:0004121!5.41e-16!95;UBERON:0000924!5.41e-16!95;UBERON:0006601!5.41e-16!95;UBERON:0003080!4.12e-15!40;UBERON:0002020!6.17e-15!34;UBERON:0000955!7.84e-15!47;UBERON:0006238!7.84e-15!47;UBERON:0002780!1.00e-14!39;UBERON:0001890!1.00e-14!39;UBERON:0006240!1.00e-14!39;UBERON:0002616!2.18e-14!46;UBERON:0003528!1.73e-12!29;UBERON:0002791!1.73e-12!29;UBERON:0001893!1.73e-12!29;UBERON:0000956!1.45e-09!21;UBERON:0001869!1.45e-09!21;UBERON:0000203!1.45e-09!21;UBERON:0010314!5.67e-09!92;UBERON:0000153!1.04e-08!43;UBERON:0002619!3.55e-07!17;UBERON:0000064!8.28e-07!99
|ontology_enrichment_uberon=UBERON:0000073!6.66e-18!54;UBERON:0002346!1.87e-17!64;UBERON:0003075!1.87e-17!64;UBERON:0007284!1.87e-17!64;UBERON:0001049!4.93e-17!52;UBERON:0005068!4.93e-17!52;UBERON:0006241!4.93e-17!52;UBERON:0007135!4.93e-17!52;UBERON:0010371!6.32e-17!73;UBERON:0001017!9.31e-17!73;UBERON:0003056!1.57e-16!49;UBERON:0001016!4.14e-16!75;UBERON:0004121!5.41e-16!95;UBERON:0000924!5.41e-16!95;UBERON:0006601!5.41e-16!95;UBERON:0003080!4.12e-15!40;UBERON:0002020!6.17e-15!34;UBERON:0000955!7.84e-15!47;UBERON:0006238!7.84e-15!47;UBERON:0002780!1.00e-14!39;UBERON:0001890!1.00e-14!39;UBERON:0006240!1.00e-14!39;UBERON:0002616!2.18e-14!46;UBERON:0003528!1.73e-12!29;UBERON:0002791!1.73e-12!29;UBERON:0001893!1.73e-12!29;UBERON:0000956!1.45e-09!21;UBERON:0001869!1.45e-09!21;UBERON:0000203!1.45e-09!21;UBERON:0010314!5.67e-09!92;UBERON:0000153!1.04e-08!43;UBERON:0002619!3.55e-07!17;UBERON:0000064!8.28e-07!99
|tfbs_overrepresentation_for_novel_motifs=1.12351,0.0531438,0.548514,0.238864,0.356286,0.250289,0.324772,0.057666,0.223561,0.563871,0.785008,0.314655,1.21867,0.890651,0.383709,0,0.505674,0.105493,0.1896,0.0839024,0.160516,1.053,0.888941,0.109412,0.561942,0.35869,0.178452,0.736859,0.139679,0.297581,0.710801,0.598971,1.14573,0.15332,0.770595,7.21409,1.1076,0.83799,0.290566,5.28648,0.107883,0.259911,0.438559,0.122151,0.147772,0.651235,0.433813,0.766153,0.356013,0.436869,0.48979,2.64774,0.521833,0.732469,0.749094,0.904193,0.452104,0.303999,0.378703,1.61447,0.580338,0.390204,0.516848,0.479581,0.925321,0.516415,0.880067,1.22155,0.576002,1.07689,0.991414,0.218482,2.34826,0.781142,0.158223,0.606791,0.153229,0.423705,0.564426,0.163487,0.0610891,1.29536,0.388944,0.443997,1.6106,2.86838,0.602992,0.868336,0.438181,1.38183,0.947651,0.676142,0.610915,0.114049,1.00206,0.257625,0.45422,0.613539,0.43404,0.469526,0.325002,0.59871,0.715894,0.490329,0.489372,1.32569,1.343,0.276621,0.499786,0.161774,0.582521,0.717588,0.493275,0.292444,0.954503,0.346836,0.288832,1.25934,0.506861,1.09242,0.786314,0.46068,0.360259,0.422901,1.00724,0.567849,0.331666,1.4708,0.8786,1.22419,0.699779,0.233152,0.850049,0.352905,0.975524,0.135562,0.212784,0.261043,0.927716,1.74768,1.35029,0.884624,0.370659,0.608735,0.483498,2.85815,0.436593,1.7082,0.614595,0.726856,0.880781,5.97168,0.733963,0.266555,0.928341,0.81211,0.382849,0.128633,0.204546,1.14751,0.93695,0.670634,0.568261,0.199399,0.480505,0.345769,0.663991,0.313326,3.30602
}}
}}

Revision as of 18:25, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:80164681..80164731,-p2@Mob3a
Mm9::chr12:109149819..109149825,-p@chr12:109149819..109149825
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Mm9::chr12:109242296..109242307,-p3@Bcl11b
Mm9::chr15:96473695..96473724,-p9@Slc38a1
Mm9::chr15:98764953..98765017,-p2@Gm5620
p2@Tuba1b
Mm9::chr16:91485298..91485311,+p5@Ifnar1
Mm9::chr16:91485312..91485350,+p2@Ifnar1
Mm9::chr17:13185451..13185464,-p5@Wtap
Mm9::chr17:13185469..13185514,-p3@Wtap
Mm9::chr17:74738040..74738089,+p1@Spast
Mm9::chr19:40588323..40588370,-p4@Sorbs1
Mm9::chr1:127332321..127332330,-p6@Actr3
Mm9::chr1:157005814..157005831,+p2@Stx6
Mm9::chr9:110019834..110019857,-p3@Dhx30
Mm9::chrX:20195322..20195344,-p@chrX:20195322..20195344
-


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:0019961interferon binding0.0441693570460601
GO:0006868glutamine transport0.0441693570460601
GO:0015186L-glutamine transmembrane transporter activity0.0441693570460601
GO:0004637phosphoribosylamine-glycine ligase activity0.0441693570460601
GO:0004904interferon receptor activity0.0441693570460601
GO:0043149stress fiber formation0.0473139401846565
GO:0015802basic amino acid transport0.0473139401846565



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
CNS neuron (sensu Vertebrata)5.27e-1223
neuroblast (sensu Vertebrata)5.27e-1223
neuron2.60e-0933
neuronal stem cell2.60e-0933
neuroblast2.60e-0933
electrically signaling cell2.60e-0933

Uber Anatomy
Ontology termp-valuen
regional part of nervous system6.66e-1854
neurectoderm1.87e-1764
neural plate1.87e-1764
presumptive neural plate1.87e-1764
neural tube4.93e-1752
neural rod4.93e-1752
future spinal cord4.93e-1752
neural keel4.93e-1752
ecto-epithelium6.32e-1773
central nervous system9.31e-1773
pre-chordal neural plate1.57e-1649
nervous system4.14e-1675
ectoderm-derived structure5.41e-1695
ectoderm5.41e-1695
presumptive ectoderm5.41e-1695
anterior neural tube4.12e-1540
gray matter6.17e-1534
brain7.84e-1547
future brain7.84e-1547
regional part of forebrain1.00e-1439
forebrain1.00e-1439
future forebrain1.00e-1439
regional part of brain2.18e-1446
brain grey matter1.73e-1229
regional part of telencephalon1.73e-1229
telencephalon1.73e-1229
cerebral cortex1.45e-0921
cerebral hemisphere1.45e-0921
pallium1.45e-0921
structure with developmental contribution from neural crest5.67e-0992
anterior region of body1.04e-0843
regional part of cerebral cortex3.55e-0717
organ part8.28e-0799


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}}}