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MCL coexpression mm9:626: Difference between revisions

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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0354470656487682,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0428469550828748,0.0230822320937266,0,0.054561543345514,0.0866689030825281,0.0250913949416665,0,0,0,0.247021199245269,0.348081283300519,0.0538027986792206,0.0380188235580625,0.153282818781362,0,0.096946505969497,0.282574418667431,0.562490009537864,0.440399548559187,0.137606919870727,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0234784353458152,0,0,0,0,0,0.0321489988824211,0,0,0,0,0,0,0,0,0,0.111524892460631,0.151949772756791,0,0,0,0,0.203892612769831,0.28216905172576,0.194287653451686,0.250441710981523,0.305966219492192,0.236570192217746,0.194720871044395,0.148404418111199,0,0,0,0,0,0,0.057207008968797,0.0419961661963089,0.0523528812100954,0.0388988969149198,0.181102009199648,0,0,0,0,0.106546909924599,0,0,0.0394157974199537,0,0,0,0.514791252035406,0.657542565781931,0.60863887609606,0.424426392861003,0.71784493310697,0.916483127195124,0.93804427164347,0.595704392040815,0.662374094201726,0.50678736303958,0.534952956260077,0.183670961651987,0.157940044576385,0.273741942845615,0.166782202209631,0.254609302117277,0.339013291819423,0,0,0.0419819959588466,0.0906941294286938,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0893741091821246,0,0.20708313509219,0.199167347384355,0.141544844194364,0.139239443693993,0.318368187474926,0.600207670865817,0.269440724159863,0,0,0,0,0,0,0,0,0,0,0.193488531055194,0,0,0,0,0,0,0,0.0652219495776001,0.0680912293502604,0.045779009027853,0.0384375578457364,0.0463679768904873,0.0387082368603573,0.0347500437836687,0.043440458408578,0.0642538110976656,0.0659019793256198,0.0964127681086069,0.0586723554240733,0,0,0,0,0.215426671903518,0.183647834491121,0,0,0,0,0,0,0,0,0,0,0,0.326036965553742,0,0,0.0655375003561515,0.0663147875126409,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.240973653066283,0,0,0.0368948187299337,0,0,0,0,0,0,0,0,0,0.0849373898696927,0.117094164992904,0.0857765460992942,0.0793274429263655,0.034489466458534,0,0.0529304404135566,0,0,0,0,0.00976254435669985,0,0.126427630498926,0.11128313411302,0.0531569878936061,0,0,0,0,0,0.0212308449966822,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.00769854306636345,0,0,0.471762062616302,0.415136100365385,0.434359137099159,0.390802920966584,0.226621173458704,0.399810008829701,0.29754841187768,0.409301586768586,0.326497187896024,0.407098602473158,0,0,0.0396364258278871,0,0,0,0.0435794416222198,0,0.120876255993453,0,0,0,0.0745542549075041,0.034166501287845,0.0357392340837099,0,0.0476191773904887,0.0766073954291401,0.074930558382725,0.0596387295197733,0,0.131923786075207,0.092873634605593,0.0589368614163519,0.0569785733435272,0.0352754493378881,0.0729583017401753,0.101427320830301,0.104353329269123,0,0.0486884105045233,0.0780974029773103,0.074491100723522,0,0.0383032227056179,0,0,0,0,0,0
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|gostat_on_MCL_coexpression=GO:0005432;calcium:sodium antiporter activity;0.0273897557378882;20541!GO:0015368;calcium:cation antiporter activity;0.0273897557378882;20541!GO:0030315;T-tubule;0.028479102603904;20541!GO:0015491;cation:cation antiporter activity;0.028479102603904;20541!GO:0002026;regulation of the force of heart contraction;0.028479102603904;20541!GO:0015298;solute:cation antiporter activity;0.0328532991235434;20541!GO:0015300;solute:solute antiporter activity;0.0328532991235434;20541!GO:0042383;sarcolemma;0.0383214950156528;20541!GO:0008016;regulation of heart contraction;0.0401287186248422;20541!GO:0015297;antiporter activity;0.0401287186248422;20541!GO:0060047;heart contraction;0.0401287186248422;20541!GO:0003015;heart process;0.0401287186248422;20541!
|gostat_on_MCL_coexpression=GO:0005432;calcium:sodium antiporter activity;0.0273897557378882;20541!GO:0015368;calcium:cation antiporter activity;0.0273897557378882;20541!GO:0030315;T-tubule;0.028479102603904;20541!GO:0015491;cation:cation antiporter activity;0.028479102603904;20541!GO:0002026;regulation of the force of heart contraction;0.028479102603904;20541!GO:0015298;solute:cation antiporter activity;0.0328532991235434;20541!GO:0015300;solute:solute antiporter activity;0.0328532991235434;20541!GO:0042383;sarcolemma;0.0383214950156528;20541!GO:0008016;regulation of heart contraction;0.0401287186248422;20541!GO:0015297;antiporter activity;0.0401287186248422;20541!GO:0060047;heart contraction;0.0401287186248422;20541!GO:0003015;heart process;0.0401287186248422;20541!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0010314!1.29e-16!92;UBERON:0000025!1.66e-15!114;UBERON:0002020!2.40e-13!34;UBERON:0004111!4.67e-13!122;UBERON:0003103!5.13e-13!43;UBERON:0000073!1.46e-12!54;UBERON:0001049!2.32e-12!52;UBERON:0005068!2.32e-12!52;UBERON:0006241!2.32e-12!52;UBERON:0007135!2.32e-12!52;UBERON:0002346!4.68e-11!64;UBERON:0003075!4.68e-11!64;UBERON:0007284!4.68e-11!64;UBERON:0007100!7.37e-11!18;UBERON:0000948!7.37e-11!18;UBERON:0005498!7.37e-11!18;UBERON:0004140!7.37e-11!18;UBERON:0009881!7.37e-11!18;UBERON:0004141!7.37e-11!18;UBERON:0003084!7.37e-11!18;UBERON:0007005!7.37e-11!18;UBERON:0004139!7.37e-11!18;UBERON:0004291!7.37e-11!18;UBERON:0003528!1.91e-10!29;UBERON:0002791!1.91e-10!29;UBERON:0001893!1.91e-10!29;UBERON:0000955!8.75e-10!47;UBERON:0006238!8.75e-10!47;UBERON:0002021!1.32e-09!10;UBERON:0000411!1.32e-09!10;UBERON:0001950!1.32e-09!10;UBERON:0002616!3.52e-09!46;UBERON:0010371!4.11e-08!73;UBERON:0003056!4.55e-08!49;UBERON:0003080!4.57e-08!40;UBERON:0000956!1.16e-07!21;UBERON:0001869!1.16e-07!21;UBERON:0000203!1.16e-07!21;UBERON:0001017!1.29e-07!73;UBERON:0002780!1.49e-07!39;UBERON:0001890!1.49e-07!39;UBERON:0006240!1.49e-07!39;UBERON:0002619!2.56e-07!17;UBERON:0004535!3.13e-07!23;UBERON:0001009!3.13e-07!23;UBERON:0001016!4.22e-07!75
}}
}}

Revision as of 21:00, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr17:81774774..81774786,-p@chr17:81774774..81774786
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Mm9::chr17:81774792..81774804,-p@chr17:81774792..81774804
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Mm9::chr17:81774861..81774874,-p@chr17:81774861..81774874
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Mm9::chr17:81775224..81775241,-p@chr17:81775224..81775241
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Mm9::chr17:81775324..81775339,-p@chr17:81775324..81775339
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Mm9::chr17:81775424..81775434,-p@chr17:81775424..81775434
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Mm9::chr17:81778386..81778400,-p@chr17:81778386..81778400
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Mm9::chr17:81778448..81778462,-p@chr17:81778448..81778462
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Mm9::chr17:81779985..81780016,-p@chr17:81779985..81780016
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Mm9::chr17:81787666..81787681,-p@chr17:81787666..81787681
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Mm9::chr17:82047194..82047205,-p@chr17:82047194..82047205
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Mm9::chr5:51849314..51849339,-p@chr5:51849314..51849339
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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:0005432calcium:sodium antiporter activity0.0273897557378882
GO:0015368calcium:cation antiporter activity0.0273897557378882
GO:0030315T-tubule0.028479102603904
GO:0015491cation:cation antiporter activity0.028479102603904
GO:0002026regulation of the force of heart contraction0.028479102603904
GO:0015298solute:cation antiporter activity0.0328532991235434
GO:0015300solute:solute antiporter activity0.0328532991235434
GO:0042383sarcolemma0.0383214950156528
GO:0008016regulation of heart contraction0.0401287186248422
GO:0015297antiporter activity0.0401287186248422
GO:0060047heart contraction0.0401287186248422
GO:0003015heart process0.0401287186248422



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
structure with developmental contribution from neural crest1.29e-1692
tube1.66e-15114
gray matter2.40e-1334
anatomical conduit4.67e-13122
compound organ5.13e-1343
regional part of nervous system1.46e-1254
neural tube2.32e-1252
neural rod2.32e-1252
future spinal cord2.32e-1252
neural keel2.32e-1252
neurectoderm4.68e-1164
neural plate4.68e-1164
presumptive neural plate4.68e-1164
primary circulatory organ7.37e-1118
heart7.37e-1118
primitive heart tube7.37e-1118
primary heart field7.37e-1118
anterior lateral plate mesoderm7.37e-1118
heart tube7.37e-1118
heart primordium7.37e-1118
cardiac mesoderm7.37e-1118
cardiogenic plate7.37e-1118
heart rudiment7.37e-1118
brain grey matter1.91e-1029
regional part of telencephalon1.91e-1029
telencephalon1.91e-1029
brain8.75e-1047
future brain8.75e-1047
occipital lobe1.32e-0910
visual cortex1.32e-0910
neocortex1.32e-0910
regional part of brain3.52e-0946
ecto-epithelium4.11e-0873
pre-chordal neural plate4.55e-0849
anterior neural tube4.57e-0840
cerebral cortex1.16e-0721
cerebral hemisphere1.16e-0721
pallium1.16e-0721
central nervous system1.29e-0773
regional part of forebrain1.49e-0739
forebrain1.49e-0739
future forebrain1.49e-0739
regional part of cerebral cortex2.56e-0717
cardiovascular system3.13e-0723
circulatory system3.13e-0723
nervous system4.22e-0775


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}}}

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