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MCL coexpression mm9:984: Difference between revisions

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{{MCL_coexpression_mm9
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channel activity;0.0212610862975629;99738,20266!GO:0005244;voltage-gated ion channel activity;0.0212610862975629;99738,20266!GO:0031420;alkali metal ion binding;0.0212610862975629;99738,20266!GO:0006810;transport;0.0212610862975629;100273,99738,20266,18802!GO:0051234;establishment of localization;0.0212610862975629;100273,99738,20266,18802!GO:0005261;cation channel activity;0.0212610862975629;99738,20266!GO:0051179;localization;0.0212610862975629;100273,99738,20266,18802!GO:0022836;gated channel activity;0.0212610862975629;99738,20266!GO:0046873;metal ion transmembrane transporter activity;0.0212610862975629;99738,20266!GO:0015672;monovalent inorganic cation transport;0.0212610862975629;99738,20266!GO:0007340;acrosome reaction;0.0212610862975629;18802!GO:0004435;phosphoinositide phospholipase C activity;0.0212610862975629;18802!GO:0004434;inositol or phosphatidylinositol phosphodiesterase activity;0.0212610862975629;18802!GO:0005216;ion channel activity;0.0230202269040457;99738,20266!GO:0022838;substrate specific channel activity;0.0230202269040457;99738,20266!GO:0022803;passive transmembrane transporter activity;0.0230202269040457;99738,20266!GO:0015267;channel activity;0.0230202269040457;99738,20266!GO:0004629;phospholipase C activity;0.0230202269040457;18802!GO:0030001;metal ion transport;0.0230774535726656;99738,20266!GO:0017156;calcium ion-dependent exocytosis;0.0275451680756006;18802!GO:0008324;cation transmembrane transporter activity;0.0275451680756006;99738,20266!GO:0006812;cation transport;0.0275451680756006;99738,20266!GO:0005272;sodium channel activity;0.0311898189645894;20266!GO:0015075;ion transmembrane transporter activity;0.0451749126702556;99738,20266!GO:0007338;single fertilization;0.0451749126702556;18802!GO:0030384;phosphoinositide metabolic process;0.0458893449675082;18802!GO:0004620;phospholipase activity;0.0458893449675082;18802!GO:0006811;ion transport;0.0465019137658845;99738,20266!GO:0009566;fertilization;0.0465019137658845;18802!GO:0022891;substrate-specific transmembrane transporter activity;0.0475471638115029;99738,20266!GO:0008076;voltage-gated potassium channel complex;0.0479144883263067;99738!GO:0006650;glycerophospholipid metabolic 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|gostat_on_MCL_coexpression=GO:0022832;voltage-gated channel activity;0.0212610862975629;99738,20266!GO:0005244;voltage-gated ion channel activity;0.0212610862975629;99738,20266!GO:0031420;alkali metal ion binding;0.0212610862975629;99738,20266!GO:0006810;transport;0.0212610862975629;100273,99738,20266,18802!GO:0051234;establishment of localization;0.0212610862975629;100273,99738,20266,18802!GO:0005261;cation channel activity;0.0212610862975629;99738,20266!GO:0051179;localization;0.0212610862975629;100273,99738,20266,18802!GO:0022836;gated channel activity;0.0212610862975629;99738,20266!GO:0046873;metal ion transmembrane transporter activity;0.0212610862975629;99738,20266!GO:0015672;monovalent inorganic cation transport;0.0212610862975629;99738,20266!GO:0007340;acrosome reaction;0.0212610862975629;18802!GO:0004435;phosphoinositide phospholipase C activity;0.0212610862975629;18802!GO:0004434;inositol or phosphatidylinositol phosphodiesterase activity;0.0212610862975629;18802!GO:0005216;ion channel activity;0.0230202269040457;99738,20266!GO:0022838;substrate specific channel activity;0.0230202269040457;99738,20266!GO:0022803;passive transmembrane transporter activity;0.0230202269040457;99738,20266!GO:0015267;channel activity;0.0230202269040457;99738,20266!GO:0004629;phospholipase C activity;0.0230202269040457;18802!GO:0030001;metal ion transport;0.0230774535726656;99738,20266!GO:0017156;calcium ion-dependent exocytosis;0.0275451680756006;18802!GO:0008324;cation transmembrane transporter activity;0.0275451680756006;99738,20266!GO:0006812;cation transport;0.0275451680756006;99738,20266!GO:0005272;sodium channel activity;0.0311898189645894;20266!GO:0015075;ion transmembrane transporter activity;0.0451749126702556;99738,20266!GO:0007338;single fertilization;0.0451749126702556;18802!GO:0030384;phosphoinositide metabolic process;0.0458893449675082;18802!GO:0004620;phospholipase activity;0.0458893449675082;18802!GO:0006811;ion transport;0.0465019137658845;99738,20266!GO:0009566;fertilization;0.0465019137658845;18802!GO:0022891;substrate-specific transmembrane transporter activity;0.0475471638115029;99738,20266!GO:0008076;voltage-gated potassium channel complex;0.0479144883263067;99738!GO:0006650;glycerophospholipid metabolic process;0.0498336203933884;18802!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004121!1.89e-17!95;UBERON:0000924!1.89e-17!95;UBERON:0006601!1.89e-17!95;UBERON:0010371!1.33e-16!73;UBERON:0000073!7.00e-16!54;UBERON:0002346!1.09e-14!64;UBERON:0003075!1.09e-14!64;UBERON:0007284!1.09e-14!64;UBERON:0001049!1.31e-14!52;UBERON:0005068!1.31e-14!52;UBERON:0006241!1.31e-14!52;UBERON:0007135!1.31e-14!52;UBERON:0001017!3.94e-14!73;UBERON:0001016!6.86e-14!75;UBERON:0000955!2.94e-12!47;UBERON:0006238!2.94e-12!47;UBERON:0010314!4.96e-12!92;UBERON:0002616!8.56e-12!46;UBERON:0003056!2.68e-10!49;UBERON:0002020!2.39e-09!34;UBERON:0003080!3.59e-09!40;UBERON:0002780!1.36e-08!39;UBERON:0001890!1.36e-08!39;UBERON:0006240!1.36e-08!39;UBERON:0003528!2.29e-07!29;UBERON:0002791!2.29e-07!29;UBERON:0001893!2.29e-07!29;UBERON:0002021!3.48e-07!10;UBERON:0000411!3.48e-07!10;UBERON:0001950!3.48e-07!10;UBERON:0003076!7.08e-07!12;UBERON:0003057!7.08e-07!12
}}

Latest revision as of 16:12, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr1:74589455..74589492,+p1@Plcd4
Mm9::chr3:107261813..107261838,-p2@Kcnc4
Mm9::chr3:107261840..107261893,-p1@Kcnc4
Mm9::chr3:107262609..107262634,-p@chr3:107262609..107262634
-
Mm9::chr4:108829312..108829367,-p2@Osbpl9
Mm9::chr6:113481495..113481506,-p2@Tmem111
Mm9::chr7:31911778..31911791,-p3@Scn1b
Mm9::chr7:31912183..31912196,-p5@Scn1b


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:0022832voltage-gated channel activity0.0212610862975629
GO:0005244voltage-gated ion channel activity0.0212610862975629
GO:0031420alkali metal ion binding0.0212610862975629
GO:0006810transport0.0212610862975629
GO:0051234establishment of localization0.0212610862975629
GO:0005261cation channel activity0.0212610862975629
GO:0051179localization0.0212610862975629
GO:0022836gated channel activity0.0212610862975629
GO:0046873metal ion transmembrane transporter activity0.0212610862975629
GO:0015672monovalent inorganic cation transport0.0212610862975629
GO:0007340acrosome reaction0.0212610862975629
GO:0004435phosphoinositide phospholipase C activity0.0212610862975629
GO:0004434inositol or phosphatidylinositol phosphodiesterase activity0.0212610862975629
GO:0005216ion channel activity0.0230202269040457
GO:0022838substrate specific channel activity0.0230202269040457
GO:0022803passive transmembrane transporter activity0.0230202269040457
GO:0015267channel activity0.0230202269040457
GO:0004629phospholipase C activity0.0230202269040457
GO:0030001metal ion transport0.0230774535726656
GO:0017156calcium ion-dependent exocytosis0.0275451680756006
GO:0008324cation transmembrane transporter activity0.0275451680756006
GO:0006812cation transport0.0275451680756006
GO:0005272sodium channel activity0.0311898189645894
GO:0015075ion transmembrane transporter activity0.0451749126702556
GO:0007338single fertilization0.0451749126702556
GO:0030384phosphoinositide metabolic process0.0458893449675082
GO:0004620phospholipase activity0.0458893449675082
GO:0006811ion transport0.0465019137658845
GO:0009566fertilization0.0465019137658845
GO:0022891substrate-specific transmembrane transporter activity0.0475471638115029
GO:0008076voltage-gated potassium channel complex0.0479144883263067
GO:0006650glycerophospholipid metabolic process0.0498336203933884



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
ectoderm-derived structure1.89e-1795
ectoderm1.89e-1795
presumptive ectoderm1.89e-1795
ecto-epithelium1.33e-1673
regional part of nervous system7.00e-1654
neurectoderm1.09e-1464
neural plate1.09e-1464
presumptive neural plate1.09e-1464
neural tube1.31e-1452
neural rod1.31e-1452
future spinal cord1.31e-1452
neural keel1.31e-1452
central nervous system3.94e-1473
nervous system6.86e-1475
brain2.94e-1247
future brain2.94e-1247
structure with developmental contribution from neural crest4.96e-1292
regional part of brain8.56e-1246
pre-chordal neural plate2.68e-1049
gray matter2.39e-0934
anterior neural tube3.59e-0940
regional part of forebrain1.36e-0839
forebrain1.36e-0839
future forebrain1.36e-0839
brain grey matter2.29e-0729
regional part of telencephalon2.29e-0729
telencephalon2.29e-0729
occipital lobe3.48e-0710
visual cortex3.48e-0710
neocortex3.48e-0710
posterior neural tube7.08e-0712
chordal neural plate7.08e-0712


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)
MA0003.12.63694
MA0004.10.434673
MA0006.10.271714
MA0007.10.419994
MA0009.10.870101
MA0014.10.162935
MA0017.10.804572
MA0019.10.688051
MA0024.11.93095
MA0025.11.10341
MA0027.12.51754
MA0028.10.281528
MA0029.10.804619
MA0030.10.811181
MA0031.10.775627
MA0038.11.41387
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.10.685543
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.11.64072
MA0056.10
MA0057.10.643187
MA0058.10.341628
MA0059.10.353484
MA0060.10.197678
MA0061.10.224905
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.0965831
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.10.934832
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.980744
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.229377
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.10.401504
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.362124
MA0103.10.827743
MA0105.10.41549
MA0106.10.626997
MA0107.10.301222
MA0108.20.710846
MA0109.10
MA0111.11.06639
MA0113.10.598933
MA0114.10.222763
MA0115.10.969632
MA0116.10.747001
MA0117.10.937363
MA0119.10.362692
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.11.63575
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.10.169849
MA0140.10.519484
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.10.900473
MA0146.10.946874
MA0147.10.236889
MA0148.10.450593
MA0149.10.367458
MA0062.20.137653
MA0035.20.524137
MA0039.20.402847
MA0138.21.61926
MA0002.20.172399
MA0137.20.863775
MA0104.20.18504
MA0047.20.576767
MA0112.20.0701537
MA0065.20.0704227
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.11.12269
MA0155.10.275377
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.10.453546
MA0161.10
MA0162.10.230918
MA0163.10.991519
MA0164.10.551114
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.22.35015
MA0102.21.59466
MA0258.10.210437
MA0259.10.227035
MA0442.10
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