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MCL coexpression mm9:799: Difference between revisions

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{{MCL_coexpression_mm9
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007035;vacuolar acidification;0.0157769315378812;11984!GO:0045851;pH reduction;0.0157769315378812;11984!GO:0051452;cellular pH reduction;0.0157769315378812;11984!GO:0051453;regulation of cellular pH;0.0157769315378812;11984!GO:0007042;lysosomal lumen acidification;0.0157769315378812;11984!GO:0030641;cellular hydrogen ion homeostasis;0.0197195436675489;11984!GO:0004630;phospholipase D activity;0.0250893514230226;18807!GO:0033176;proton-transporting V-type ATPase complex;0.0250893514230226;11984!GO:0016471;vacuolar proton-transporting V-type ATPase complex;0.0250893514230226;11984!GO:0030004;cellular monovalent inorganic cation homeostasis;0.0250893514230226;11984!GO:0055067;monovalent inorganic cation homeostasis;0.0250893514230226;11984!GO:0045309;protein phosphorylated amino acid binding;0.0262819222260888;19261!GO:0006910;phagocytosis, recognition;0.0331763951638302;19261!GO:0051219;phosphoprotein binding;0.0331763951638302;19261!GO:0006911;phagocytosis, 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|gostat_on_MCL_coexpression=GO:0007035;vacuolar acidification;0.0157769315378812;11984!GO:0045851;pH reduction;0.0157769315378812;11984!GO:0051452;cellular pH reduction;0.0157769315378812;11984!GO:0051453;regulation of cellular pH;0.0157769315378812;11984!GO:0007042;lysosomal lumen acidification;0.0157769315378812;11984!GO:0030641;cellular hydrogen ion homeostasis;0.0197195436675489;11984!GO:0004630;phospholipase D activity;0.0250893514230226;18807!GO:0033176;proton-transporting V-type ATPase complex;0.0250893514230226;11984!GO:0016471;vacuolar proton-transporting V-type ATPase complex;0.0250893514230226;11984!GO:0030004;cellular monovalent inorganic cation homeostasis;0.0250893514230226;11984!GO:0055067;monovalent inorganic cation homeostasis;0.0250893514230226;11984!GO:0045309;protein phosphorylated amino acid binding;0.0262819222260888;19261!GO:0006910;phagocytosis, recognition;0.0331763951638302;19261!GO:0051219;phosphoprotein binding;0.0331763951638302;19261!GO:0006911;phagocytosis, engulfment;0.0331763951638302;19261!GO:0007040;lysosome organization and biogenesis;0.0331763951638302;11984!GO:0050766;positive regulation of phagocytosis;0.0331763951638302;19261!GO:0050764;regulation of phagocytosis;0.0331763951638302;19261!GO:0005774;vacuolar membrane;0.0331763951638302;11984!GO:0006885;regulation of pH;0.035451443793266;11984!GO:0007033;vacuole organization and biogenesis;0.0356360882026992;11984!GO:0044437;vacuolar part;0.0358036526335401;11984!GO:0045807;positive regulation of endocytosis;0.0359563649399432;19261!GO:0008553;hydrogen-exporting ATPase activity, phosphorylative mechanism;0.0393710703231679;11984!GO:0015985;energy coupled proton transport, down electrochemical gradient;0.0426270730378642;11984!GO:0015986;ATP synthesis coupled proton transport;0.0426270730378642;11984!GO:0051050;positive regulation of transport;0.0426270730378642;19261!GO:0030100;regulation of endocytosis;0.0426270730378642;19261!GO:0006754;ATP biosynthetic process;0.0426270730378642;11984!GO:0006753;nucleoside phosphate metabolic process;0.0426270730378642;11984!GO:0046933;hydrogen ion transporting ATP synthase activity, rotational mechanism;0.0426270730378642;11984!GO:0016469;proton-transporting two-sector ATPase complex;0.0426270730378642;11984!GO:0046961;hydrogen ion transporting ATPase activity, rotational mechanism;0.0426270730378642;11984!GO:0006909;phagocytosis;0.0426270730378642;19261!GO:0007015;actin filament organization;0.0426270730378642;19261!GO:0046034;ATP metabolic process;0.0426270730378642;11984!GO:0008037;cell recognition;0.0426270730378642;19261!GO:0009145;purine nucleoside triphosphate biosynthetic process;0.0426270730378642;11984!GO:0009206;purine ribonucleoside triphosphate biosynthetic process;0.0426270730378642;11984!GO:0009201;ribonucleoside triphosphate biosynthetic process;0.0426270730378642;11984!GO:0004620;phospholipase activity;0.0426270730378642;18807!GO:0019829;cation-transporting ATPase activity;0.0426270730378642;11984!GO:0009142;nucleoside triphosphate biosynthetic process;0.0426270730378642;11984!GO:0009205;purine ribonucleoside triphosphate metabolic process;0.0426270730378642;11984!GO:0009199;ribonucleoside triphosphate metabolic process;0.0426270730378642;11984!GO:0006119;oxidative phosphorylation;0.0426270730378642;11984!GO:0009144;purine nucleoside triphosphate metabolic process;0.0426270730378642;11984!GO:0015992;proton transport;0.0432289395035572;11984!GO:0006752;group transfer coenzyme metabolic process;0.0432289395035572;11984!GO:0009141;nucleoside triphosphate metabolic process;0.0432289395035572;11984!GO:0009152;purine ribonucleotide biosynthetic process;0.0432289395035572;11984!GO:0006818;hydrogen transport;0.0432289395035572;11984!GO:0015662;ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism;0.0432289395035572;11984!GO:0009260;ribonucleotide biosynthetic process;0.0432289395035572;11984!GO:0016298;lipase activity;0.0432289395035572;18807!GO:0007160;cell-matrix adhesion;0.0432289395035572;19261!GO:0009150;purine ribonucleotide metabolic process;0.0432289395035572;11984!GO:0008081;phosphoric diester hydrolase activity;0.0432289395035572;18807!GO:0006164;purine nucleotide biosynthetic process;0.0432289395035572;11984!GO:0031589;cell-substrate adhesion;0.0438092038771068;19261!GO:0009259;ribonucleotide metabolic process;0.0450093633137073;11984!GO:0006163;purine nucleotide metabolic process;0.0467984890472701;11984!
}}

Latest revision as of 15:54, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:95574072..95574082,-p1@ENSMUST00000155531
p1@uc007lao.1
Mm9::chr15:98571806..98571818,-p@chr15:98571806..98571818
-
Mm9::chr16:4879810..4879836,-p1@Fam100a
Mm9::chr17:24306359..24306395,-p1@Atp6v0c
Mm9::chr17:24306593..24306658,-p2@Atp6v0c
Mm9::chr2:129419264..129419336,+p2@Sirpa
Mm9::chr5:139960374..139960427,-p1@Zfand2a
Mm9::chr7:28326103..28326131,+p@chr7:28326103..28326131
+
Mm9::chr7:28327793..28327828,-p1@Pld3


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:0007035vacuolar acidification0.0157769315378812
GO:0045851pH reduction0.0157769315378812
GO:0051452cellular pH reduction0.0157769315378812
GO:0051453regulation of cellular pH0.0157769315378812
GO:0007042lysosomal lumen acidification0.0157769315378812
GO:0030641cellular hydrogen ion homeostasis0.0197195436675489
GO:0004630phospholipase D activity0.0250893514230226
GO:0033176proton-transporting V-type ATPase complex0.0250893514230226
GO:0016471vacuolar proton-transporting V-type ATPase complex0.0250893514230226
GO:0030004cellular monovalent inorganic cation homeostasis0.0250893514230226
GO:0055067monovalent inorganic cation homeostasis0.0250893514230226
GO:0045309protein phosphorylated amino acid binding0.0262819222260888
GO:0006910phagocytosis, recognition0.0331763951638302
GO:0051219phosphoprotein binding0.0331763951638302
GO:0006911phagocytosis, engulfment0.0331763951638302
GO:0007040lysosome organization and biogenesis0.0331763951638302
GO:0050766positive regulation of phagocytosis0.0331763951638302
GO:0050764regulation of phagocytosis0.0331763951638302
GO:0005774vacuolar membrane0.0331763951638302
GO:0006885regulation of pH0.035451443793266
GO:0007033vacuole organization and biogenesis0.0356360882026992
GO:0044437vacuolar part0.0358036526335401
GO:0045807positive regulation of endocytosis0.0359563649399432
GO:0008553hydrogen-exporting ATPase activity, phosphorylative mechanism0.0393710703231679
GO:0015985energy coupled proton transport, down electrochemical gradient0.0426270730378642
GO:0015986ATP synthesis coupled proton transport0.0426270730378642
GO:0051050positive regulation of transport0.0426270730378642
GO:0030100regulation of endocytosis0.0426270730378642
GO:0006754ATP biosynthetic process0.0426270730378642
GO:0006753nucleoside phosphate metabolic process0.0426270730378642
GO:0046933hydrogen ion transporting ATP synthase activity, rotational mechanism0.0426270730378642
GO:0016469proton-transporting two-sector ATPase complex0.0426270730378642
GO:0046961hydrogen ion transporting ATPase activity, rotational mechanism0.0426270730378642
GO:0006909phagocytosis0.0426270730378642
GO:0007015actin filament organization0.0426270730378642
GO:0046034ATP metabolic process0.0426270730378642
GO:0008037cell recognition0.0426270730378642
GO:0009145purine nucleoside triphosphate biosynthetic process0.0426270730378642
GO:0009206purine ribonucleoside triphosphate biosynthetic process0.0426270730378642
GO:0009201ribonucleoside triphosphate biosynthetic process0.0426270730378642
GO:0004620phospholipase activity0.0426270730378642
GO:0019829cation-transporting ATPase activity0.0426270730378642
GO:0009142nucleoside triphosphate biosynthetic process0.0426270730378642
GO:0009205purine ribonucleoside triphosphate metabolic process0.0426270730378642
GO:0009199ribonucleoside triphosphate metabolic process0.0426270730378642
GO:0006119oxidative phosphorylation0.0426270730378642
GO:0009144purine nucleoside triphosphate metabolic process0.0426270730378642
GO:0015992proton transport0.0432289395035572
GO:0006752group transfer coenzyme metabolic process0.0432289395035572
GO:0009141nucleoside triphosphate metabolic process0.0432289395035572
GO:0009152purine ribonucleotide biosynthetic process0.0432289395035572
GO:0006818hydrogen transport0.0432289395035572
GO:0015662ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism0.0432289395035572
GO:0009260ribonucleotide biosynthetic process0.0432289395035572
GO:0016298lipase activity0.0432289395035572
GO:0007160cell-matrix adhesion0.0432289395035572
GO:0009150purine ribonucleotide metabolic process0.0432289395035572
GO:0008081phosphoric diester hydrolase activity0.0432289395035572
GO:0006164purine nucleotide biosynthetic process0.0432289395035572
GO:0031589cell-substrate adhesion0.0438092038771068
GO:0009259ribonucleotide metabolic process0.0450093633137073
GO:0006163purine nucleotide metabolic process0.0467984890472701



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
central nervous system2.46e-2373
ectoderm-derived structure3.06e-2395
ectoderm3.06e-2395
presumptive ectoderm3.06e-2395
regional part of nervous system4.38e-2354
nervous system6.54e-2375
neural tube7.04e-2252
neural rod7.04e-2252
future spinal cord7.04e-2252
neural keel7.04e-2252
brain2.98e-1947
future brain2.98e-1947
regional part of brain1.34e-1846
ecto-epithelium1.82e-1873
neurectoderm4.08e-1864
neural plate4.08e-1864
presumptive neural plate4.08e-1864
gray matter6.00e-1634
anterior neural tube1.41e-1540
structure with developmental contribution from neural crest2.55e-1592
regional part of forebrain5.52e-1539
forebrain5.52e-1539
future forebrain5.52e-1539
brain grey matter1.88e-1329
regional part of telencephalon1.88e-1329
telencephalon1.88e-1329
anatomical conduit2.24e-13122
pre-chordal neural plate4.46e-1349
tube4.52e-12114
cerebral cortex1.07e-0921
cerebral hemisphere1.07e-0921
pallium1.07e-0921
regional part of cerebral cortex1.42e-0917
occipital lobe8.98e-0810
visual cortex8.98e-0810
neocortex8.98e-0810
adult organism1.29e-0751
posterior neural tube4.73e-0712
chordal neural plate4.73e-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)
MA0003.13.51844
MA0004.10.394951
MA0006.10.670874
MA0007.10.38073
MA0009.10.82278
MA0014.13.05062
MA0017.10.26239
MA0019.10.642876
MA0024.10.779446
MA0025.11.05446
MA0027.12.46647
MA0028.10.24786
MA0029.10.757957
MA0030.10.764448
MA0031.10.729293
MA0038.10.534262
MA0040.10.835181
MA0041.10.323687
MA0042.10.311486
MA0043.10.918718
MA0046.10.858391
MA0048.10.589612
MA0050.10.431976
MA0051.10.542972
MA0052.10.84317
MA0055.10.424109
MA0056.10
MA0057.11.93392
MA0058.10.305206
MA0059.10.316585
MA0060.10.169058
MA0061.10.194456
MA0063.10
MA0066.10.523573
MA0067.11.16502
MA0068.10.563625
MA0069.10.843506
MA0070.10.833895
MA0071.10.431174
MA0072.10.825495
MA0073.15.13002
MA0074.10.488775
MA0076.10.279739
MA0077.10.804033
MA0078.10.575205
MA0081.10.338098
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.10.728131
MA0089.10
MA0090.10.362551
MA0091.10.407455
MA0092.10.362847
MA0093.10.2553
MA0095.10
MA0098.10
MA0100.10.477594
MA0101.10.324888
MA0103.10.272167
MA0105.10.109964
MA0106.10.582805
MA0107.10.266586
MA0108.20.665343
MA0109.10
MA0111.10.375908
MA0113.10.555251
MA0114.10.561811
MA0115.10.921497
MA0116.10.238371
MA0117.10.88947
MA0119.10.325434
MA0122.10.909168
MA0124.11.11203
MA0125.11.03833
MA0130.10
MA0131.10.638414
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.10.508047
MA0139.10.441109
MA0140.10.477483
MA0141.10.29014
MA0142.10.714976
MA0143.10.571221
MA0144.10.195095
MA0145.10.77191
MA0146.11.09957
MA0147.10.205697
MA0148.10.410398
MA0149.10.330018
MA0062.20.113962
MA0035.21.21101
MA0039.21.67243
MA0138.20.630612
MA0002.20.145685
MA0137.20.287486
MA0104.20.157347
MA0047.20.533516
MA0112.20.200175
MA0065.20.200864
MA0150.10.380623
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.581988
MA0155.10.490492
MA0156.10.278949
MA0157.10.683365
MA0158.10
MA0159.10.214506
MA0160.10.413266
MA0161.10
MA0162.11.61761
MA0163.12.42374
MA0164.11.26737
MA0080.20.267388
MA0018.21.28741
MA0099.20.624421
MA0079.25.6867
MA0102.21.5442
MA0258.10.180934
MA0259.10.571417
MA0442.10
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