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MCL coexpression mm9:1532: Difference between revisions

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{{MCL_coexpression_mm9
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process;0.0290678163773041;66043!GO:0006753;nucleoside phosphate metabolic process;0.0290678163773041;66043!GO:0046933;hydrogen ion transporting ATP synthase activity, rotational mechanism;0.0290678163773041;66043!GO:0016469;proton-transporting two-sector ATPase complex;0.0290678163773041;66043!GO:0046961;hydrogen ion transporting ATPase activity, rotational mechanism;0.0290678163773041;66043!GO:0046034;ATP metabolic process;0.0290678163773041;66043!GO:0005739;mitochondrion;0.0290678163773041;66477,66043!GO:0009206;purine ribonucleoside triphosphate biosynthetic process;0.0290678163773041;66043!GO:0009201;ribonucleoside triphosphate biosynthetic process;0.0290678163773041;66043!GO:0009145;purine nucleoside triphosphate biosynthetic process;0.0290678163773041;66043!GO:0019829;cation-transporting ATPase activity;0.0290678163773041;66043!GO:0009142;nucleoside triphosphate biosynthetic process;0.0290678163773041;66043!GO:0009205;purine ribonucleoside triphosphate metabolic 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|gostat_on_MCL_coexpression=GO:0005743;mitochondrial inner membrane;0.0143950233737972;66477,66043!GO:0019866;organelle inner membrane;0.0143950233737972;66477,66043!GO:0031966;mitochondrial membrane;0.0143950233737972;66477,66043!GO:0005740;mitochondrial envelope;0.0143950233737972;66477,66043!GO:0044429;mitochondrial part;0.0143950233737972;66477,66043!GO:0045261;proton-transporting ATP synthase complex, catalytic core F(1);0.0143950233737972;66043!GO:0033178;proton-transporting two-sector ATPase complex, catalytic domain;0.0143950233737972;66043!GO:0031975;envelope;0.0143950233737972;66477,66043!GO:0031967;organelle envelope;0.0143950233737972;66477,66043!GO:0031090;organelle membrane;0.0249855892454239;66477,66043!GO:0045259;proton-transporting ATP synthase complex;0.0279444512698392;66043!GO:0015985;energy coupled proton transport, down electrochemical gradient;0.0290678163773041;66043!GO:0015986;ATP synthesis coupled proton transport;0.0290678163773041;66043!GO:0006754;ATP biosynthetic process;0.0290678163773041;66043!GO:0006753;nucleoside phosphate metabolic process;0.0290678163773041;66043!GO:0046933;hydrogen ion transporting ATP synthase activity, rotational mechanism;0.0290678163773041;66043!GO:0016469;proton-transporting two-sector ATPase complex;0.0290678163773041;66043!GO:0046961;hydrogen ion transporting ATPase activity, rotational mechanism;0.0290678163773041;66043!GO:0046034;ATP metabolic process;0.0290678163773041;66043!GO:0005739;mitochondrion;0.0290678163773041;66477,66043!GO:0009206;purine ribonucleoside triphosphate biosynthetic process;0.0290678163773041;66043!GO:0009201;ribonucleoside triphosphate biosynthetic process;0.0290678163773041;66043!GO:0009145;purine nucleoside triphosphate biosynthetic process;0.0290678163773041;66043!GO:0019829;cation-transporting ATPase activity;0.0290678163773041;66043!GO:0009142;nucleoside triphosphate biosynthetic process;0.0290678163773041;66043!GO:0009205;purine ribonucleoside triphosphate metabolic process;0.0290678163773041;66043!GO:0009199;ribonucleoside triphosphate metabolic process;0.0290678163773041;66043!GO:0009144;purine nucleoside triphosphate metabolic process;0.0290678163773041;66043!GO:0006119;oxidative phosphorylation;0.0290678163773041;66043!GO:0015992;proton transport;0.0290678163773041;66043!GO:0006752;group transfer coenzyme metabolic process;0.0290678163773041;66043!GO:0009141;nucleoside triphosphate metabolic process;0.0290678163773041;66043!GO:0009152;purine ribonucleotide biosynthetic process;0.0290678163773041;66043!GO:0006818;hydrogen transport;0.0290678163773041;66043!GO:0009260;ribonucleotide biosynthetic process;0.0296929715106224;66043!GO:0009150;purine ribonucleotide metabolic process;0.0299232124906377;66043!GO:0006164;purine nucleotide biosynthetic process;0.0299232124906377;66043!GO:0009259;ribonucleotide metabolic process;0.0313683668974196;66043!GO:0006163;purine nucleotide metabolic process;0.032303477403647;66043!GO:0042625;ATPase activity, coupled to transmembrane movement of ions;0.03444783581511;66043!GO:0009108;coenzyme biosynthetic process;0.03444783581511;66043!GO:0015078;hydrogen ion transmembrane transporter activity;0.0368526864043736;66043!GO:0015077;monovalent inorganic cation transmembrane transporter activity;0.0371002154178416;66043!GO:0051188;cofactor biosynthetic process;0.0371002154178416;66043!GO:0042626;ATPase activity, coupled to transmembrane movement of substances;0.041921923177726;66043!GO:0043492;ATPase activity, coupled to movement of substances;0.041921923177726;66043!GO:0016820;hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances;0.041921923177726;66043!GO:0009165;nucleotide biosynthetic process;0.0431575302318435;66043!GO:0015399;primary active transmembrane transporter activity;0.0434545106322518;66043!GO:0015405;P-P-bond-hydrolysis-driven transmembrane transporter activity;0.0434545106322518;66043!GO:0022890;inorganic cation transmembrane transporter activity;0.0435937737411297;66043!GO:0005737;cytoplasm;0.0493307875638466;66477,15254,66043!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000160!7.92e-08!31;UBERON:0003914!1.04e-07!47;UBERON:0000344!1.29e-07!15
|tfbs_overrepresentation_for_novel_motifs=0.557864,0.087078,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.310789,0.115752,0.668936,0.702872,0.300533,1.72941,0.424775,0,0.930881,0.397593,0.283802,0.185796,0.489529,0.44579,1.72742,0.404661,1.32977,0.757752,0.274609,0.641282,1.15581,0.227599,0.626183,1.03545,0.395107,0.253145,0.425309,0.0566307,0.384813,0.699032,0.360612,0.328675,0.401916,0.631725,0.134724,0.426986,0.227872,1.44282,0.847828,0.658142,0.115788,0.459555,0.912738,0.786094,0.627649,1.18062,1.19842,0.73621,1.18377,0.689304,0.26467,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.30684,0.46305,1.23259,0.714607,0.245132,0.253065,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.796301,4.09681,0.0793594,1.03552,0.227755,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,1.60426,1.46478,1.05152,0.848095,0.20438,0.384901,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,1.24825,0.491483,0.550229,1.16464,0.495367,0.674448,1.41481,1.03353,0.328405,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.143464,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,1.5287,3.28302,2.18247,0.569503,0.408309,0.230371,0.416978,1.18223,0.343194,0.749664,1.26545,0.787153,1.95382,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,1.75672,0.383572,0.701187,0.191104
}}

Latest revision as of 17:05, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:79605024..79605035,+p5@Atp5d
Mm9::chr10:79605040..79605056,+p4@Atp5d
Mm9::chr10:79605079..79605098,+p2@Atp5d
Mm9::chr11:54679876..54679894,+p2@Hint1
Mm9::chr19:47165168..47165173,-p2@Gm14539
p2@LOC100504912
p2@Usmg5


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:0005743mitochondrial inner membrane0.0143950233737972
GO:0019866organelle inner membrane0.0143950233737972
GO:0031966mitochondrial membrane0.0143950233737972
GO:0005740mitochondrial envelope0.0143950233737972
GO:0044429mitochondrial part0.0143950233737972
GO:0045261proton-transporting ATP synthase complex, catalytic core F(1)0.0143950233737972
GO:0033178proton-transporting two-sector ATPase complex, catalytic domain0.0143950233737972
GO:0031975envelope0.0143950233737972
GO:0031967organelle envelope0.0143950233737972
GO:0031090organelle membrane0.0249855892454239
GO:0045259proton-transporting ATP synthase complex0.0279444512698392
GO:0015985energy coupled proton transport, down electrochemical gradient0.0290678163773041
GO:0015986ATP synthesis coupled proton transport0.0290678163773041
GO:0006754ATP biosynthetic process0.0290678163773041
GO:0006753nucleoside phosphate metabolic process0.0290678163773041
GO:0046933hydrogen ion transporting ATP synthase activity, rotational mechanism0.0290678163773041
GO:0016469proton-transporting two-sector ATPase complex0.0290678163773041
GO:0046961hydrogen ion transporting ATPase activity, rotational mechanism0.0290678163773041
GO:0046034ATP metabolic process0.0290678163773041
GO:0005739mitochondrion0.0290678163773041
GO:0009206purine ribonucleoside triphosphate biosynthetic process0.0290678163773041
GO:0009201ribonucleoside triphosphate biosynthetic process0.0290678163773041
GO:0009145purine nucleoside triphosphate biosynthetic process0.0290678163773041
GO:0019829cation-transporting ATPase activity0.0290678163773041
GO:0009142nucleoside triphosphate biosynthetic process0.0290678163773041
GO:0009205purine ribonucleoside triphosphate metabolic process0.0290678163773041
GO:0009199ribonucleoside triphosphate metabolic process0.0290678163773041
GO:0009144purine nucleoside triphosphate metabolic process0.0290678163773041
GO:0006119oxidative phosphorylation0.0290678163773041
GO:0015992proton transport0.0290678163773041
GO:0006752group transfer coenzyme metabolic process0.0290678163773041
GO:0009141nucleoside triphosphate metabolic process0.0290678163773041
GO:0009152purine ribonucleotide biosynthetic process0.0290678163773041
GO:0006818hydrogen transport0.0290678163773041
GO:0009260ribonucleotide biosynthetic process0.0296929715106224
GO:0009150purine ribonucleotide metabolic process0.0299232124906377
GO:0006164purine nucleotide biosynthetic process0.0299232124906377
GO:0009259ribonucleotide metabolic process0.0313683668974196
GO:0006163purine nucleotide metabolic process0.032303477403647
GO:0042625ATPase activity, coupled to transmembrane movement of ions0.03444783581511
GO:0009108coenzyme biosynthetic process0.03444783581511
GO:0015078hydrogen ion transmembrane transporter activity0.0368526864043736
GO:0015077monovalent inorganic cation transmembrane transporter activity0.0371002154178416
GO:0051188cofactor biosynthetic process0.0371002154178416
GO:0042626ATPase activity, coupled to transmembrane movement of substances0.041921923177726
GO:0043492ATPase activity, coupled to movement of substances0.041921923177726
GO:0016820hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances0.041921923177726
GO:0009165nucleotide biosynthetic process0.0431575302318435
GO:0015399primary active transmembrane transporter activity0.0434545106322518
GO:0015405P-P-bond-hydrolysis-driven transmembrane transporter activity0.0434545106322518
GO:0022890inorganic cation transmembrane transporter activity0.0435937737411297
GO:0005737cytoplasm0.0493307875638466



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
intestine7.92e-0831
epithelial tube1.04e-0747
mucosa1.29e-0715


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)
MA0003.10.0833043
MA0004.10.603793
MA0006.11.89254
MA0007.10.587678
MA0009.11.06266
MA0014.10.0502051
MA0017.10.449113
MA0019.10.874061
MA0024.11.01759
MA0025.11.30092
MA0027.12.72141
MA0028.10.43138
MA0029.10.995171
MA0030.11.00195
MA0031.10.965177
MA0038.10.757669
MA0040.11.07552
MA0041.11.29634
MA0042.10.507715
MA0043.11.1618
MA0046.11.09955
MA0048.10.205696
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.10.0851423
MA0056.10
MA0057.10.192781
MA0058.10.50032
MA0059.10.513699
MA0060.10.330907
MA0061.10.364227
MA0063.10
MA0066.10.746072
MA0067.11.41352
MA0068.10.197245
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.10.000589538
MA0074.10.708108
MA0076.11.1853
MA0077.11.04318
MA0078.10.801834
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.15.20048
MA0089.10
MA0090.10.566938
MA0091.10.617887
MA0092.10.567278
MA0093.10.440484
MA0095.10
MA0098.10
MA0100.10.695835
MA0101.10.523409
MA0103.10.460936
MA0105.10.248108
MA0106.10.809991
MA0107.10.454197
MA0108.20.897859
MA0109.10
MA0111.10.582193
MA0113.10.780358
MA0114.10.361633
MA0115.11.16466
MA0116.10.419688
MA0117.11.13165
MA0119.10.524046
MA0122.11.15196
MA0124.11.35963
MA0125.11.28445
MA0130.10
MA0131.10.869325
MA0132.10
MA0133.10
MA0135.11.19898
MA0136.10.729175
MA0139.10.295945
MA0140.10.695713
MA0141.10.482463
MA0142.10.950155
MA0143.10.797553
MA0144.10.365053
MA0145.10.157686
MA0146.10.0604336
MA0147.10.986917
MA0148.10.621195
MA0149.10.529387
MA0062.20.706751
MA0035.20.700704
MA0039.20.285933
MA0138.20.861035
MA0002.20.299191
MA0137.21.20517
MA0104.20.845917
MA0047.20.75686
MA0112.20.157681
MA0065.20.477991
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.10.203217
MA0155.10.515751
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.10.0699535
MA0163.10.0644585
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.20.00606655
MA0102.21.79669
MA0258.10.346619
MA0259.11.71005
MA0442.10
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