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MCL coexpression mm9:1972: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000344!3.13e-10!15;UBERON:0001242!4.22e-09!13;UBERON:0000060!4.22e-09!13;UBERON:0001262!4.22e-09!13;UBERON:0004786!4.22e-09!13;UBERON:0000160!7.55e-09!31;UBERON:0003914!2.13e-08!47
|ontology_enrichment_uberon=UBERON:0000344!3.13e-10!15;UBERON:0001242!4.22e-09!13;UBERON:0000060!4.22e-09!13;UBERON:0001262!4.22e-09!13;UBERON:0004786!4.22e-09!13;UBERON:0000160!7.55e-09!31;UBERON:0003914!2.13e-08!47
|tfbs_overrepresentation_for_novel_motifs=0.641384,0.402508,0.612053,0.688265,0.483253,0.704257,0.803568,0.370124,0.381467,0.489964,0.755749,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,0.928768,0.683591,0.570433,1.08884,0.815872,0.481455,0.620553,0.846564,0.342316,0.727368,0.535752,0.790816,0.711848,1.12823,0.471365,0.854272,1.2563,0.30022,0.460474,0.786577,0.434783,0.40068,0.478558,0.717547,0.185353,0.504971,0.325217,0.675898,0.938241,0.744678,0.162985,0.539131,1.0041,0.875451,0.282443,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,0.205546,1.32691,0.323563,0.834514,0.854076,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,0.11855,0.129654,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,0.576517,0.7614,1.51002,1.1991,0.143825,1.65428,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,1.2358,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.293812,0.542121,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,0.589293
|tfbs_overrepresentation_for_novel_motifs=0.641384,0.402508,0.612053,0.688265,0.483253,0.704257,0.803568,0.370124,0.381467,0.489964,0.755749,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,0.928768,0.683591,0.570433,1.08884,0.815872,0.481455,0.620553,0.846564,0.342316,0.727368,0.535752,0.790816,0.711848,1.12823,0.471365,0.854272,1.2563,0.30022,0.460474,0.786577,0.434783,0.40068,0.478558,0.717547,0.185353,0.504971,0.325217,0.675898,0.938241,0.744678,0.162985,0.539131,1.0041,0.875451,0.282443,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,0.205546,1.32691,0.323563,0.834514,0.854076,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,0.11855,0.129654,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,0.576517,0.7614,1.51002,1.1991,0.143825,1.65428,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,1.2358,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.293812,0.542121,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,0.589293
|tfbs_overrepresentation_jaspar=MA0003.1;0.142214,MA0004.1;0.6888,MA0006.1;0.497533,MA0007.1;0.672186,MA0009.1;1.15569,MA0014.1;0.581929,MA0017.1;0.528196,MA0019.1;0.964875,MA0024.1;1.11019,MA0025.1;1.39562,MA0027.1;2.81824,MA0028.1;2.19266,MA0029.1;1.08753,MA0030.1;1.09438,MA0031.1;1.05719,MA0038.1;0.846479,MA0040.1;1.16866,MA0041.1;0.604221,MA0042.1;0.589368,MA0043.1;1.25564,MA0046.1;1.1929,MA0048.1;0.735223,MA0050.1;0.731539,MA0051.1;0.856094,MA0052.1;1.17701,MA0055.1;1.28762,MA0056.1;0,MA0057.1;0.701847,MA0058.1;0.581673,MA0059.1;0.59559,MA0060.1;1.04037,MA0061.1;0.438628,MA0063.1;0,MA0066.1;0.834648,MA0067.1;1.50873,MA0068.1;0.713436,MA0069.1;1.17737,MA0070.1;1.16732,MA0071.1;0.73062,MA0072.1;1.15853,MA0073.1;0.00221226,MA0074.1;0.795862,MA0076.1;4.59949,MA0077.1;1.13603,MA0078.1;0.891476,MA0081.1;1.5065,MA0083.1;1.25482,MA0084.1;1.84013,MA0087.1;1.21037,MA0088.1;0.201215,MA0089.1;0,MA0090.1;0.650768,MA0091.1;0.703314,MA0092.1;0.651119,MA0093.1;1.29026,MA0095.1;0,MA0098.1;0,MA0100.1;0.783305,MA0101.1;0.605676,MA0103.1;0.540576,MA0105.1;0.313353,MA0106.1;0.899777,MA0107.1;0.533522,MA0108.2;0.989014,MA0109.1;0,MA0111.1;0.666525,MA0113.1;0.869608,MA0114.1;0.43587,MA0115.1;1.25852,MA0116.1;1.24367,MA0117.1;1.22527,MA0119.1;0.606338,MA0122.1;1.24573,MA0124.1;1.45461,MA0125.1;1.37907,MA0130.1;0,MA0131.1;0.960068,MA0132.1;0,MA0133.1;0,MA0135.1;1.29308,MA0136.1;0.817395,MA0139.1;0.365453,MA0140.1;0.78318,MA0141.1;1.38335,MA0142.1;1.04199,MA0143.1;0.887119,MA0144.1;1.11951,MA0145.1;0.608454,MA0146.1;1.5929,MA0147.1;1.15069,MA0148.1;0.706718,MA0149.1;0.611881,MA0062.2;3.24307,MA0035.2;0.788288,MA0039.2;2.41467,MA0138.2;0.951653,MA0002.2;0.368961,MA0137.2;1.37638,MA0104.2;1.0034,MA0047.2;0.845655,MA0112.2;0.211985,MA0065.2;0.212467,MA0150.1;0.67206,MA0151.1;0,MA0152.1;0.84577,MA0153.1;1.31015,MA0154.1;0.728853,MA0155.1;1.8891,MA0156.1;1.35382,MA0157.1;1.0083,MA0158.1;0,MA0159.1;1.1762,MA0160.1;0.71003,MA0161.1;0,MA0162.1;0.704935,MA0163.1;0.0996272,MA0164.1;0.817786,MA0080.2;0.534538,MA0018.2;0.828253,MA0099.2;0.944966,MA0079.2;0.300141,MA0102.2;1.8929,MA0258.1;0.419871,MA0259.1;0.441366,MA0442.1;0
}}
}}

Revision as of 14:09, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:53244281..53244340,-p1@Uqcrq
Mm9::chr2:174289540..174289551,-p2@Atp5e
Mm9::chr4:40226373..40226414,-p1@Ndufb6
Mm9::chr6:125142195..125142228,+p1@Mrpl51


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:0005739mitochondrion0.000878702121549544
GO:0044429mitochondrial part0.00139034920464052
GO:0044455mitochondrial membrane part0.00155129181801757
GO:0015078hydrogen ion transmembrane transporter activity0.0044695623510328
GO:0015077monovalent inorganic cation transmembrane transporter activity0.0044695623510328
GO:0022890inorganic cation transmembrane transporter activity0.00693727815077478
GO:0005753mitochondrial proton-transporting ATP synthase complex0.0128646546783533
GO:0044444cytoplasmic part0.0134689523553146
GO:0005743mitochondrial inner membrane0.0134941987268441
GO:0019866organelle inner membrane0.0134941987268441
GO:0031966mitochondrial membrane0.0134941987268441
GO:0005740mitochondrial envelope0.0138508279464587
GO:0045261proton-transporting ATP synthase complex, catalytic core F(1)0.0138508279464587
GO:0033178proton-transporting two-sector ATPase complex, catalytic domain0.0150038303946409
GO:0016681oxidoreductase activity, acting on diphenols and related substances as donors, cytochrome as acceptor0.0177202870675471
GO:0008121ubiquinol-cytochrome-c reductase activity0.0177202870675471
GO:0016679oxidoreductase activity, acting on diphenols and related substances as donors0.0177202870675471
GO:0031975envelope0.0177202870675471
GO:0031967organelle envelope0.0177202870675471
GO:0006091generation of precursor metabolites and energy0.0199794080386367
GO:0008324cation transmembrane transporter activity0.0235762164430165
GO:0045259proton-transporting ATP synthase complex0.0245295343418053
GO:0031090organelle membrane0.0273003996548574
GO:0008553hydrogen-exporting ATPase activity, phosphorylative mechanism0.0273003996548574
GO:0005746mitochondrial respiratory chain0.0273003996548574
GO:0015075ion transmembrane transporter activity0.0273003996548574
GO:0015985energy coupled proton transport, down electrochemical gradient0.0273003996548574
GO:0015986ATP synthesis coupled proton transport0.0273003996548574
GO:0044446intracellular organelle part0.0273003996548574
GO:0005737cytoplasm0.0273003996548574
GO:0044422organelle part0.0273003996548574
GO:0006754ATP biosynthetic process0.0273003996548574
GO:0006753nucleoside phosphate metabolic process0.0273003996548574
GO:0046933hydrogen ion transporting ATP synthase activity, rotational mechanism0.0273003996548574
GO:0016469proton-transporting two-sector ATPase complex0.0273003996548574
GO:0046961hydrogen ion transporting ATPase activity, rotational mechanism0.0273003996548574
GO:0022891substrate-specific transmembrane transporter activity0.0273003996548574
GO:0000313organellar ribosome0.0273003996548574
GO:0046034ATP metabolic process0.0273003996548574
GO:0005761mitochondrial ribosome0.0273003996548574
GO:0016491oxidoreductase activity0.0273003996548574
GO:0009145purine nucleoside triphosphate biosynthetic process0.0273003996548574
GO:0009206purine ribonucleoside triphosphate biosynthetic process0.0273003996548574
GO:0009201ribonucleoside triphosphate biosynthetic process0.0273003996548574
GO:0050136NADH dehydrogenase (quinone) activity0.0273003996548574
GO:0008137NADH dehydrogenase (ubiquinone) activity0.0273003996548574
GO:0003954NADH dehydrogenase activity0.0273003996548574
GO:0019829cation-transporting ATPase activity0.0273003996548574
GO:0009142nucleoside triphosphate biosynthetic process0.0273003996548574
GO:0009205purine ribonucleoside triphosphate metabolic process0.0273003996548574
GO:0016655oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor0.0273003996548574
GO:0009199ribonucleoside triphosphate metabolic process0.0273003996548574
GO:0006119oxidative phosphorylation0.0273003996548574
GO:0009144purine nucleoside triphosphate metabolic process0.0273003996548574
GO:0031980mitochondrial lumen0.0273003996548574
GO:0015992proton transport0.0273003996548574
GO:0005759mitochondrial matrix0.0273003996548574
GO:0022857transmembrane transporter activity0.0273003996548574
GO:0006752group transfer coenzyme metabolic process0.0273003996548574
GO:0044249cellular biosynthetic process0.0273003996548574
GO:0009141nucleoside triphosphate metabolic process0.0274130749186557
GO:0009152purine ribonucleotide biosynthetic process0.0274130749186557
GO:0006818hydrogen transport0.0274130749186557
GO:0015662ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism0.0274130749186557
GO:0009260ribonucleotide biosynthetic process0.0274130749186557
GO:0043231intracellular membrane-bound organelle0.0274130749186557
GO:0043227membrane-bound organelle0.0274130749186557
GO:0022892substrate-specific transporter activity0.0277030697338808
GO:0009150purine ribonucleotide metabolic process0.0277030697338808
GO:0006164purine nucleotide biosynthetic process0.0277317077783534
GO:0016651oxidoreductase activity, acting on NADH or NADPH0.0277594701017158
GO:0009259ribonucleotide metabolic process0.0290233988590009
GO:0006163purine nucleotide metabolic process0.0302516260249248
GO:0042625ATPase activity, coupled to transmembrane movement of ions0.0326469894789926
GO:0009108coenzyme biosynthetic process0.0330016178530571
GO:0051188cofactor biosynthetic process0.0376280457883119
GO:0009058biosynthetic process0.0381003043476087
GO:0043229intracellular organelle0.0381807149439813
GO:0043226organelle0.0381807149439813
GO:0043492ATPase activity, coupled to movement of substances0.0420710765210653
GO:0042626ATPase activity, coupled to transmembrane movement of substances0.0420710765210653
GO:0016820hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances0.0420710765210653
GO:0009165nucleotide biosynthetic process0.0436924945731703
GO:0015399primary active transmembrane transporter activity0.0447405944058265
GO:0015405P-P-bond-hydrolysis-driven transmembrane transporter activity0.0447405944058265
GO:0009055electron carrier activity0.0469532093348615



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
epithelial cell3.98e-0725

Uber Anatomy
Ontology termp-valuen
mucosa3.13e-1015
intestinal mucosa4.22e-0913
anatomical wall4.22e-0913
wall of intestine4.22e-0913
gastrointestinal system mucosa4.22e-0913
intestine7.55e-0931
epithelial tube2.13e-0847


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)
MA0003.10.142214
MA0004.10.6888
MA0006.10.497533
MA0007.10.672186
MA0009.11.15569
MA0014.10.581929
MA0017.10.528196
MA0019.10.964875
MA0024.11.11019
MA0025.11.39562
MA0027.12.81824
MA0028.12.19266
MA0029.11.08753
MA0030.11.09438
MA0031.11.05719
MA0038.10.846479
MA0040.11.16866
MA0041.10.604221
MA0042.10.589368
MA0043.11.25564
MA0046.11.1929
MA0048.10.735223
MA0050.10.731539
MA0051.10.856094
MA0052.11.17701
MA0055.11.28762
MA0056.10
MA0057.10.701847
MA0058.10.581673
MA0059.10.59559
MA0060.11.04037
MA0061.10.438628
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.10.713436
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.10.00221226
MA0074.10.795862
MA0076.14.59949
MA0077.11.13603
MA0078.10.891476
MA0081.11.5065
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.10.201215
MA0089.10
MA0090.10.650768
MA0091.10.703314
MA0092.10.651119
MA0093.11.29026
MA0095.10
MA0098.10
MA0100.10.783305
MA0101.10.605676
MA0103.10.540576
MA0105.10.313353
MA0106.10.899777
MA0107.10.533522
MA0108.20.989014
MA0109.10
MA0111.10.666525
MA0113.10.869608
MA0114.10.43587
MA0115.11.25852
MA0116.11.24367
MA0117.11.22527
MA0119.10.606338
MA0122.11.24573
MA0124.11.45461
MA0125.11.37907
MA0130.10
MA0131.10.960068
MA0132.10
MA0133.10
MA0135.11.29308
MA0136.10.817395
MA0139.10.365453
MA0140.10.78318
MA0141.11.38335
MA0142.11.04199
MA0143.10.887119
MA0144.11.11951
MA0145.10.608454
MA0146.11.5929
MA0147.11.15069
MA0148.10.706718
MA0149.10.611881
MA0062.23.24307
MA0035.20.788288
MA0039.22.41467
MA0138.20.951653
MA0002.20.368961
MA0137.21.37638
MA0104.21.0034
MA0047.20.845655
MA0112.20.211985
MA0065.20.212467
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.10.728853
MA0155.11.8891
MA0156.11.35382
MA0157.11.0083
MA0158.10
MA0159.11.1762
MA0160.10.71003
MA0161.10
MA0162.10.704935
MA0163.10.0996272
MA0164.10.817786
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.20.300141
MA0102.21.8929
MA0258.10.419871
MA0259.10.441366
MA0442.10
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