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MCL coexpression mm9:1236: Difference between revisions

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{{MCL_coexpression_mm9
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acceptor activity;0.0159947409747897;66841!GO:0016649;oxidoreductase activity, acting on the CH-NH group of donors, quinone or similar compound as acceptor;0.0159947409747897;66841!GO:0004174;electron-transferring-flavoprotein dehydrogenase activity;0.0159947409747897;66841!GO:0005739;mitochondrion;0.0159947409747897;64058,18103,66841!GO:0017133;mitochondrial electron transfer flavoprotein complex;0.0159947409747897;66841!GO:0045251;electron transfer flavoprotein complex;0.0159947409747897;66841!GO:0044444;cytoplasmic part;0.0164043131918743;64058,280408,18103,66841!GO:0046039;GTP metabolic process;0.0179852122329424;18103!GO:0006228;UTP biosynthetic process;0.0179852122329424;18103!GO:0006183;GTP biosynthetic process;0.0179852122329424;18103!GO:0046036;CTP metabolic process;0.0179852122329424;18103!GO:0009209;pyrimidine ribonucleoside triphosphate biosynthetic process;0.0179852122329424;18103!GO:0046051;UTP metabolic process;0.0179852122329424;18103!GO:0009208;pyrimidine ribonucleoside triphosphate metabolic process;0.0179852122329424;18103!GO:0006241;CTP biosynthetic process;0.0179852122329424;18103!GO:0004550;nucleoside diphosphate kinase activity;0.0179852122329424;18103!GO:0009220;pyrimidine ribonucleotide biosynthetic process;0.019536278097304;18103!GO:0009218;pyrimidine ribonucleotide metabolic process;0.019536278097304;18103!GO:0009147;pyrimidine nucleoside triphosphate metabolic process;0.0201889437298985;18103!GO:0006221;pyrimidine nucleotide biosynthetic process;0.0275909713205747;18103!GO:0006220;pyrimidine nucleotide metabolic process;0.0275909713205747;18103!GO:0051539;4 iron, 4 sulfur cluster binding;0.0275909713205747;66841!GO:0016645;oxidoreductase activity, acting on the CH-NH group of donors;0.0277780995794519;66841!GO:0016776;phosphotransferase activity, phosphate group as acceptor;0.0372444493694653;18103!GO:0005737;cytoplasm;0.0419193300402541;64058,280408,18103,66841!GO:0019205;nucleobase, nucleoside, nucleotide kinase 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|gostat_on_MCL_coexpression=GO:0009054;electron acceptor activity;0.0159947409747897;66841!GO:0016649;oxidoreductase activity, acting on the CH-NH group of donors, quinone or similar compound as acceptor;0.0159947409747897;66841!GO:0004174;electron-transferring-flavoprotein dehydrogenase activity;0.0159947409747897;66841!GO:0005739;mitochondrion;0.0159947409747897;64058,18103,66841!GO:0017133;mitochondrial electron transfer flavoprotein complex;0.0159947409747897;66841!GO:0045251;electron transfer flavoprotein complex;0.0159947409747897;66841!GO:0044444;cytoplasmic part;0.0164043131918743;64058,280408,18103,66841!GO:0046039;GTP metabolic process;0.0179852122329424;18103!GO:0006228;UTP biosynthetic process;0.0179852122329424;18103!GO:0006183;GTP biosynthetic process;0.0179852122329424;18103!GO:0046036;CTP metabolic process;0.0179852122329424;18103!GO:0009209;pyrimidine ribonucleoside triphosphate biosynthetic process;0.0179852122329424;18103!GO:0046051;UTP metabolic process;0.0179852122329424;18103!GO:0009208;pyrimidine ribonucleoside triphosphate metabolic process;0.0179852122329424;18103!GO:0006241;CTP biosynthetic process;0.0179852122329424;18103!GO:0004550;nucleoside diphosphate kinase activity;0.0179852122329424;18103!GO:0009220;pyrimidine ribonucleotide biosynthetic process;0.019536278097304;18103!GO:0009218;pyrimidine ribonucleotide metabolic process;0.019536278097304;18103!GO:0009147;pyrimidine nucleoside triphosphate metabolic process;0.0201889437298985;18103!GO:0006221;pyrimidine nucleotide biosynthetic process;0.0275909713205747;18103!GO:0006220;pyrimidine nucleotide metabolic process;0.0275909713205747;18103!GO:0051539;4 iron, 4 sulfur cluster binding;0.0275909713205747;66841!GO:0016645;oxidoreductase activity, acting on the CH-NH group of donors;0.0277780995794519;66841!GO:0016776;phosphotransferase activity, phosphate group as acceptor;0.0372444493694653;18103!GO:0005737;cytoplasm;0.0419193300402541;64058,280408,18103,66841!GO:0019205;nucleobase, nucleoside, nucleotide kinase activity;0.0441731426607082;18103!GO:0051536;iron-sulfur cluster binding;0.0456348127013525;66841!GO:0051540;metal cluster binding;0.0456348127013525;66841!GO:0009145;purine nucleoside triphosphate biosynthetic process;0.0456348127013525;18103!GO:0009206;purine ribonucleoside triphosphate biosynthetic process;0.0456348127013525;18103!GO:0009201;ribonucleoside triphosphate biosynthetic process;0.0456348127013525;18103!GO:0009142;nucleoside triphosphate biosynthetic process;0.0456348127013525;18103!GO:0009205;purine ribonucleoside triphosphate metabolic process;0.0456348127013525;18103!GO:0009199;ribonucleoside triphosphate metabolic process;0.0456348127013525;18103!GO:0009144;purine nucleoside triphosphate metabolic process;0.0456348127013525;18103!GO:0031980;mitochondrial lumen;0.0456348127013525;66841!GO:0005759;mitochondrial matrix;0.0456348127013525;66841!GO:0009141;nucleoside triphosphate metabolic process;0.0465467683456577;18103!GO:0009152;purine ribonucleotide biosynthetic process;0.0465467683456577;18103!GO:0009260;ribonucleotide biosynthetic process;0.0466031801971308;18103!GO:0043231;intracellular membrane-bound organelle;0.0466031801971308;64058,280408,18103,66841!GO:0043227;membrane-bound organelle;0.0466031801971308;64058,280408,18103,66841!GO:0009150;purine ribonucleotide metabolic process;0.0470169299095507;18103!GO:0006164;purine nucleotide biosynthetic process;0.0470169299095507;18103!GO:0009259;ribonucleotide metabolic process;0.0494880727989972;18103!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003914!8.60e-13!47;UBERON:0002365!5.53e-10!25;UBERON:0002330!5.53e-10!25;UBERON:0009854!4.03e-09!23;UBERON:0009856!4.03e-09!23;UBERON:0002107!7.07e-09!22;UBERON:0007499!7.07e-09!22;UBERON:0006925!7.07e-09!22;UBERON:0009497!7.07e-09!22;UBERON:0000015!7.07e-09!22;UBERON:0002423!7.07e-09!22;UBERON:0006235!7.07e-09!22;UBERON:0008835!7.07e-09!22;UBERON:0003894!7.07e-09!22;UBERON:0004161!7.07e-09!22;UBERON:0008836!7.07e-09!22;UBERON:0000160!3.69e-07!31
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.819928,0.464605,0.535892,0.346849,0.550971,0.645383,0.691572,0.257202,0.0835344,0.599767,0.632897,0.247704,0.6581,0.364314,0,0.856992,0.338549,0.656199,0.86893,0.426133,0.713088,0.657163,0.345236,0.472505,0.686615,0.63639,0.572827,0.394364,0.534301,0.558142,0.960397,0.892985,0.589948,0.364821,0.0363535,0.326478,0.629145,0.820134,0.752287,0.342638,0.56353,0.671603,0.959963,0.368882,0.524258,0.77511,0.589246,0.284064,0.397446,0.839084,0.714419,0.517905,1.10437,1.12205,0.66551,0.406788,0.619643,0.614918,0.663395,0.939962,0.724164,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.253541,0.11437,1.156,0.208101,0.19692,1.11463,0.763395,0.922432,0.430551,0.708505,0.874787,0.722675,0.676326,1.03903,0.198949,0.479018,0.181203,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.2995,0.769162,0.244935,0.976308,0.775372,0.160254,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,0.428007,0.484547,1.0885,0.431734,0.605144,1.33732,0.90315,3.10162,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.106956,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,1.83209,2.10357,0.503174,2.48865,1.03315,0.667976,1.10596,0.287383,0.678689,1.18867,1.70209,0.376898,0.48935,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.325308,0.63125,0.30995
|tfbs_overrepresentation_jaspar=MA0003.1;0.730824,MA0004.1;1.3269,MA0006.1;0.945134,MA0007.1;0.52077,MA0009.1;0.987341,MA0014.1;0.883128,MA0017.1;0.387481,MA0019.1;0.800946,MA0024.1;0.942716,MA0025.1;1.22395,MA0027.1;2.64231,MA0028.1;0.370592,MA0029.1;0.920529,MA0030.1;0.927235,MA0031.1;0.890871,MA0038.1;0.686534,MA0040.1;1.00009,MA0041.1;1.15799,MA0042.1;1.12834,MA0043.1;1.08567,MA0046.1;1.02391,MA0048.1;0.486223,MA0050.1;0.57678,MA0051.1;0.695779,MA0052.1;1.00829,MA0055.1;0.0585191,MA0056.1;0,MA0057.1;0.149949,MA0058.1;2.90242,MA0059.1;1.99202,MA0060.1;1.38604,MA0061.1;0.307097,MA0063.1;0,MA0066.1;0.675169,MA0067.1;1.33603,MA0068.1;0.153907,MA0069.1;1.00864,MA0070.1;0.998765,MA0071.1;2.40974,MA0072.1;0.990133,MA0073.1;1.22055,MA0074.1;1.54084,MA0076.1;1.04996,MA0077.1;0.968053,MA0078.1;0.729877,MA0081.1;0.473489,MA0083.1;1.08487,MA0084.1;1.66561,MA0087.1;1.04109,MA0088.1;0.358337,MA0089.1;0,MA0090.1;0.500693,MA0091.1;0.55008,MA0092.1;1.25163,MA0093.1;1.75322,MA0095.1;0,MA0098.1;0,MA0100.1;0.626021,MA0101.1;0.458688,MA0103.1;0.398766,MA0105.1;1.09694,MA0106.1;0.737893,MA0107.1;0.392331,MA0108.2;0.824407,MA0109.1;0,MA0111.1;1.2824,MA0113.1;0.708789,MA0114.1;0.822296,MA0115.1;2.46592,MA0116.1;0.944657,MA0117.1;1.05576,MA0119.1;1.16221,MA0122.1;1.07591,MA0124.1;1.28237,MA0125.1;1.20757,MA0130.1;0,MA0131.1;0.796279,MA0132.1;0,MA0133.1;0,MA0135.1;1.1226,MA0136.1;0.658622,MA0139.1;0.682297,MA0140.1;0.625902,MA0141.1;2.82312,MA0142.1;0.876028,MA0143.1;0.725672,MA0144.1;2.2889,MA0145.1;0.761789,MA0146.1;0.635245,MA0147.1;0.858298,MA0148.1;0.553294,MA0149.1;0.464445,MA0062.2;0.204999,MA0035.2;0.630778,MA0039.2;2.17024,MA0138.2;0.788113,MA0002.2;0.246463,MA0137.2;0.416331,MA0104.2;0.723439,MA0047.2;0.685741,MA0112.2;0.37938,MA0065.2;0.380324,MA0150.1;0.520653,MA0151.1;0,MA0152.1;0.685852,MA0153.1;1.13945,MA0154.1;0.159217,MA0155.1;0.132921,MA0156.1;1.04798,MA0157.1;0.843181,MA0158.1;0,MA0159.1;1.58527,MA0160.1;2.34632,MA0161.1;0,MA0162.1;0.397553,MA0163.1;1.03138,MA0164.1;0.658997,MA0080.2;1.01893,MA0018.2;0.669032,MA0099.2;0.781628,MA0079.2;0.0267793,MA0102.2;1.7182,MA0258.1;0.290587,MA0259.1;0.833237,MA0442.1;0
}}

Latest revision as of 16:36, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:18564818..18564829,+p3@Perp
Mm9::chr11:75323579..75323606,+p1@Rilp
Mm9::chr11:75323608..75323630,+p3@Rilp
Mm9::chr11:93816942..93817021,-p3@Nme2
Mm9::chr17:56256960..56256974,-p2@Plin5
Mm9::chr3:79432674..79432685,-p3@Etfdh


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:0009054electron acceptor activity0.0159947409747897
GO:0016649oxidoreductase activity, acting on the CH-NH group of donors, quinone or similar compound as acceptor0.0159947409747897
GO:0004174electron-transferring-flavoprotein dehydrogenase activity0.0159947409747897
GO:0005739mitochondrion0.0159947409747897
GO:0017133mitochondrial electron transfer flavoprotein complex0.0159947409747897
GO:0045251electron transfer flavoprotein complex0.0159947409747897
GO:0044444cytoplasmic part0.0164043131918743
GO:0046039GTP metabolic process0.0179852122329424
GO:0006228UTP biosynthetic process0.0179852122329424
GO:0006183GTP biosynthetic process0.0179852122329424
GO:0046036CTP metabolic process0.0179852122329424
GO:0009209pyrimidine ribonucleoside triphosphate biosynthetic process0.0179852122329424
GO:0046051UTP metabolic process0.0179852122329424
GO:0009208pyrimidine ribonucleoside triphosphate metabolic process0.0179852122329424
GO:0006241CTP biosynthetic process0.0179852122329424
GO:0004550nucleoside diphosphate kinase activity0.0179852122329424
GO:0009220pyrimidine ribonucleotide biosynthetic process0.019536278097304
GO:0009218pyrimidine ribonucleotide metabolic process0.019536278097304
GO:0009147pyrimidine nucleoside triphosphate metabolic process0.0201889437298985
GO:0006221pyrimidine nucleotide biosynthetic process0.0275909713205747
GO:0006220pyrimidine nucleotide metabolic process0.0275909713205747
GO:00515394 iron, 4 sulfur cluster binding0.0275909713205747
GO:0016645oxidoreductase activity, acting on the CH-NH group of donors0.0277780995794519
GO:0016776phosphotransferase activity, phosphate group as acceptor0.0372444493694653
GO:0005737cytoplasm0.0419193300402541
GO:0019205nucleobase, nucleoside, nucleotide kinase activity0.0441731426607082
GO:0051536iron-sulfur cluster binding0.0456348127013525
GO:0051540metal cluster binding0.0456348127013525
GO:0009145purine nucleoside triphosphate biosynthetic process0.0456348127013525
GO:0009206purine ribonucleoside triphosphate biosynthetic process0.0456348127013525
GO:0009201ribonucleoside triphosphate biosynthetic process0.0456348127013525
GO:0009142nucleoside triphosphate biosynthetic process0.0456348127013525
GO:0009205purine ribonucleoside triphosphate metabolic process0.0456348127013525
GO:0009199ribonucleoside triphosphate metabolic process0.0456348127013525
GO:0009144purine nucleoside triphosphate metabolic process0.0456348127013525
GO:0031980mitochondrial lumen0.0456348127013525
GO:0005759mitochondrial matrix0.0456348127013525
GO:0009141nucleoside triphosphate metabolic process0.0465467683456577
GO:0009152purine ribonucleotide biosynthetic process0.0465467683456577
GO:0009260ribonucleotide biosynthetic process0.0466031801971308
GO:0043231intracellular membrane-bound organelle0.0466031801971308
GO:0043227membrane-bound organelle0.0466031801971308
GO:0009150purine ribonucleotide metabolic process0.0470169299095507
GO:0006164purine nucleotide biosynthetic process0.0470169299095507
GO:0009259ribonucleotide metabolic process0.0494880727989972



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
epithelial tube8.60e-1347
exocrine gland5.53e-1025
exocrine system5.53e-1025
digestive tract diverticulum4.03e-0923
sac4.03e-0923
liver7.07e-0922
epithelial sac7.07e-0922
digestive gland7.07e-0922
epithelium of foregut-midgut junction7.07e-0922
anatomical boundary7.07e-0922
hepatobiliary system7.07e-0922
foregut-midgut junction7.07e-0922
hepatic diverticulum7.07e-0922
liver primordium7.07e-0922
septum transversum7.07e-0922
liver bud7.07e-0922
intestine3.69e-0731


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)
MA0003.10.730824
MA0004.11.3269
MA0006.10.945134
MA0007.10.52077
MA0009.10.987341
MA0014.10.883128
MA0017.10.387481
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.370592
MA0029.10.920529
MA0030.10.927235
MA0031.10.890871
MA0038.10.686534
MA0040.11.00009
MA0041.11.15799
MA0042.11.12834
MA0043.11.08567
MA0046.11.02391
MA0048.10.486223
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.0585191
MA0056.10
MA0057.10.149949
MA0058.12.90242
MA0059.11.99202
MA0060.11.38604
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.153907
MA0069.11.00864
MA0070.10.998765
MA0071.12.40974
MA0072.10.990133
MA0073.11.22055
MA0074.11.54084
MA0076.11.04996
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.358337
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.11.25163
MA0093.11.75322
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.10.458688
MA0103.10.398766
MA0105.11.09694
MA0106.10.737893
MA0107.10.392331
MA0108.20.824407
MA0109.10
MA0111.11.2824
MA0113.10.708789
MA0114.10.822296
MA0115.12.46592
MA0116.10.944657
MA0117.11.05576
MA0119.11.16221
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.10.796279
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.10.658622
MA0139.10.682297
MA0140.10.625902
MA0141.12.82312
MA0142.10.876028
MA0143.10.725672
MA0144.12.2889
MA0145.10.761789
MA0146.10.635245
MA0147.10.858298
MA0148.10.553294
MA0149.10.464445
MA0062.20.204999
MA0035.20.630778
MA0039.22.17024
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.20.723439
MA0047.20.685741
MA0112.20.37938
MA0065.20.380324
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.159217
MA0155.10.132921
MA0156.11.04798
MA0157.10.843181
MA0158.10
MA0159.11.58527
MA0160.12.34632
MA0161.10
MA0162.10.397553
MA0163.11.03138
MA0164.10.658997
MA0080.21.01893
MA0018.20.669032
MA0099.20.781628
MA0079.20.0267793
MA0102.21.7182
MA0258.10.290587
MA0259.10.833237
MA0442.10
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