MCL coexpression mm9:561: Difference between revisions
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{{MCL_coexpression_mm9| | 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assembly or disassembly;0.00167154048853748;12412,20588,56086!GO:0006259;DNA metabolic process;0.00267532743741777;12412,53610,20588,56086!GO:0006325;establishment and/or maintenance of chromatin architecture;0.00382075892357918;12412,20588,56086!GO:0006323;DNA packaging;0.00382075892357918;12412,20588,56086!GO:0051276;chromosome organization and biogenesis;0.00782676507747672;12412,20588,56086!GO:0005634;nucleus;0.010352760363296;12412,53610,20588,16906,56086,51886!GO:0003682;chromatin binding;0.010352760363296;12412,20588!GO:0043283;biopolymer metabolic process;0.010352760363296;12412,53610,20588,109079,56086,51886!GO:0004756;selenide, water dikinase activity;0.010352760363296;109079!GO:0016781;phosphotransferase activity, paired acceptors;0.010352760363296;109079!GO:0005701;polytene chromosome chromocenter;0.0129388234465679;12412!GO:0005700;polytene chromosome;0.0129388234465679;12412!GO:0005721;centric heterochromatin;0.0137991432826624;12412!GO:0005638;lamin filament;0.0137991432826624;16906!GO:0001940;male pronucleus;0.0137991432826624;12412!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0140998553424081;12412,53610,20588,56086,51886!GO:0001939;female pronucleus;0.0152171418786361;12412!GO:0000785;chromatin;0.0155189337054456;12412,20588!GO:0010369;chromocenter;0.0155189337054456;12412!GO:0016514;SWI/SNF complex;0.0155189337054456;20588!GO:0003677;DNA binding;0.0179870528483271;53610,20588,56086,51886!GO:0005652;nuclear lamina;0.0179870528483271;16906!GO:0005637;nuclear inner membrane;0.0179870528483271;16906!GO:0043170;macromolecule metabolic process;0.018211026510159;12412,53610,20588,109079,56086,51886!GO:0044428;nuclear part;0.0242749379943623;12412,20588,16906!GO:0044427;chromosomal part;0.026787604125647;12412,20588!GO:0045120;pronucleus;0.026787604125647;12412!GO:0006996;organelle organization and biogenesis;0.0305470632527692;12412,20588,56086!GO:0044238;primary metabolic process;0.0305470632527692;12412,53610,20588,109079,56086,51886!GO:0044237;cellular metabolic process;0.0305470632527692;12412,53610,20588,109079,56086,51886!GO:0005694;chromosome;0.0305470632527692;12412,20588!GO:0016585;chromatin remodeling complex;0.0305470632527692;20588!GO:0043231;intracellular membrane-bound organelle;0.0305470632527692;12412,53610,20588,16906,56086,51886!GO:0043227;membrane-bound organelle;0.0305470632527692;12412,53610,20588,16906,56086,51886!GO:0005720;nuclear heterochromatin;0.0338990160233967;12412!GO:0003676;nucleic acid binding;0.0420275964709632;53610,20588,56086,51886!GO:0000790;nuclear chromatin;0.0420275964709632;12412!GO:0008430;selenium binding;0.0420275964709632;109079!GO:0000792;heterochromatin;0.0463176859807975;12412!GO:0043232;intracellular non-membrane-bound organelle;0.0463176859807975;12412,20588,16906!GO:0043228;non-membrane-bound organelle;0.0463176859807975;12412,20588,16906!GO:0043229;intracellular organelle;0.0480738099214408;12412,53610,20588,16906,56086,51886!GO:0043226;organelle;0.0480738099214408;12412,53610,20588,16906,56086,51886!GO:0003723;RNA binding;0.0499254134235463;53610,51886!|ontology_enrichment_celltype=|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0000153!5.61e-08!43|tfbs_overrepresentation_for_novel_motifs=0.684947,0.341626,1.18988,0.765013,0.430128,0.291576,0.370193,0.0778908,0.283485,1.40965,1.58702,0.35958,0.567414,0.992198,0.15081,0,0.557619,0.133477,0.069633,0.119642,0.194751,0.634211,1.75669,0.137915,0.64994,0.405649,0.0651848,0.833023,0.985516,0.169823,0.805906,0.653099,1.9209,0.779896,2.78029,3.25115,0.790102,1.6738,0.111088,2.16092,0.136186,0.815844,0.0142091,0.152251,0.577849,0.743728,1.2144,0.863451,0.0100673,0.173974,0.541299,0.429887,0.160439,0.788877,0.805733,0.387424,0.18067,0.920073,0.0605105,0.385607,0.634076,1.1172,0.090369,0.5308,1.02791,0.568642,0.938213,1.28193,0.629645,1.13654,0.600538,0.277751,3.33687,0.838198,3.4832,0.427563,0.0552358,0.473159,0.617814,0.198007,0.0819833,0.573903,0.437131,0.0742829,0.72691,3.97567,0.552224,0.0444451,0.488122,1.44275,1.0064,0.731688,0.665283,0.143149,0.713238,0.0973538,0.0764965,0.667958,0.483845,1.80811,0.125632,0.652833,0.772062,0.541854,0.54087,1.47882,2.47776,0.319507,0.584153,1.08317,0.238877,0.773781,0.19888,0.336214,1.01331,0.134943,2.93557,0.282562,0.558838,0.123076,0.843435,0.511336,0.407285,0.472327,1.06644,1.50588,0.377415,0.658832,0.936732,0.875241,0.755703,0.273302,0.907893,0.399614,1.03449,0.377676,0.251471,0.303003,0.986296,1.80931,1.41113,0.942814,0.418119,0.66306,0.53483,0.816716,0.486482,1.76978,0.253405,1.98864,1.51728,5.44212,1.85698,0.331601,0.398786,0.869538,1.10066,0.159498,0.680297,0.700333,0.995609,0.726089,0.621734,0.237049,0.531751,0.392164,0.786757,0.358185,4.01131|tfbs_overrepresentation_jaspar=MA0003.1;6.72247,MA0004.1;1.40032,MA0006.1;0.451962,MA0007.1;0.737361,MA0009.1;0.678286,MA0014.1;4.46847,MA0017.1;0.166909,MA0019.1;0.506787,MA0024.1;0.636635,MA0025.1;0.9035,MA0027.1;2.3071,MA0028.1;2.10691,MA0029.1;0.616052,MA0030.1;0.622264,MA0031.1;0.588678,MA0038.1;0.405578,MA0040.1;0.690239,MA0041.1;0.218039,MA0042.1;0.207696,MA0043.1;0.771094,MA0046.1;0.712646,MA0048.1;0.332541,MA0050.1;0.312673,MA0051.1;0.413609,MA0052.1;0.697946,MA0055.1;0.183408,MA0056.1;0,MA0057.1;0.878515,MA0058.1;1.73925,MA0059.1;0.608499,MA0060.1;3.52264,MA0061.1;0.113212,MA0063.1;0,MA0066.1;0.395746,MA0067.1;1.01206,MA0068.1;0.0328198,MA0069.1;0.698271,MA0070.1;0.688999,MA0071.1;0.311956,MA0072.1;0.680902,MA0073.1;0.191412,MA0074.1;0.363923,MA0076.1;1.02349,MA0077.1;1.58726,MA0078.1;0.443468,MA0081.1;0.651709,MA0083.1;0.77033,MA0084.1;1.33532,MA0087.1;0.728855,MA0088.1;0.965806,MA0089.1;0,MA0090.1;0.251458,MA0091.1;0.290854,MA0092.1;0.251716,MA0093.1;1.50408,MA0095.1;0,MA0098.1;0,MA0100.1;0.931999,MA0101.1;0.625174,MA0103.1;0.174916,MA0105.1;1.16392,MA0106.1;0.450539,MA0107.1;0.508149,MA0108.2;0.527977,MA0109.1;0,MA0111.1;0.263095,MA0113.1;0.424958,MA0114.1;0.359761,MA0115.1;0.773793,MA0116.1;0.451594,MA0117.1;0.742722,MA0119.1;0.219527,MA0122.1;0.761823,MA0124.1;0.959967,MA0125.1;0.887718,MA0130.1;0,MA0131.1;0.502588,MA0132.1;0,MA0133.1;0,MA0135.1;0.806261,MA0136.1;0.38151,MA0139.1;0.5556,MA0140.1;0.353662,MA0141.1;0.18979,MA0142.1;0.575041,MA0143.1;0.439766,MA0144.1;0.1137,MA0145.1;0.223975,MA0146.1;7.29725,MA0147.1;0.386218,MA0148.1;0.293462,MA0149.1;0.223436,MA0062.2;1.19443,MA0035.2;0.357786,MA0039.2;2.57266,MA0138.2;0.495254,MA0002.2;0.0773396,MA0137.2;0.187581,MA0104.2;1.01662,MA0047.2;0.404891,MA0112.2;0.223965,MA0065.2;0.429377,MA0150.1;0.267221,MA0151.1;0,MA0152.1;0.404987,MA0153.1;0.822355,MA0154.1;0.0349712,MA0155.1;1.54988,MA0156.1;0.180505,MA0157.1;0.545026,MA0158.1;0,MA0159.1;0.403827,MA0160.1;0.296006,MA0161.1;0,MA0162.1;1.52018,MA0163.1;1.42454,MA0164.1;0.381832,MA0080.2;0.170995,MA0018.2;0.390455,MA0099.2;0.489441,MA0079.2;6.8499,MA0102.2;1.38728,MA0258.1;0.103004,MA0259.1;0.367748,MA0442.1;0}} | ||
Latest revision as of 15:30, 17 September 2013
Phase1 CAGE Peaks
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 ID | GO name | FDR corrected p-value |
|---|---|---|
| GO:0006333 | chromatin assembly or disassembly | 0.00167154048853748 |
| GO:0006259 | DNA metabolic process | 0.00267532743741777 |
| GO:0006325 | establishment and/or maintenance of chromatin architecture | 0.00382075892357918 |
| GO:0006323 | DNA packaging | 0.00382075892357918 |
| GO:0051276 | chromosome organization and biogenesis | 0.00782676507747672 |
| GO:0005634 | nucleus | 0.010352760363296 |
| GO:0003682 | chromatin binding | 0.010352760363296 |
| GO:0043283 | biopolymer metabolic process | 0.010352760363296 |
| GO:0004756 | selenide, water dikinase activity | 0.010352760363296 |
| GO:0016781 | phosphotransferase activity, paired acceptors | 0.010352760363296 |
| GO:0005701 | polytene chromosome chromocenter | 0.0129388234465679 |
| GO:0005700 | polytene chromosome | 0.0129388234465679 |
| GO:0005721 | centric heterochromatin | 0.0137991432826624 |
| GO:0005638 | lamin filament | 0.0137991432826624 |
| GO:0001940 | male pronucleus | 0.0137991432826624 |
| GO:0006139 | nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.0140998553424081 |
| GO:0001939 | female pronucleus | 0.0152171418786361 |
| GO:0000785 | chromatin | 0.0155189337054456 |
| GO:0010369 | chromocenter | 0.0155189337054456 |
| GO:0016514 | SWI/SNF complex | 0.0155189337054456 |
| GO:0003677 | DNA binding | 0.0179870528483271 |
| GO:0005652 | nuclear lamina | 0.0179870528483271 |
| GO:0005637 | nuclear inner membrane | 0.0179870528483271 |
| GO:0043170 | macromolecule metabolic process | 0.018211026510159 |
| GO:0044428 | nuclear part | 0.0242749379943623 |
| GO:0044427 | chromosomal part | 0.026787604125647 |
| GO:0045120 | pronucleus | 0.026787604125647 |
| GO:0006996 | organelle organization and biogenesis | 0.0305470632527692 |
| GO:0044238 | primary metabolic process | 0.0305470632527692 |
| GO:0044237 | cellular metabolic process | 0.0305470632527692 |
| GO:0005694 | chromosome | 0.0305470632527692 |
| GO:0016585 | chromatin remodeling complex | 0.0305470632527692 |
| GO:0043231 | intracellular membrane-bound organelle | 0.0305470632527692 |
| GO:0043227 | membrane-bound organelle | 0.0305470632527692 |
| GO:0005720 | nuclear heterochromatin | 0.0338990160233967 |
| GO:0003676 | nucleic acid binding | 0.0420275964709632 |
| GO:0000790 | nuclear chromatin | 0.0420275964709632 |
| GO:0008430 | selenium binding | 0.0420275964709632 |
| GO:0000792 | heterochromatin | 0.0463176859807975 |
| GO:0043232 | intracellular non-membrane-bound organelle | 0.0463176859807975 |
| GO:0043228 | non-membrane-bound organelle | 0.0463176859807975 |
| GO:0043229 | intracellular organelle | 0.0480738099214408 |
| GO:0043226 | organelle | 0.0480738099214408 |
| GO:0003723 | RNA binding | 0.0499254134235463 |
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>
| Ontology term | p-value | n |
|---|---|---|
| anterior region of body | 5.61e-08 | 43 |
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) |
|---|---|
| MA0003.1 | 6.72247 |
| MA0004.1 | 1.40032 |
| MA0006.1 | 0.451962 |
| MA0007.1 | 0.737361 |
| MA0009.1 | 0.678286 |
| MA0014.1 | 4.46847 |
| MA0017.1 | 0.166909 |
| MA0019.1 | 0.506787 |
| MA0024.1 | 0.636635 |
| MA0025.1 | 0.9035 |
| MA0027.1 | 2.3071 |
| MA0028.1 | 2.10691 |
| MA0029.1 | 0.616052 |
| MA0030.1 | 0.622264 |
| MA0031.1 | 0.588678 |
| MA0038.1 | 0.405578 |
| MA0040.1 | 0.690239 |
| MA0041.1 | 0.218039 |
| MA0042.1 | 0.207696 |
| MA0043.1 | 0.771094 |
| MA0046.1 | 0.712646 |
| MA0048.1 | 0.332541 |
| MA0050.1 | 0.312673 |
| MA0051.1 | 0.413609 |
| MA0052.1 | 0.697946 |
| MA0055.1 | 0.183408 |
| MA0056.1 | 0 |
| MA0057.1 | 0.878515 |
| MA0058.1 | 1.73925 |
| MA0059.1 | 0.608499 |
| MA0060.1 | 3.52264 |
| MA0061.1 | 0.113212 |
| MA0063.1 | 0 |
| MA0066.1 | 0.395746 |
| MA0067.1 | 1.01206 |
| MA0068.1 | 0.0328198 |
| MA0069.1 | 0.698271 |
| MA0070.1 | 0.688999 |
| MA0071.1 | 0.311956 |
| MA0072.1 | 0.680902 |
| MA0073.1 | 0.191412 |
| MA0074.1 | 0.363923 |
| MA0076.1 | 1.02349 |
| MA0077.1 | 1.58726 |
| MA0078.1 | 0.443468 |
| MA0081.1 | 0.651709 |
| MA0083.1 | 0.77033 |
| MA0084.1 | 1.33532 |
| MA0087.1 | 0.728855 |
| MA0088.1 | 0.965806 |
| MA0089.1 | 0 |
| MA0090.1 | 0.251458 |
| MA0091.1 | 0.290854 |
| MA0092.1 | 0.251716 |
| MA0093.1 | 1.50408 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.931999 |
| MA0101.1 | 0.625174 |
| MA0103.1 | 0.174916 |
| MA0105.1 | 1.16392 |
| MA0106.1 | 0.450539 |
| MA0107.1 | 0.508149 |
| MA0108.2 | 0.527977 |
| MA0109.1 | 0 |
| MA0111.1 | 0.263095 |
| MA0113.1 | 0.424958 |
| MA0114.1 | 0.359761 |
| MA0115.1 | 0.773793 |
| MA0116.1 | 0.451594 |
| MA0117.1 | 0.742722 |
| MA0119.1 | 0.219527 |
| MA0122.1 | 0.761823 |
| MA0124.1 | 0.959967 |
| MA0125.1 | 0.887718 |
| MA0130.1 | 0 |
| MA0131.1 | 0.502588 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 0.806261 |
| MA0136.1 | 0.38151 |
| MA0139.1 | 0.5556 |
| MA0140.1 | 0.353662 |
| MA0141.1 | 0.18979 |
| MA0142.1 | 0.575041 |
| MA0143.1 | 0.439766 |
| MA0144.1 | 0.1137 |
| MA0145.1 | 0.223975 |
| MA0146.1 | 7.29725 |
| MA0147.1 | 0.386218 |
| MA0148.1 | 0.293462 |
| MA0149.1 | 0.223436 |
| MA0062.2 | 1.19443 |
| MA0035.2 | 0.357786 |
| MA0039.2 | 2.57266 |
| MA0138.2 | 0.495254 |
| MA0002.2 | 0.0773396 |
| MA0137.2 | 0.187581 |
| MA0104.2 | 1.01662 |
| MA0047.2 | 0.404891 |
| MA0112.2 | 0.223965 |
| MA0065.2 | 0.429377 |
| MA0150.1 | 0.267221 |
| MA0151.1 | 0 |
| MA0152.1 | 0.404987 |
| MA0153.1 | 0.822355 |
| MA0154.1 | 0.0349712 |
| MA0155.1 | 1.54988 |
| MA0156.1 | 0.180505 |
| MA0157.1 | 0.545026 |
| MA0158.1 | 0 |
| MA0159.1 | 0.403827 |
| MA0160.1 | 0.296006 |
| MA0161.1 | 0 |
| MA0162.1 | 1.52018 |
| MA0163.1 | 1.42454 |
| MA0164.1 | 0.381832 |
| MA0080.2 | 0.170995 |
| MA0018.2 | 0.390455 |
| MA0099.2 | 0.489441 |
| MA0079.2 | 6.8499 |
| MA0102.2 | 1.38728 |
| MA0258.1 | 0.103004 |
| MA0259.1 | 0.367748 |
| MA0442.1 | 0 |
