MCL coexpression mm9:519: Difference between revisions
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{{MCL_coexpression_mm9| | 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292944,0.0959076470095132,0.0668683739633331,0.0905641158318875|gostat_on_MCL_coexpression=GO:0048663;neuron fate commitment;0.00328124834416348;50913,50914!GO:0044451;nucleoplasm part;0.0216479470319356;64383,50913,50914!GO:0045165;cell fate commitment;0.0216479470319356;50913,50914!GO:0005654;nucleoplasm;0.0216479470319356;64383,50913,50914!GO:0031981;nuclear lumen;0.0255129623200036;64383,50913,50914!GO:0004609;phosphatidylserine decarboxylase activity;0.0255129623200036;320951!GO:0031974;membrane-enclosed lumen;0.0255129623200036;64383,50913,50914!GO:0043233;organelle lumen;0.0255129623200036;64383,50913,50914!GO:0045892;negative regulation of transcription, DNA-dependent;0.029467491566657;64383,50913!GO:0016481;negative regulation of transcription;0.0338399603669903;64383,50913!GO:0005677;chromatin silencing complex;0.0338399603669903;64383!GO:0044428;nuclear part;0.0338399603669903;64383,50913,50914!GO:0045934;negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0338399603669903;64383,50913!GO:0044446;intracellular organelle part;0.0338399603669903;64383,50913,50914,71803!GO:0044422;organelle part;0.0338399603669903;64383,50913,50914,71803!GO:0048709;oligodendrocyte differentiation;0.0338399603669903;50913!GO:0030182;neuron differentiation;0.0338399603669903;50913,50914!GO:0031324;negative regulation of cellular metabolic process;0.0353489451883645;64383,50913!GO:0048699;generation of neurons;0.0353489451883645;50913,50914!GO:0006342;chromatin silencing;0.0353489451883645;64383!GO:0031507;heterochromatin formation;0.0353489451883645;64383!GO:0009892;negative regulation of metabolic process;0.035679063989088;64383,50913!GO:0022008;neurogenesis;0.035679063989088;50913,50914!GO:0045814;negative regulation of gene expression, epigenetic;0.035679063989088;64383!GO:0003705;RNA polymerase II transcription factor activity, enhancer binding;0.0433619796683617;50913!GO:0016585;chromatin remodeling complex;0.04388263289812;64383!GO:0005667;transcription factor complex;0.0466304394042769;50913,50914!GO:0004950;chemokine receptor activity;0.0466304394042769;13051!GO:0019956;chemokine binding;0.0466304394042769;13051!GO:0001637;G-protein chemoattractant receptor activity;0.0466304394042769;13051!GO:0016831;carboxy-lyase activity;0.0466304394042769;320951!GO:0042552;myelination;0.0466304394042769;50913!GO:0016458;gene silencing;0.0466304394042769;64383!GO:0007272;ensheathment of neurons;0.0472096397336174;50913!GO:0008366;axon ensheathment;0.0472096397336174;50913!GO:0043234;protein complex;0.0492691316908081;64383,50913,50914!|ontology_enrichment_celltype=CL:0000221!3.30e-17!44;CL:0000133!3.30e-17!44;CL:0002319!9.27e-17!43;CL:0000117!1.00e-16!23;CL:0000337!1.00e-16!23;CL:0000055!2.46e-13!49;CL:0000540!3.91e-11!33;CL:0000047!3.91e-11!33;CL:0000031!3.91e-11!33;CL:0000404!3.91e-11!33;CL:0000393!2.90e-08!39;CL:0000211!2.90e-08!39;CL:0000333!5.99e-07!10;CL:0000095!5.99e-07!10;CL:0000243!5.99e-07!10;CL:0000123!5.99e-07!10;CL:0000125!5.99e-07!10;CL:0000030!5.99e-07!10;CL:0000339!5.99e-07!10;CL:0002321!6.99e-07!70|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0001016!2.28e-38!75;UBERON:0001017!1.38e-37!73;UBERON:0000073!9.76e-35!54;UBERON:0001049!1.41e-32!52;UBERON:0005068!1.41e-32!52;UBERON:0006241!1.41e-32!52;UBERON:0007135!1.41e-32!52;UBERON:0004121!4.05e-31!95;UBERON:0000924!4.05e-31!95;UBERON:0006601!4.05e-31!95;UBERON:0002346!5.42e-28!64;UBERON:0003075!5.42e-28!64;UBERON:0007284!5.42e-28!64;UBERON:0000955!1.59e-27!47;UBERON:0006238!1.59e-27!47;UBERON:0002020!9.58e-27!34;UBERON:0002616!1.43e-26!46;UBERON:0010371!2.13e-23!73;UBERON:0003080!1.06e-22!40;UBERON:0003528!5.34e-22!29;UBERON:0002791!5.34e-22!29;UBERON:0001893!5.34e-22!29;UBERON:0002780!8.33e-22!39;UBERON:0001890!8.33e-22!39;UBERON:0006240!8.33e-22!39;UBERON:0003056!1.20e-20!49;UBERON:0000956!1.98e-15!21;UBERON:0001869!1.98e-15!21;UBERON:0000203!1.98e-15!21;UBERON:0010314!5.31e-15!92;UBERON:0002619!3.22e-13!17;UBERON:0002021!2.75e-10!10;UBERON:0000411!2.75e-10!10;UBERON:0001950!2.75e-10!10;UBERON:0003076!3.33e-10!12;UBERON:0003057!3.33e-10!12;UBERON:0002420!9.95e-08!8;UBERON:0007245!9.95e-08!8;UBERON:0010009!9.95e-08!8;UBERON:0010011!9.95e-08!8;UBERON:0000454!9.95e-08!8;UBERON:0002240!5.47e-07!6;UBERON:0005174!5.47e-07!6;UBERON:0001137!5.47e-07!6|tfbs_overrepresentation_for_novel_motifs=0.6379,0.153651,0.589984,0.25808,0.391122,0.269875,0.346405,0.237242,0.0719629,0.0394224,0.831817,0.336042,0.511203,0.357027,0.830717,0,0.530547,0.118546,0.215337,0.465097,0.176628,0.329508,0.356242,0.122718,0.210021,0.381085,0.781016,0.287195,0.154744,0.957486,0.75617,0.624931,0.117091,0.397142,0.135203,0.155394,0.358314,0.885722,0.097604,0.276416,0.121091,0.279796,0.145909,0.136236,0.949756,0.24907,0.457618,0.812613,0.0394476,0.156829,0.514446,0.404841,0.137142,0.759566,0.776306,0.363247,0.163199,0.325117,0.424359,0.36147,0.606104,0.413233,0.26973,0.504093,0.974413,0.541429,0.908031,1.25063,1.46477,1.10561,0.189925,0.526777,0.587721,0.808562,0.0481979,3.12194,0.0464428,0.447339,0.590017,0.179738,0.0707051,0.546623,0.411949,0.0636668,0.69807,0.132803,0.0697055,0.958261,0.462057,1.41118,0.975915,0.702809,0.636995,0.799202,1.08418,1.01076,0.503836,0.639644,2.02057,0.286529,0.111186,0.624668,1.75886,0.514993,0.514023,0.76508,0.569344,0.296997,0.183341,0.526725,0.218949,0.744577,1.61675,0.841652,0.982794,0.76501,0.342134,3.75093,0.53175,0.352143,0.813766,1.21719,3.62997,0.446521,1.03573,3.60647,0.353461,0.630607,0.906557,0.406303,0.726634,1.29819,0.877862,0.375176,1.0039,0.012643,0.231086,0.768569,0.955897,1.77738,1.3796,0.91261,0.393303,0.634793,0.508066,0.280171,0.460443,1.73788,1.22575,1.2821,0.621133,0.293013,0.761071,1.0355,0.374365,0.839715,0.405736,1.39573,0.222538,0.230865,0.96517,0.697256,0.593895,0.21719,0.50503,0.367885,0.356446,0.33468,1.97604|tfbs_overrepresentation_jaspar=MA0003.1;1.16498,MA0004.1;0.258473,MA0006.1;0.817804,MA0007.1;0.246385,MA0009.1;0.649874,MA0014.1;0.546364,MA0017.1;0.150118,MA0019.1;0.480432,MA0024.1;0.608636,MA0025.1;0.873493,MA0027.1;2.275,MA0028.1;0.138956,MA0029.1;0.588275,MA0030.1;0.594419,MA0031.1;0.561217,MA0038.1;0.381016,MA0040.1;0.661716,MA0041.1;0.198922,MA0042.1;0.189008,MA0043.1;0.74191,MA0046.1;0.683926,MA0048.1;0.534002,MA0050.1;0.290354,MA0051.1;0.388883,MA0052.1;0.669354,MA0055.1;0.0652519,MA0056.1;0,MA0057.1;0.107353,MA0058.1;0.183941,MA0059.1;0.19314,MA0060.1;4.79328,MA0061.1;1.11472,MA0063.1;0,MA0066.1;0.371389,MA0067.1;0.981551,MA0068.1;0.271058,MA0069.1;0.669676,MA0070.1;0.660488,MA0071.1;0.289658,MA0072.1;0.652465,MA0073.1;2.48172e-05,MA0074.1;0.340281,MA0076.1;0.163664,MA0077.1;0.632005,MA0078.1;0.418168,MA0081.1;1.14043,MA0083.1;0.741151,MA0084.1;1.30392,MA0087.1;0.699999,MA0088.1;0.569713,MA0089.1;0,MA0090.1;0.231074,MA0091.1;0.269175,MA0092.1;1.21955,MA0093.1;0.144649,MA0095.1;0,MA0098.1;0,MA0100.1;0.330364,MA0101.1;1.72541,MA0103.1;0.927638,MA0105.1;1.05934,MA0106.1;0.425111,MA0107.1;2.80186,MA0108.2;1.25225,MA0109.1;0,MA0111.1;0.242308,MA0113.1;0.400008,MA0114.1;0.0981613,MA0115.1;0.744589,MA0116.1;0.131762,MA0117.1;0.713754,MA0119.1;0.200349,MA0122.1;0.732707,MA0124.1;0.929684,MA0125.1;0.857794,MA0130.1;0,MA0131.1;0.476296,MA0132.1;0,MA0133.1;0,MA0135.1;0.77683,MA0136.1;0.357464,MA0139.1;0.231431,MA0140.1;0.330266,MA0141.1;0.171891,MA0142.1;0.547747,MA0143.1;0.414534,MA0144.1;0.100037,MA0145.1;0.614688,MA0146.1;0.662029,MA0147.1;0.107632,MA0148.1;0.271704,MA0149.1;0.589705,MA0062.2;0.177386,MA0035.2;0.33429,MA0039.2;0.04606,MA0138.2;0.469076,MA0002.2;2.39888,MA0137.2;0.169785,MA0104.2;0.0740839,MA0047.2;0.380343,MA0112.2;0.614664,MA0065.2;0.616691,MA0150.1;0.246295,MA0151.1;0,MA0152.1;0.990823,MA0153.1;0.792819,MA0154.1;0.118426,MA0155.1;0.423059,MA0156.1;0.490212,MA0157.1;0.518122,MA0158.1;0,MA0159.1;0.114033,MA0160.1;0.274172,MA0161.1;0,MA0162.1;0.0453371,MA0163.1;0.70702,MA0164.1;0.357779,MA0080.2;0.467794,MA0018.2;0.366212,MA0099.2;0.463355,MA0079.2;0.0981045,MA0102.2;1.35579,MA0258.1;0.0900907,MA0259.1;0.101001,MA0442.1;0}} | ||
Latest revision as of 15:26, 17 September 2013
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Mm9::chr10:77815034..77815062,- | p4@Agpat3 |
| Mm9::chr16:91225691..91225700,+ | p5@Olig2 |
| Mm9::chr16:91225808..91225824,+ | p1@Olig2 |
| Mm9::chr16:91269972..91269978,+ | p3@Olig1 |
| Mm9::chr16:91270004..91270023,+ | p1@Olig1 |
| Mm9::chr16:91270091..91270143,+ | p2@Olig1 |
| Mm9::chr5:33084895..33084903,- | p5@Pisd |
| Mm9::chr6:120723567..120723597,+ | p1@Slc25a18 |
| Mm9::chr6:120723602..120723604,+ | p3@Slc25a18 |
| Mm9::chr6:120723629..120723642,+ | p2@Slc25a18 |
| Mm9::chr6:120723651..120723654,+ | p4@Slc25a18 |
| Mm9::chr6:85163894..85163900,- | p@chr6:85163894..85163900 - |
| Mm9::chr7:29551766..29551841,+ | p1@Sirt2 |
| Mm9::chr9:119977381..119977409,- | p1@Cx3cr1 |
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:0048663 | neuron fate commitment | 0.00328124834416348 |
| GO:0044451 | nucleoplasm part | 0.0216479470319356 |
| GO:0045165 | cell fate commitment | 0.0216479470319356 |
| GO:0005654 | nucleoplasm | 0.0216479470319356 |
| GO:0031981 | nuclear lumen | 0.0255129623200036 |
| GO:0004609 | phosphatidylserine decarboxylase activity | 0.0255129623200036 |
| GO:0031974 | membrane-enclosed lumen | 0.0255129623200036 |
| GO:0043233 | organelle lumen | 0.0255129623200036 |
| GO:0045892 | negative regulation of transcription, DNA-dependent | 0.029467491566657 |
| GO:0016481 | negative regulation of transcription | 0.0338399603669903 |
| GO:0005677 | chromatin silencing complex | 0.0338399603669903 |
| GO:0044428 | nuclear part | 0.0338399603669903 |
| GO:0045934 | negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.0338399603669903 |
| GO:0044446 | intracellular organelle part | 0.0338399603669903 |
| GO:0044422 | organelle part | 0.0338399603669903 |
| GO:0048709 | oligodendrocyte differentiation | 0.0338399603669903 |
| GO:0030182 | neuron differentiation | 0.0338399603669903 |
| GO:0031324 | negative regulation of cellular metabolic process | 0.0353489451883645 |
| GO:0048699 | generation of neurons | 0.0353489451883645 |
| GO:0006342 | chromatin silencing | 0.0353489451883645 |
| GO:0031507 | heterochromatin formation | 0.0353489451883645 |
| GO:0009892 | negative regulation of metabolic process | 0.035679063989088 |
| GO:0022008 | neurogenesis | 0.035679063989088 |
| GO:0045814 | negative regulation of gene expression, epigenetic | 0.035679063989088 |
| GO:0003705 | RNA polymerase II transcription factor activity, enhancer binding | 0.0433619796683617 |
| GO:0016585 | chromatin remodeling complex | 0.04388263289812 |
| GO:0005667 | transcription factor complex | 0.0466304394042769 |
| GO:0004950 | chemokine receptor activity | 0.0466304394042769 |
| GO:0019956 | chemokine binding | 0.0466304394042769 |
| GO:0001637 | G-protein chemoattractant receptor activity | 0.0466304394042769 |
| GO:0016831 | carboxy-lyase activity | 0.0466304394042769 |
| GO:0042552 | myelination | 0.0466304394042769 |
| GO:0016458 | gene silencing | 0.0466304394042769 |
| GO:0007272 | ensheathment of neurons | 0.0472096397336174 |
| GO:0008366 | axon ensheathment | 0.0472096397336174 |
| GO:0043234 | protein complex | 0.0492691316908081 |
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>
| Ontology term | p-value | n |
|---|---|---|
| ectodermal cell | 3.30e-17 | 44 |
| neurectodermal cell | 3.30e-17 | 44 |
| neural cell | 9.27e-17 | 43 |
| CNS neuron (sensu Vertebrata) | 1.00e-16 | 23 |
| neuroblast (sensu Vertebrata) | 1.00e-16 | 23 |
| non-terminally differentiated cell | 2.46e-13 | 49 |
| neuron | 3.91e-11 | 33 |
| neuronal stem cell | 3.91e-11 | 33 |
| neuroblast | 3.91e-11 | 33 |
| electrically signaling cell | 3.91e-11 | 33 |
| electrically responsive cell | 2.90e-08 | 39 |
| electrically active cell | 2.90e-08 | 39 |
| migratory neural crest cell | 5.99e-07 | 10 |
| neuron associated cell | 5.99e-07 | 10 |
| glial cell (sensu Vertebrata) | 5.99e-07 | 10 |
| neuron associated cell (sensu Vertebrata) | 5.99e-07 | 10 |
| glial cell | 5.99e-07 | 10 |
| glioblast | 5.99e-07 | 10 |
| glioblast (sensu Vertebrata) | 5.99e-07 | 10 |
| embryonic cell | 6.99e-07 | 70 |
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 | 1.16498 |
| MA0004.1 | 0.258473 |
| MA0006.1 | 0.817804 |
| MA0007.1 | 0.246385 |
| MA0009.1 | 0.649874 |
| MA0014.1 | 0.546364 |
| MA0017.1 | 0.150118 |
| MA0019.1 | 0.480432 |
| MA0024.1 | 0.608636 |
| MA0025.1 | 0.873493 |
| MA0027.1 | 2.275 |
| MA0028.1 | 0.138956 |
| MA0029.1 | 0.588275 |
| MA0030.1 | 0.594419 |
| MA0031.1 | 0.561217 |
| MA0038.1 | 0.381016 |
| MA0040.1 | 0.661716 |
| MA0041.1 | 0.198922 |
| MA0042.1 | 0.189008 |
| MA0043.1 | 0.74191 |
| MA0046.1 | 0.683926 |
| MA0048.1 | 0.534002 |
| MA0050.1 | 0.290354 |
| MA0051.1 | 0.388883 |
| MA0052.1 | 0.669354 |
| MA0055.1 | 0.0652519 |
| MA0056.1 | 0 |
| MA0057.1 | 0.107353 |
| MA0058.1 | 0.183941 |
| MA0059.1 | 0.19314 |
| MA0060.1 | 4.79328 |
| MA0061.1 | 1.11472 |
| MA0063.1 | 0 |
| MA0066.1 | 0.371389 |
| MA0067.1 | 0.981551 |
| MA0068.1 | 0.271058 |
| MA0069.1 | 0.669676 |
| MA0070.1 | 0.660488 |
| MA0071.1 | 0.289658 |
| MA0072.1 | 0.652465 |
| MA0073.1 | 2.48172e-05 |
| MA0074.1 | 0.340281 |
| MA0076.1 | 0.163664 |
| MA0077.1 | 0.632005 |
| MA0078.1 | 0.418168 |
| MA0081.1 | 1.14043 |
| MA0083.1 | 0.741151 |
| MA0084.1 | 1.30392 |
| MA0087.1 | 0.699999 |
| MA0088.1 | 0.569713 |
| MA0089.1 | 0 |
| MA0090.1 | 0.231074 |
| MA0091.1 | 0.269175 |
| MA0092.1 | 1.21955 |
| MA0093.1 | 0.144649 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.330364 |
| MA0101.1 | 1.72541 |
| MA0103.1 | 0.927638 |
| MA0105.1 | 1.05934 |
| MA0106.1 | 0.425111 |
| MA0107.1 | 2.80186 |
| MA0108.2 | 1.25225 |
| MA0109.1 | 0 |
| MA0111.1 | 0.242308 |
| MA0113.1 | 0.400008 |
| MA0114.1 | 0.0981613 |
| MA0115.1 | 0.744589 |
| MA0116.1 | 0.131762 |
| MA0117.1 | 0.713754 |
| MA0119.1 | 0.200349 |
| MA0122.1 | 0.732707 |
| MA0124.1 | 0.929684 |
| MA0125.1 | 0.857794 |
| MA0130.1 | 0 |
| MA0131.1 | 0.476296 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 0.77683 |
| MA0136.1 | 0.357464 |
| MA0139.1 | 0.231431 |
| MA0140.1 | 0.330266 |
| MA0141.1 | 0.171891 |
| MA0142.1 | 0.547747 |
| MA0143.1 | 0.414534 |
| MA0144.1 | 0.100037 |
| MA0145.1 | 0.614688 |
| MA0146.1 | 0.662029 |
| MA0147.1 | 0.107632 |
| MA0148.1 | 0.271704 |
| MA0149.1 | 0.589705 |
| MA0062.2 | 0.177386 |
| MA0035.2 | 0.33429 |
| MA0039.2 | 0.04606 |
| MA0138.2 | 0.469076 |
| MA0002.2 | 2.39888 |
| MA0137.2 | 0.169785 |
| MA0104.2 | 0.0740839 |
| MA0047.2 | 0.380343 |
| MA0112.2 | 0.614664 |
| MA0065.2 | 0.616691 |
| MA0150.1 | 0.246295 |
| MA0151.1 | 0 |
| MA0152.1 | 0.990823 |
| MA0153.1 | 0.792819 |
| MA0154.1 | 0.118426 |
| MA0155.1 | 0.423059 |
| MA0156.1 | 0.490212 |
| MA0157.1 | 0.518122 |
| MA0158.1 | 0 |
| MA0159.1 | 0.114033 |
| MA0160.1 | 0.274172 |
| MA0161.1 | 0 |
| MA0162.1 | 0.0453371 |
| MA0163.1 | 0.70702 |
| MA0164.1 | 0.357779 |
| MA0080.2 | 0.467794 |
| MA0018.2 | 0.366212 |
| MA0099.2 | 0.463355 |
| MA0079.2 | 0.0981045 |
| MA0102.2 | 1.35579 |
| MA0258.1 | 0.0900907 |
| MA0259.1 | 0.101001 |
| MA0442.1 | 0 |
