MCL coexpression mm9:2774: Difference between revisions
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{{MCL_coexpression_mm9 | 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of histone H3-K4 methylation;0.00602640661809018;214162!GO:0051568;histone H3-K4 methylation;0.00602640661809018;214162!GO:0031060;regulation of histone methylation;0.00803498870553531;214162!GO:0031056;regulation of histone modification;0.0120518227025482;214162!GO:0035162;embryonic hemopoiesis;0.0144613948161521;214162!GO:0006306;DNA methylation;0.0225903576485567;214162!GO:0006305;DNA alkylation;0.0225903576485567;214162!GO:0016571;histone methylation;0.0225903576485567;214162!GO:0006304;DNA modification;0.0240944004245295;214162!GO:0051052;regulation of DNA metabolic process;0.0246237656104948;214162!GO:0044428;nuclear part;0.0246237656104948;214162,20688!GO:0008213;protein amino acid alkylation;0.0246237656104948;214162!GO:0006479;protein amino acid methylation;0.0246237656104948;214162!GO:0016570;histone modification;0.0246237656104948;214162!GO:0008016;regulation of heart contraction;0.0246237656104948;20688!GO:0048568;embryonic organ development;0.0246237656104948;214162!GO:0016569;covalent chromatin modification;0.0246237656104948;214162!GO:0043414;biopolymer methylation;0.0246237656104948;214162!GO:0040029;regulation of gene expression, epigenetic;0.0246237656104948;214162!GO:0060047;heart contraction;0.0246237656104948;20688!GO:0003015;heart process;0.0246237656104948;20688!GO:0032259;methylation;0.0246237656104948;214162!GO:0051128;regulation of cellular component organization and biogenesis;0.0282568237247241;214162!GO:0003713;transcription coactivator activity;0.033112143142528;20688!GO:0003702;RNA polymerase II transcription factor activity;0.033112143142528;20688!GO:0006730;one-carbon compound metabolic process;0.033112143142528;214162!GO:0006355;regulation of transcription, DNA-dependent;0.033112143142528;214162,20688!GO:0006351;transcription, DNA-dependent;0.033112143142528;214162,20688!GO:0032774;RNA biosynthetic process;0.033112143142528;214162,20688!GO:0008270;zinc ion binding;0.033112143142528;214162,20688!GO:0003677;DNA binding;0.033112143142528;214162,20688!GO:0009952;anterior/posterior pattern formation;0.033112143142528;214162!GO:0008015;blood circulation;0.033112143142528;20688!GO:0003013;circulatory system process;0.033112143142528;20688!GO:0045449;regulation of transcription;0.033112143142528;214162,20688!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.033429706950182;214162,20688!GO:0006350;transcription;0.033429706950182;214162,20688!GO:0010468;regulation of gene expression;0.0347729438238879;214162,20688!GO:0031323;regulation of cellular metabolic process;0.0367158307621688;214162,20688!GO:0019222;regulation of metabolic process;0.0383625493068262;214162,20688!GO:0016070;RNA metabolic process;0.0383625493068262;214162,20688!GO:0003712;transcription cofactor activity;0.0383625493068262;20688!GO:0046914;transition metal ion binding;0.0383625493068262;214162,20688!GO:0044446;intracellular organelle part;0.0383625493068262;214162,20688!GO:0044422;organelle part;0.0383625493068262;214162,20688!GO:0003002;regionalization;0.0383625493068262;214162!GO:0016568;chromatin modification;0.0421229695873964;214162!GO:0016563;transcription activator activity;0.044479128579898;20688!GO:0008134;transcription factor binding;0.045763098535396;20688!GO:0010467;gene expression;0.0464610196380316;214162,20688!GO:0003676;nucleic acid binding;0.0477746153611416;214162,20688!GO:0030097;hemopoiesis;0.0479378656622439;214162!|ontology_enrichment_celltype=CL:0000117!4.36e-09!23;CL:0000337!4.36e-09!23;CL:0000540!2.08e-07!33;CL:0000047!2.08e-07!33;CL:0000031!2.08e-07!33;CL:0000404!2.08e-07!33|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0002346!5.30e-14!64;UBERON:0003075!5.30e-14!64;UBERON:0007284!5.30e-14!64;UBERON:0000073!7.86e-13!54;UBERON:0003056!3.08e-12!49;UBERON:0001049!6.54e-12!52;UBERON:0005068!6.54e-12!52;UBERON:0006241!6.54e-12!52;UBERON:0007135!6.54e-12!52;UBERON:0001017!2.87e-11!73;UBERON:0000955!6.80e-11!47;UBERON:0006238!6.80e-11!47;UBERON:0010371!8.50e-11!73;UBERON:0002020!2.25e-10!34;UBERON:0002616!2.57e-10!46;UBERON:0001016!3.65e-10!75;UBERON:0003080!5.32e-10!40;UBERON:0002780!1.40e-09!39;UBERON:0001890!1.40e-09!39;UBERON:0006240!1.40e-09!39;UBERON:0004121!3.08e-09!95;UBERON:0000924!3.08e-09!95;UBERON:0006601!3.08e-09!95;UBERON:0003528!3.21e-09!29;UBERON:0002791!3.21e-09!29;UBERON:0001893!3.21e-09!29;UBERON:0010314!6.77e-08!92|tfbs_overrepresentation_for_novel_motifs=0.752782,0.564138,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,1.23467,2.0216,0.906098,1.18012,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.328717,0.679146,0.275782,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,1.55113,0.380786,0.825437,1.24901,1.40911,0.411696,0.608816,0.444545,1.38481,0.902078,0.536514,1.24975,0.582863,0.831295,0.261619,0.610669,0.474221,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,1.41919,1.44925,1.882,0.402065,0.411601,1.04436,1.20986,0.684144,1.19917,1.16055,1.00151,0.459035,1.32978,2.30787,0.195254,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,1.26911,0.464141,1.26539,1.05692,0.928366,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,1.63106,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,1.1471,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.999018,1.32874,1.39822,2.21624,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,1.75703,1.11251,0.94678,0.562367,0.904334,1.34909|tfbs_overrepresentation_jaspar=MA0003.1;3.77865,MA0004.1;0.801718,MA0006.1;0.60285,MA0007.1;0.784593,MA0009.1;1.27673,MA0014.1;4.96439,MA0017.1;0.635031,MA0019.1;1.08369,MA0024.1;1.23079,MA0025.1;1.51835,MA0027.1;2.9431,MA0028.1;0.61552,MA0029.1;1.20789,MA0030.1;1.21482,MA0031.1;1.17722,MA0038.1;0.963265,MA0040.1;1.28983,MA0041.1;0.714279,MA0042.1;0.69885,MA0043.1;1.3775,MA0046.1;1.31428,MA0048.1;0.932001,MA0050.1;0.845669,MA0051.1;0.973068,MA0052.1;1.29825,MA0055.1;0.190475,MA0056.1;0,MA0057.1;1.60767,MA0058.1;0.690848,MA0059.1;0.705317,MA0060.1;1.25521,MA0061.1;0.5406,MA0063.1;0,MA0066.1;0.951196,MA0067.1;1.63197,MA0068.1;0.343188,MA0069.1;1.29861,MA0070.1;1.28847,MA0071.1;0.844726,MA0072.1;1.2796,MA0073.1;4.16062,MA0074.1;0.911576,MA0076.1;0.657929,MA0077.1;1.2569,MA0078.1;1.0091,MA0081.1;0.732313,MA0083.1;1.37668,MA0084.1;1.96428,MA0087.1;1.33189,MA0088.1;0.27999,MA0089.1;0,MA0090.1;0.762482,MA0091.1;0.816659,MA0092.1;0.762845,MA0093.1;0.62555,MA0095.1;0,MA0098.1;0,MA0100.1;0.89873,MA0101.1;0.71579,MA0103.1;0.647985,MA0105.1;2.75918,MA0106.1;1.01755,MA0107.1;0.640607,MA0108.2;1.10817,MA0109.1;0,MA0111.1;0.778753,MA0113.1;0.986839,MA0114.1;1.3296,MA0115.1;1.38041,MA0116.1;0.602598,MA0117.1;1.34691,MA0119.1;0.716476,MA0122.1;1.36752,MA0124.1;1.57762,MA0125.1;1.5017,MA0130.1;0,MA0131.1;1.07881,MA0132.1;0,MA0133.1;0,MA0135.1;1.4152,MA0136.1;0.933582,MA0139.1;2.03543,MA0140.1;0.898603,MA0141.1;0.671467,MA0142.1;1.16183,MA0143.1;1.00467,MA0144.1;0.541532,MA0145.1;3.06815,MA0146.1;2.07553,MA0147.1;0.556853,MA0148.1;0.820161,MA0149.1;0.722227,MA0062.2;0.412742,MA0035.2;0.903829,MA0039.2;3.25387,MA0138.2;1.07027,MA0002.2;0.466067,MA0137.2;0.668025,MA0104.2;0.48458,MA0047.2;0.962424,MA0112.2;0.29236,MA0065.2;3.07166,MA0150.1;0.784464,MA0151.1;0,MA0152.1;0.962542,MA0153.1;1.43238,MA0154.1;0.35067,MA0155.1;1.52001,MA0156.1;0.656895,MA0157.1;1.12772,MA0158.1;0,MA0159.1;0.569393,MA0160.1;0.823568,MA0161.1;0,MA0162.1;1.53682,MA0163.1;4.46088,MA0164.1;0.933981,MA0080.2;0.64167,MA0018.2;0.944669,MA0099.2;1.06348,MA0079.2;11.3089,MA0102.2;2.01714,MA0258.1;0.520639,MA0259.1;0.543506,MA0442.1;0}} | ||
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| |||
| | |||
}} | |||
Latest revision as of 19:03, 17 September 2013
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Mm9::chr12:119539843..119539899,- | p1@Sp4 |
| Mm9::chr12:119539902..119539931,- | p2@Sp4 |
| Mm9::chr9:44689360..44689406,- | p1@Mll1 |
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:0051569 | regulation of histone H3-K4 methylation | 0.00602640661809018 |
| GO:0051568 | histone H3-K4 methylation | 0.00602640661809018 |
| GO:0031060 | regulation of histone methylation | 0.00803498870553531 |
| GO:0031056 | regulation of histone modification | 0.0120518227025482 |
| GO:0035162 | embryonic hemopoiesis | 0.0144613948161521 |
| GO:0006306 | DNA methylation | 0.0225903576485567 |
| GO:0006305 | DNA alkylation | 0.0225903576485567 |
| GO:0016571 | histone methylation | 0.0225903576485567 |
| GO:0006304 | DNA modification | 0.0240944004245295 |
| GO:0051052 | regulation of DNA metabolic process | 0.0246237656104948 |
| GO:0044428 | nuclear part | 0.0246237656104948 |
| GO:0008213 | protein amino acid alkylation | 0.0246237656104948 |
| GO:0006479 | protein amino acid methylation | 0.0246237656104948 |
| GO:0016570 | histone modification | 0.0246237656104948 |
| GO:0008016 | regulation of heart contraction | 0.0246237656104948 |
| GO:0048568 | embryonic organ development | 0.0246237656104948 |
| GO:0016569 | covalent chromatin modification | 0.0246237656104948 |
| GO:0043414 | biopolymer methylation | 0.0246237656104948 |
| GO:0040029 | regulation of gene expression, epigenetic | 0.0246237656104948 |
| GO:0060047 | heart contraction | 0.0246237656104948 |
| GO:0003015 | heart process | 0.0246237656104948 |
| GO:0032259 | methylation | 0.0246237656104948 |
| GO:0051128 | regulation of cellular component organization and biogenesis | 0.0282568237247241 |
| GO:0003713 | transcription coactivator activity | 0.033112143142528 |
| GO:0003702 | RNA polymerase II transcription factor activity | 0.033112143142528 |
| GO:0006730 | one-carbon compound metabolic process | 0.033112143142528 |
| GO:0006355 | regulation of transcription, DNA-dependent | 0.033112143142528 |
| GO:0006351 | transcription, DNA-dependent | 0.033112143142528 |
| GO:0032774 | RNA biosynthetic process | 0.033112143142528 |
| GO:0008270 | zinc ion binding | 0.033112143142528 |
| GO:0003677 | DNA binding | 0.033112143142528 |
| GO:0009952 | anterior/posterior pattern formation | 0.033112143142528 |
| GO:0008015 | blood circulation | 0.033112143142528 |
| GO:0003013 | circulatory system process | 0.033112143142528 |
| GO:0045449 | regulation of transcription | 0.033112143142528 |
| GO:0019219 | regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.033429706950182 |
| GO:0006350 | transcription | 0.033429706950182 |
| GO:0010468 | regulation of gene expression | 0.0347729438238879 |
| GO:0031323 | regulation of cellular metabolic process | 0.0367158307621688 |
| GO:0019222 | regulation of metabolic process | 0.0383625493068262 |
| GO:0016070 | RNA metabolic process | 0.0383625493068262 |
| GO:0003712 | transcription cofactor activity | 0.0383625493068262 |
| GO:0046914 | transition metal ion binding | 0.0383625493068262 |
| GO:0044446 | intracellular organelle part | 0.0383625493068262 |
| GO:0044422 | organelle part | 0.0383625493068262 |
| GO:0003002 | regionalization | 0.0383625493068262 |
| GO:0016568 | chromatin modification | 0.0421229695873964 |
| GO:0016563 | transcription activator activity | 0.044479128579898 |
| GO:0008134 | transcription factor binding | 0.045763098535396 |
| GO:0010467 | gene expression | 0.0464610196380316 |
| GO:0003676 | nucleic acid binding | 0.0477746153611416 |
| GO:0030097 | hemopoiesis | 0.0479378656622439 |
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 |
|---|---|---|
| CNS neuron (sensu Vertebrata) | 4.36e-09 | 23 |
| neuroblast (sensu Vertebrata) | 4.36e-09 | 23 |
| neuron | 2.08e-07 | 33 |
| neuronal stem cell | 2.08e-07 | 33 |
| neuroblast | 2.08e-07 | 33 |
| electrically signaling cell | 2.08e-07 | 33 |
| Ontology term | p-value | n |
|---|---|---|
| neurectoderm | 5.30e-14 | 64 |
| neural plate | 5.30e-14 | 64 |
| presumptive neural plate | 5.30e-14 | 64 |
| regional part of nervous system | 7.86e-13 | 54 |
| pre-chordal neural plate | 3.08e-12 | 49 |
| neural tube | 6.54e-12 | 52 |
| neural rod | 6.54e-12 | 52 |
| future spinal cord | 6.54e-12 | 52 |
| neural keel | 6.54e-12 | 52 |
| central nervous system | 2.87e-11 | 73 |
| brain | 6.80e-11 | 47 |
| future brain | 6.80e-11 | 47 |
| ecto-epithelium | 8.50e-11 | 73 |
| gray matter | 2.25e-10 | 34 |
| regional part of brain | 2.57e-10 | 46 |
| nervous system | 3.65e-10 | 75 |
| anterior neural tube | 5.32e-10 | 40 |
| regional part of forebrain | 1.40e-09 | 39 |
| forebrain | 1.40e-09 | 39 |
| future forebrain | 1.40e-09 | 39 |
| ectoderm-derived structure | 3.08e-09 | 95 |
| ectoderm | 3.08e-09 | 95 |
| presumptive ectoderm | 3.08e-09 | 95 |
| brain grey matter | 3.21e-09 | 29 |
| regional part of telencephalon | 3.21e-09 | 29 |
| telencephalon | 3.21e-09 | 29 |
| structure with developmental contribution from neural crest | 6.77e-08 | 92 |
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 | 3.77865 |
| MA0004.1 | 0.801718 |
| MA0006.1 | 0.60285 |
| MA0007.1 | 0.784593 |
| MA0009.1 | 1.27673 |
| MA0014.1 | 4.96439 |
| MA0017.1 | 0.635031 |
| MA0019.1 | 1.08369 |
| MA0024.1 | 1.23079 |
| MA0025.1 | 1.51835 |
| MA0027.1 | 2.9431 |
| MA0028.1 | 0.61552 |
| MA0029.1 | 1.20789 |
| MA0030.1 | 1.21482 |
| MA0031.1 | 1.17722 |
| MA0038.1 | 0.963265 |
| MA0040.1 | 1.28983 |
| MA0041.1 | 0.714279 |
| MA0042.1 | 0.69885 |
| MA0043.1 | 1.3775 |
| MA0046.1 | 1.31428 |
| MA0048.1 | 0.932001 |
| MA0050.1 | 0.845669 |
| MA0051.1 | 0.973068 |
| MA0052.1 | 1.29825 |
| MA0055.1 | 0.190475 |
| MA0056.1 | 0 |
| MA0057.1 | 1.60767 |
| MA0058.1 | 0.690848 |
| MA0059.1 | 0.705317 |
| MA0060.1 | 1.25521 |
| MA0061.1 | 0.5406 |
| MA0063.1 | 0 |
| MA0066.1 | 0.951196 |
| MA0067.1 | 1.63197 |
| MA0068.1 | 0.343188 |
| MA0069.1 | 1.29861 |
| MA0070.1 | 1.28847 |
| MA0071.1 | 0.844726 |
| MA0072.1 | 1.2796 |
| MA0073.1 | 4.16062 |
| MA0074.1 | 0.911576 |
| MA0076.1 | 0.657929 |
| MA0077.1 | 1.2569 |
| MA0078.1 | 1.0091 |
| MA0081.1 | 0.732313 |
| MA0083.1 | 1.37668 |
| MA0084.1 | 1.96428 |
| MA0087.1 | 1.33189 |
| MA0088.1 | 0.27999 |
| MA0089.1 | 0 |
| MA0090.1 | 0.762482 |
| MA0091.1 | 0.816659 |
| MA0092.1 | 0.762845 |
| MA0093.1 | 0.62555 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.89873 |
| MA0101.1 | 0.71579 |
| MA0103.1 | 0.647985 |
| MA0105.1 | 2.75918 |
| MA0106.1 | 1.01755 |
| MA0107.1 | 0.640607 |
| MA0108.2 | 1.10817 |
| MA0109.1 | 0 |
| MA0111.1 | 0.778753 |
| MA0113.1 | 0.986839 |
| MA0114.1 | 1.3296 |
| MA0115.1 | 1.38041 |
| MA0116.1 | 0.602598 |
| MA0117.1 | 1.34691 |
| MA0119.1 | 0.716476 |
| MA0122.1 | 1.36752 |
| MA0124.1 | 1.57762 |
| MA0125.1 | 1.5017 |
| MA0130.1 | 0 |
| MA0131.1 | 1.07881 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.4152 |
| MA0136.1 | 0.933582 |
| MA0139.1 | 2.03543 |
| MA0140.1 | 0.898603 |
| MA0141.1 | 0.671467 |
| MA0142.1 | 1.16183 |
| MA0143.1 | 1.00467 |
| MA0144.1 | 0.541532 |
| MA0145.1 | 3.06815 |
| MA0146.1 | 2.07553 |
| MA0147.1 | 0.556853 |
| MA0148.1 | 0.820161 |
| MA0149.1 | 0.722227 |
| MA0062.2 | 0.412742 |
| MA0035.2 | 0.903829 |
| MA0039.2 | 3.25387 |
| MA0138.2 | 1.07027 |
| MA0002.2 | 0.466067 |
| MA0137.2 | 0.668025 |
| MA0104.2 | 0.48458 |
| MA0047.2 | 0.962424 |
| MA0112.2 | 0.29236 |
| MA0065.2 | 3.07166 |
| MA0150.1 | 0.784464 |
| MA0151.1 | 0 |
| MA0152.1 | 0.962542 |
| MA0153.1 | 1.43238 |
| MA0154.1 | 0.35067 |
| MA0155.1 | 1.52001 |
| MA0156.1 | 0.656895 |
| MA0157.1 | 1.12772 |
| MA0158.1 | 0 |
| MA0159.1 | 0.569393 |
| MA0160.1 | 0.823568 |
| MA0161.1 | 0 |
| MA0162.1 | 1.53682 |
| MA0163.1 | 4.46088 |
| MA0164.1 | 0.933981 |
| MA0080.2 | 0.64167 |
| MA0018.2 | 0.944669 |
| MA0099.2 | 1.06348 |
| MA0079.2 | 11.3089 |
| MA0102.2 | 2.01714 |
| MA0258.1 | 0.520639 |
| MA0259.1 | 0.543506 |
| MA0442.1 | 0 |
