MCL coexpression mm9:1096: Difference between revisions
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{{MCL_coexpression_mm9| | 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development;0.00352670701653998;15399,15402,103889!GO:0006355;regulation of transcription, DNA-dependent;0.00352698103268352;15399,15402,103889!GO:0048701;embryonic cranial skeleton morphogenesis;0.00352698103268352;15399!GO:0042474;middle ear morphogenesis;0.00352698103268352;15399!GO:0006351;transcription, DNA-dependent;0.00352698103268352;15399,15402,103889!GO:0032774;RNA biosynthetic process;0.00352698103268352;15399,15402,103889!GO:0003677;DNA binding;0.00352698103268352;15399,15402,103889!GO:0045449;regulation of transcription;0.00352698103268352;15399,15402,103889!GO:0048856;anatomical structure development;0.00352698103268352;15399,15402,103889!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.00352698103268352;15399,15402,103889!GO:0006350;transcription;0.00352698103268352;15399,15402,103889!GO:0032991;macromolecular complex;0.00353528059212516;15399,15402,103889!GO:0010468;regulation of gene expression;0.00360600608291956;15399,15402,103889!GO:0031323;regulation of cellular metabolic process;0.00392269358044763;15399,15402,103889!GO:0007275;multicellular organismal development;0.00395090403194017;15399,15402,103889!GO:0030878;thyroid gland development;0.00395090403194017;15402!GO:0019222;regulation of metabolic process;0.00395090403194017;15399,15402,103889!GO:0016070;RNA metabolic process;0.0040519072570119;15399,15402,103889!GO:0048704;embryonic skeletal morphogenesis;0.0040519072570119;15399!GO:0044446;intracellular organelle part;0.00419771021870457;15399,15402,103889!GO:0044422;organelle part;0.00419771021870457;15399,15402,103889!GO:0009887;organ morphogenesis;0.00449832583067754;15399,103889!GO:0048706;embryonic skeletal development;0.00525508818876713;15399!GO:0010467;gene expression;0.00597361517483295;15399,15402,103889!GO:0003676;nucleic acid binding;0.00625208640842819;15399,15402,103889!GO:0032502;developmental process;0.00670053665632696;15399,15402,103889!GO:0048705;skeletal morphogenesis;0.0068145802385791;15399!GO:0001709;cell fate determination;0.00694117952400784;15399!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.00709741175974999;15399,15402,103889!GO:0050794;regulation of cellular process;0.00855503059975862;15399,15402,103889!GO:0050789;regulation of biological process;0.0115558544551607;15399,15402,103889!GO:0035270;endocrine system development;0.0126585304750465;15402!GO:0065007;biological regulation;0.0147516341067968;15399,15402,103889!GO:0042471;ear morphogenesis;0.0147516341067968;15399!GO:0035264;multicellular organism growth;0.0147516341067968;15402!GO:0005634;nucleus;0.0147516341067968;15399,15402,103889!GO:0032501;multicellular organismal process;0.0147516341067968;15399,15402,103889!GO:0009653;anatomical structure morphogenesis;0.0151095004532011;15399,103889!GO:0043283;biopolymer metabolic process;0.0152994450375327;15399,15402,103889!GO:0048732;gland development;0.0166003981102075;15402!GO:0043583;ear development;0.016737238024913;15399!GO:0045165;cell fate commitment;0.0216009514315933;15399!GO:0043170;macromolecule metabolic process;0.0322573700262882;15399,15402,103889!GO:0007423;sensory organ development;0.0386095019991401;15399!GO:0048598;embryonic morphogenesis;0.040982185860779;15399!GO:0043009;chordate embryonic development;0.0441184110103377;15399!GO:0009792;embryonic development ending in birth or egg hatching;0.0441184110103377;15399!GO:0044238;primary metabolic process;0.0448612696373388;15399,15402,103889!GO:0044237;cellular metabolic process;0.0448612696373388;15399,15402,103889!GO:0043231;intracellular membrane-bound organelle;0.0448612696373388;15399,15402,103889!GO:0043227;membrane-bound organelle;0.0448612696373388;15399,15402,103889!|ontology_enrichment_celltype=|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0005178!1.34e-11!17;UBERON:0005181!1.34e-11!17;UBERON:0002224!1.34e-11!17;UBERON:0000915!1.34e-11!17;UBERON:0008947!1.34e-11!17;UBERON:0003258!1.34e-11!17;UBERON:0002048!6.50e-10!14;UBERON:0000117!6.50e-10!14;UBERON:0000171!6.50e-10!14;UBERON:0000170!6.50e-10!14;UBERON:0005597!6.50e-10!14;UBERON:0000118!6.50e-10!14;UBERON:0005157!3.00e-09!20;UBERON:0005153!5.08e-07!17;UBERON:0005177!7.76e-07!79|tfbs_overrepresentation_for_novel_motifs=0.438063,0.369498,0.411716,0.480627,0.299217,0.495263,0.587291,0.206208,0.215218,0.0609112,0.542749,0.575086,0.206435,0.599731,0.315771,0,0.795315,0.792229,0.19222,0.112498,0.374752,0.08187,0.598814,0.29769,0.419327,0.62766,0.184473,0.516511,0.344372,0.145661,1.25421,0.897561,0.289148,0.166577,0.848378,0.101236,1.40094,0.57142,0.717242,0.230656,0.295233,0.507468,0.258106,0.317766,0.0275764,0.469348,0.714592,1.31862,0.0609361,0.917701,1.83068,0.654933,0.139618,1.04034,1.0579,0.606984,0.356236,0.56214,0.522357,0.604914,0.877332,0.664501,0.642748,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.21183,3.39997,1.09164,0.507615,0.159969,0.166511,0.703064,0.859987,0.378988,0.212973,1.90329,0.663039,0.580284,0.975495,0.960306,0.374181,0.447265,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.237542,1.11365,0.913319,0.71485,0.127063,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.998363,0.376549,0.430942,1.02459,0.380122,0.547992,1.27206,0.293461,0.418498,0.484437,1.86983,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.0806013,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,2.09861,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.147909,1.38961,1.04192,1.26486,0.619892,1.12411,0.655955,0.327731,1.11101,1.13413,1.25393,0.974632,0.864173,1.92222,0.767269,0.612377,0.763807,0.573477,0.227149|tfbs_overrepresentation_jaspar=MA0003.1;0.54119,MA0004.1;1.20906,MA0006.1;0.311391,MA0007.1;0.465969,MA0009.1;0.92425,MA0014.1;0.694761,MA0017.1;0.337808,MA0019.1;0.740036,MA0024.1;0.880057,MA0025.1;1.15921,MA0027.1;2.57545,MA0028.1;0.321735,MA0029.1;0.858105,MA0030.1;0.864739,MA0031.1;0.828781,MA0038.1;0.62758,MA0040.1;0.936879,MA0041.1;0.404721,MA0042.1;0.391504,MA0043.1;1.02178,MA0046.1;0.960497,MA0048.1;0.128106,MA0050.1;0.520357,MA0051.1;0.636645,MA0052.1;0.945011,MA0055.1;0.648475,MA0056.1;0,MA0057.1;1.23731,MA0058.1;2.66057,MA0059.1;1.81442,MA0060.1;0.232592,MA0061.1;0.261749,MA0063.1;0,MA0066.1;0.616444,MA0067.1;1.27078,MA0068.1;0.385183,MA0069.1;0.945354,MA0070.1;0.93557,MA0071.1;0.519509,MA0072.1;0.927016,MA0073.1;11.2967,MA0074.1;0.580087,MA0076.1;0.356883,MA0077.1;0.905143,MA0078.1;0.670113,MA0081.1;0.420276,MA0083.1;7.11247,MA0084.1;1.59945,MA0087.1;0.977537,MA0088.1;0.598004,MA0089.1;0,MA0090.1;0.446539,MA0091.1;0.494398,MA0092.1;0.446857,MA0093.1;1.58083,MA0095.1;0,MA0098.1;0,MA0100.1;0.568369,MA0101.1;0.406019,MA0103.1;0.348572,MA0105.1;0.488671,MA0106.1;0.677988,MA0107.1;0.342432,MA0108.2;0.763162,MA0109.1;0,MA0111.1;0.460823,MA0113.1;0.649407,MA0114.1;0.259463,MA0115.1;1.0246,MA0116.1;0.836994,MA0117.1;0.992087,MA0119.1;0.40661,MA0122.1;1.01209,MA0124.1;1.21735,MA0125.1;1.14291,MA0130.1;0,MA0131.1;0.735438,MA0132.1;0,MA0133.1;0,MA0135.1;1.05845,MA0136.1;0.600242,MA0139.1;1.7399,MA0140.1;0.568252,MA0141.1;0.368264,MA0142.1;0.814115,MA0143.1;0.665982,MA0144.1;0.262477,MA0145.1;0.0910975,MA0146.1;0.264322,MA0147.1;0.274511,MA0148.1;0.49752,MA0149.1;0.411562,MA0062.2;0.167299,MA0035.2;0.573016,MA0039.2;1.37408,MA0138.2;0.727395,MA0002.2;0.205289,MA0137.2;0.365364,MA0104.2;0.218974,MA0047.2;0.626803,MA0112.2;0.0910939,MA0065.2;0.305574,MA0150.1;0.465855,MA0151.1;0,MA0152.1;0.626912,MA0153.1;1.07519,MA0154.1;0.126143,MA0155.1;0.102995,MA0156.1;0.356017,MA0157.1;0.781683,MA0158.1;0,MA0159.1;0.284457,MA0160.1;0.50056,MA0161.1;0,MA0162.1;2.75316,MA0163.1;5.85525,MA0164.1;0.600609,MA0080.2;0.343316,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;7.04343,MA0102.2;1.65195,MA0258.1;0.246285,MA0259.1;0.729797,MA0442.1;0}} | ||
Latest revision as of 16:23, 17 September 2013
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Mm9::chr11:96214200..96214214,+ | p@chr11:96214200..96214214 + |
| Mm9::chr6:52114821..52114828,- | p1@Hoxa2 |
| Mm9::chr6:52125954..52125994,- | p@chr6:52125954..52125994 - |
| Mm9::chr6:52141617..52141644,- | p@chr6:52141617..52141644 - |
| Mm9::chr6:52154314..52154337,- | p@chr6:52154314..52154337 - |
| Mm9::chr6:52154386..52154407,- | p2@Hoxa5 |
| Mm9::chr6:52154414..52154462,- | p1@Hoxa5 |
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:0007389 | pattern specification process | 0.000153943056126016 |
| GO:0005667 | transcription factor complex | 0.000315835053414219 |
| GO:0043565 | sequence-specific DNA binding | 0.000315835053414219 |
| GO:0044451 | nucleoplasm part | 0.00039402010379568 |
| GO:0005654 | nucleoplasm | 0.00039402010379568 |
| GO:0031981 | nuclear lumen | 0.000551916113459114 |
| GO:0031974 | membrane-enclosed lumen | 0.000594239712410312 |
| GO:0043233 | organelle lumen | 0.000594239712410312 |
| GO:0003700 | transcription factor activity | 0.000700170475403781 |
| GO:0044428 | nuclear part | 0.00111763160844294 |
| GO:0001501 | skeletal development | 0.00193913542639484 |
| GO:0048513 | organ development | 0.00234322078843713 |
| GO:0043234 | protein complex | 0.00347439578904433 |
| GO:0048703 | embryonic viscerocranium morphogenesis | 0.00347439578904433 |
| GO:0048731 | system development | 0.00352670701653998 |
| GO:0006355 | regulation of transcription, DNA-dependent | 0.00352698103268352 |
| GO:0048701 | embryonic cranial skeleton morphogenesis | 0.00352698103268352 |
| GO:0042474 | middle ear morphogenesis | 0.00352698103268352 |
| GO:0006351 | transcription, DNA-dependent | 0.00352698103268352 |
| GO:0032774 | RNA biosynthetic process | 0.00352698103268352 |
| GO:0003677 | DNA binding | 0.00352698103268352 |
| GO:0045449 | regulation of transcription | 0.00352698103268352 |
| GO:0048856 | anatomical structure development | 0.00352698103268352 |
| GO:0019219 | regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.00352698103268352 |
| GO:0006350 | transcription | 0.00352698103268352 |
| GO:0032991 | macromolecular complex | 0.00353528059212516 |
| GO:0010468 | regulation of gene expression | 0.00360600608291956 |
| GO:0031323 | regulation of cellular metabolic process | 0.00392269358044763 |
| GO:0007275 | multicellular organismal development | 0.00395090403194017 |
| GO:0030878 | thyroid gland development | 0.00395090403194017 |
| GO:0019222 | regulation of metabolic process | 0.00395090403194017 |
| GO:0016070 | RNA metabolic process | 0.0040519072570119 |
| GO:0048704 | embryonic skeletal morphogenesis | 0.0040519072570119 |
| GO:0044446 | intracellular organelle part | 0.00419771021870457 |
| GO:0044422 | organelle part | 0.00419771021870457 |
| GO:0009887 | organ morphogenesis | 0.00449832583067754 |
| GO:0048706 | embryonic skeletal development | 0.00525508818876713 |
| GO:0010467 | gene expression | 0.00597361517483295 |
| GO:0003676 | nucleic acid binding | 0.00625208640842819 |
| GO:0032502 | developmental process | 0.00670053665632696 |
| GO:0048705 | skeletal morphogenesis | 0.0068145802385791 |
| GO:0001709 | cell fate determination | 0.00694117952400784 |
| GO:0006139 | nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.00709741175974999 |
| GO:0050794 | regulation of cellular process | 0.00855503059975862 |
| GO:0050789 | regulation of biological process | 0.0115558544551607 |
| GO:0035270 | endocrine system development | 0.0126585304750465 |
| GO:0065007 | biological regulation | 0.0147516341067968 |
| GO:0042471 | ear morphogenesis | 0.0147516341067968 |
| GO:0035264 | multicellular organism growth | 0.0147516341067968 |
| GO:0005634 | nucleus | 0.0147516341067968 |
| GO:0032501 | multicellular organismal process | 0.0147516341067968 |
| GO:0009653 | anatomical structure morphogenesis | 0.0151095004532011 |
| GO:0043283 | biopolymer metabolic process | 0.0152994450375327 |
| GO:0048732 | gland development | 0.0166003981102075 |
| GO:0043583 | ear development | 0.016737238024913 |
| GO:0045165 | cell fate commitment | 0.0216009514315933 |
| GO:0043170 | macromolecule metabolic process | 0.0322573700262882 |
| GO:0007423 | sensory organ development | 0.0386095019991401 |
| GO:0048598 | embryonic morphogenesis | 0.040982185860779 |
| GO:0043009 | chordate embryonic development | 0.0441184110103377 |
| GO:0009792 | embryonic development ending in birth or egg hatching | 0.0441184110103377 |
| GO:0044238 | primary metabolic process | 0.0448612696373388 |
| GO:0044237 | cellular metabolic process | 0.0448612696373388 |
| GO:0043231 | intracellular membrane-bound organelle | 0.0448612696373388 |
| GO:0043227 | membrane-bound organelle | 0.0448612696373388 |
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 |
|---|---|---|
| thoracic cavity element | 1.34e-11 | 17 |
| thoracic segment organ | 1.34e-11 | 17 |
| thoracic cavity | 1.34e-11 | 17 |
| thoracic segment of trunk | 1.34e-11 | 17 |
| respiratory primordium | 1.34e-11 | 17 |
| endoderm of foregut | 1.34e-11 | 17 |
| lung | 6.50e-10 | 14 |
| respiratory tube | 6.50e-10 | 14 |
| respiration organ | 6.50e-10 | 14 |
| pair of lungs | 6.50e-10 | 14 |
| lung primordium | 6.50e-10 | 14 |
| lung bud | 6.50e-10 | 14 |
| epithelial fold | 3.00e-09 | 20 |
| epithelial bud | 5.08e-07 | 17 |
| trunk region element | 7.76e-07 | 79 |
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 | 0.54119 |
| MA0004.1 | 1.20906 |
| MA0006.1 | 0.311391 |
| MA0007.1 | 0.465969 |
| MA0009.1 | 0.92425 |
| MA0014.1 | 0.694761 |
| MA0017.1 | 0.337808 |
| MA0019.1 | 0.740036 |
| MA0024.1 | 0.880057 |
| MA0025.1 | 1.15921 |
| MA0027.1 | 2.57545 |
| MA0028.1 | 0.321735 |
| MA0029.1 | 0.858105 |
| MA0030.1 | 0.864739 |
| MA0031.1 | 0.828781 |
| MA0038.1 | 0.62758 |
| MA0040.1 | 0.936879 |
| MA0041.1 | 0.404721 |
| MA0042.1 | 0.391504 |
| MA0043.1 | 1.02178 |
| MA0046.1 | 0.960497 |
| MA0048.1 | 0.128106 |
| MA0050.1 | 0.520357 |
| MA0051.1 | 0.636645 |
| MA0052.1 | 0.945011 |
| MA0055.1 | 0.648475 |
| MA0056.1 | 0 |
| MA0057.1 | 1.23731 |
| MA0058.1 | 2.66057 |
| MA0059.1 | 1.81442 |
| MA0060.1 | 0.232592 |
| MA0061.1 | 0.261749 |
| MA0063.1 | 0 |
| MA0066.1 | 0.616444 |
| MA0067.1 | 1.27078 |
| MA0068.1 | 0.385183 |
| MA0069.1 | 0.945354 |
| MA0070.1 | 0.93557 |
| MA0071.1 | 0.519509 |
| MA0072.1 | 0.927016 |
| MA0073.1 | 11.2967 |
| MA0074.1 | 0.580087 |
| MA0076.1 | 0.356883 |
| MA0077.1 | 0.905143 |
| MA0078.1 | 0.670113 |
| MA0081.1 | 0.420276 |
| MA0083.1 | 7.11247 |
| MA0084.1 | 1.59945 |
| MA0087.1 | 0.977537 |
| MA0088.1 | 0.598004 |
| MA0089.1 | 0 |
| MA0090.1 | 0.446539 |
| MA0091.1 | 0.494398 |
| MA0092.1 | 0.446857 |
| MA0093.1 | 1.58083 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.568369 |
| MA0101.1 | 0.406019 |
| MA0103.1 | 0.348572 |
| MA0105.1 | 0.488671 |
| MA0106.1 | 0.677988 |
| MA0107.1 | 0.342432 |
| MA0108.2 | 0.763162 |
| MA0109.1 | 0 |
| MA0111.1 | 0.460823 |
| MA0113.1 | 0.649407 |
| MA0114.1 | 0.259463 |
| MA0115.1 | 1.0246 |
| MA0116.1 | 0.836994 |
| MA0117.1 | 0.992087 |
| MA0119.1 | 0.40661 |
| MA0122.1 | 1.01209 |
| MA0124.1 | 1.21735 |
| MA0125.1 | 1.14291 |
| MA0130.1 | 0 |
| MA0131.1 | 0.735438 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.05845 |
| MA0136.1 | 0.600242 |
| MA0139.1 | 1.7399 |
| MA0140.1 | 0.568252 |
| MA0141.1 | 0.368264 |
| MA0142.1 | 0.814115 |
| MA0143.1 | 0.665982 |
| MA0144.1 | 0.262477 |
| MA0145.1 | 0.0910975 |
| MA0146.1 | 0.264322 |
| MA0147.1 | 0.274511 |
| MA0148.1 | 0.49752 |
| MA0149.1 | 0.411562 |
| MA0062.2 | 0.167299 |
| MA0035.2 | 0.573016 |
| MA0039.2 | 1.37408 |
| MA0138.2 | 0.727395 |
| MA0002.2 | 0.205289 |
| MA0137.2 | 0.365364 |
| MA0104.2 | 0.218974 |
| MA0047.2 | 0.626803 |
| MA0112.2 | 0.0910939 |
| MA0065.2 | 0.305574 |
| MA0150.1 | 0.465855 |
| MA0151.1 | 0 |
| MA0152.1 | 0.626912 |
| MA0153.1 | 1.07519 |
| MA0154.1 | 0.126143 |
| MA0155.1 | 0.102995 |
| MA0156.1 | 0.356017 |
| MA0157.1 | 0.781683 |
| MA0158.1 | 0 |
| MA0159.1 | 0.284457 |
| MA0160.1 | 0.50056 |
| MA0161.1 | 0 |
| MA0162.1 | 2.75316 |
| MA0163.1 | 5.85525 |
| MA0164.1 | 0.600609 |
| MA0080.2 | 0.343316 |
| MA0018.2 | 0.610433 |
| MA0099.2 | 0.721008 |
| MA0079.2 | 7.04343 |
| MA0102.2 | 1.65195 |
| MA0258.1 | 0.246285 |
| MA0259.1 | 0.729797 |
| MA0442.1 | 0 |
