MCL coexpression mm9:1300: Difference between revisions
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{{MCL_coexpression_mm9| | 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regulation of astrocyte differentiation;0.00878367895802332;12156!GO:0048710;regulation of astrocyte differentiation;0.00878367895802332;12156!GO:0014015;positive regulation of gliogenesis;0.00878367895802332;12156!GO:0045687;positive regulation of glial cell differentiation;0.00878367895802332;12156!GO:0045778;positive regulation of ossification;0.00878367895802332;12156!GO:0048708;astrocyte differentiation;0.00878367895802332;12156!GO:0046852;positive regulation of bone remodeling;0.00878367895802332;12156!GO:0045669;positive regulation of osteoblast differentiation;0.00878367895802332;12156!GO:0001837;epithelial to mesenchymal transition;0.00878367895802332;12156!GO:0045685;regulation of glial cell differentiation;0.00878367895802332;12156!GO:0014013;regulation of gliogenesis;0.00878367895802332;12156!GO:0045667;regulation of osteoblast differentiation;0.0107347251399441;12156!GO:0035051;cardiac cell differentiation;0.0123852030744534;12156!GO:0001658;ureteric bud branching;0.0137995202431396;12156!GO:0030278;regulation of ossification;0.0160967928574096;12156!GO:0030282;bone mineralization;0.0160967928574096;12156!GO:0001649;osteoblast differentiation;0.0163769478384945;12156!GO:0030509;BMP signaling pathway;0.0163769478384945;12156!GO:0046850;regulation of bone remodeling;0.0163769478384945;12156!GO:0001657;ureteric bud development;0.0167337812634476;12156!GO:0042475;odontogenesis of dentine-containing teeth;0.0167337812634476;12156!GO:0042476;odontogenesis;0.0167337812634476;12156!GO:0010001;glial cell differentiation;0.0167337812634476;12156!GO:0048762;mesenchymal cell differentiation;0.0167337812634476;12156!GO:0014031;mesenchymal cell development;0.0167337812634476;12156!GO:0042063;gliogenesis;0.0169143837043772;12156!GO:0001656;metanephros development;0.0170116307788382;12156!GO:0045597;positive regulation of cell differentiation;0.0170116307788382;12156!GO:0007179;transforming growth factor beta receptor signaling pathway;0.0170116307788382;12156!GO:0051216;cartilage development;0.0171586166958898;12156!GO:0048754;branching morphogenesis of a tube;0.0200590078487712;12156!GO:0001763;morphogenesis of a branching structure;0.0211044547701272;12156!GO:0051094;positive regulation of developmental process;0.0224102760419235;12156!GO:0001822;kidney development;0.0230095602216914;12156!GO:0001655;urogenital system development;0.0235135084794501;12156!GO:0007178;transmembrane receptor protein serine/threonine kinase signaling pathway;0.0235135084794501;12156!GO:0001503;ossification;0.02649465235916;12156!GO:0031214;biomineral formation;0.02649465235916;12156!GO:0045165;cell fate commitment;0.0274585620368124;12156!GO:0046849;bone remodeling;0.0275729885512682;12156!GO:0051240;positive regulation of multicellular organismal process;0.0300718626747224;12156!GO:0008285;negative regulation of cell proliferation;0.0300718626747224;12156!GO:0048771;tissue remodeling;0.0301167926939151;12156!GO:0035239;tube morphogenesis;0.0354104308655744;12156!GO:0008083;growth factor activity;0.0354104308655744;12156!GO:0045595;regulation of cell differentiation;0.0355666753409223;12156!GO:0007507;heart development;0.0386596207918497;12156!GO:0001501;skeletal development;0.0400698994370635;12156!GO:0035295;tube development;0.0438062238145681;12156!GO:0006954;inflammatory response;0.0444166115299627;12156!GO:0005125;cytokine activity;0.0447944175979461;12156!GO:0007417;central nervous system development;0.0474007754684157;12156!|ontology_enrichment_celltype=CL:0000239!4.95e-10!6;CL:0000677!4.95e-10!6;CL:0000212!4.95e-10!6;CL:0000584!4.95e-10!6;CL:0002563!2.03e-08!9;CL:0002251!2.03e-08!9;CL:0000075!2.03e-08!7|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0000160!1.22e-24!31;UBERON:0005409!8.72e-19!47;UBERON:0000344!4.09e-16!15;UBERON:0001242!2.13e-13!13;UBERON:0000060!2.13e-13!13;UBERON:0001262!2.13e-13!13;UBERON:0004786!2.13e-13!13;UBERON:0004923!6.20e-13!24;UBERON:0004119!1.87e-11!118;UBERON:0000925!1.87e-11!118;UBERON:0006595!1.87e-11!118;UBERON:0001007!5.42e-11!116;UBERON:0001555!5.42e-11!116;UBERON:0007026!5.42e-11!116;UBERON:0004921!1.40e-09!114;UBERON:0003350!2.03e-08!9;UBERON:0004808!2.03e-08!9;UBERON:0001277!2.03e-08!9|tfbs_overrepresentation_for_novel_motifs=0.491922,0.217198,0.464605,0.535892,0.346849,0.550971,0.645383,0.247459,0.257202,0.283981,0.599767,0.632897,0.247704,0.6581,0.364314,0,0.856992,0.89822,0.232269,0.143775,0.426133,0.713088,0.657163,0.345236,1.19059,0.686615,0.223823,0.572827,0.394364,0.534301,0.558142,0.960397,0.892985,0.589948,0.364821,0.335531,0.871288,0.629145,0.303703,0.27383,0.342638,0.56353,0.0995018,0.959963,0.368882,0.524258,0.77511,0.589246,0.0835644,1.02809,0.839084,0.714419,0.517905,1.10437,1.12205,0.66551,0.406788,0.619643,0.21472,0.663395,0.939962,0.724164,0.742129,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.70565,0.366795,1.156,0.599223,0.19692,0.589776,0.763395,0.922432,0.430551,0.708505,0.874787,0.722675,0.240896,1.03903,0.439832,0.220054,0.181203,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.2995,0.281222,0.685716,0.976308,0.775372,0.160254,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,1.09461,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,0.528609,0.53982,0.858327,0.322606,1.16147,0.805995,1.6461,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.106956,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.348692,0.183562,0.667976,1.10596,0.287383,0.678689,1.18867,1.70209,0.376898,0.48935,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,1.60971,0.325308,0.63125,0.0323861|tfbs_overrepresentation_jaspar=MA0003.1;0.730824,MA0004.1;0.536396,MA0006.1;0.359699,MA0007.1;0.52077,MA0009.1;0.987341,MA0014.1;1.71935,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;0.457338,MA0042.1;0.443591,MA0043.1;1.08567,MA0046.1;2.3347,MA0048.1;0.943003,MA0050.1;0.57678,MA0051.1;0.695779,MA0052.1;1.00829,MA0055.1;0.0585191,MA0056.1;0,MA0057.1;0.457693,MA0058.1;0.436487,MA0059.1;0.449345,MA0060.1;0.275911,MA0061.1;3.16246,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;0.575909,MA0072.1;0.990133,MA0073.1;0.000157319,MA0074.1;0.638014,MA0076.1;0.407465,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;0.111145,MA0089.1;0,MA0090.1;0.500693,MA0091.1;0.55008,MA0092.1;0.501022,MA0093.1;0.379257,MA0095.1;0,MA0098.1;0,MA0100.1;0.626021,MA0101.1;1.16089,MA0103.1;0.398766,MA0105.1;2.43957,MA0106.1;0.737893,MA0107.1;1.79828,MA0108.2;0.824407,MA0109.1;0,MA0111.1;0.515457,MA0113.1;0.708789,MA0114.1;0.822296,MA0115.1;1.08851,MA0116.1;0.359483,MA0117.1;1.05576,MA0119.1;0.459301,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;0.243463,MA0140.1;0.625902,MA0141.1;0.419361,MA0142.1;0.876028,MA0143.1;0.725672,MA0144.1;1.502,MA0145.1;0.119202,MA0146.1;0.153598,MA0147.1;0.320675,MA0148.1;0.553294,MA0149.1;0.464445,MA0062.2;0.204999,MA0035.2;0.630778,MA0039.2;0.525037,MA0138.2;0.788113,MA0002.2;0.246463,MA0137.2;1.06926,MA0104.2;0.261255,MA0047.2;0.685741,MA0112.2;0.119197,MA0065.2;0.763394,MA0150.1;0.520653,MA0151.1;0,MA0152.1;0.685852,MA0153.1;1.13945,MA0154.1;0.480757,MA0155.1;0.414701,MA0156.1;0.406559,MA0157.1;0.843181,MA0158.1;0,MA0159.1;0.331229,MA0160.1;0.556423,MA0161.1;0,MA0162.1;0.0465447,MA0163.1;0.0423021,MA0164.1;0.658997,MA0080.2;0.393257,MA0018.2;0.669032,MA0099.2;0.781628,MA0079.2;0.0520572,MA0102.2;1.7182,MA0258.1;0.290587,MA0259.1;0.309517,MA0442.1;0}} | ||
Latest revision as of 16:42, 17 September 2013
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Mm9::chr11:70272480..70272491,+ | p9@Zmynd15 |
| Mm9::chr15:44258946..44258959,+ | p@chr15:44258946..44258959 + |
| Mm9::chr16:45455027..45455039,- | p4@Gm17783 p4@Gm609 |
| Mm9::chr18:20714918..20714920,+ | p@chr18:20714918..20714920 + |
| Mm9::chr2:133377954..133377973,+ | p1@Bmp2 |
| Mm9::chr4:115500720..115500735,+ | p2@Mob3c |
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:0048711 | positive regulation of astrocyte differentiation | 0.00878367895802332 |
| GO:0048710 | regulation of astrocyte differentiation | 0.00878367895802332 |
| GO:0014015 | positive regulation of gliogenesis | 0.00878367895802332 |
| GO:0045687 | positive regulation of glial cell differentiation | 0.00878367895802332 |
| GO:0045778 | positive regulation of ossification | 0.00878367895802332 |
| GO:0048708 | astrocyte differentiation | 0.00878367895802332 |
| GO:0046852 | positive regulation of bone remodeling | 0.00878367895802332 |
| GO:0045669 | positive regulation of osteoblast differentiation | 0.00878367895802332 |
| GO:0001837 | epithelial to mesenchymal transition | 0.00878367895802332 |
| GO:0045685 | regulation of glial cell differentiation | 0.00878367895802332 |
| GO:0014013 | regulation of gliogenesis | 0.00878367895802332 |
| GO:0045667 | regulation of osteoblast differentiation | 0.0107347251399441 |
| GO:0035051 | cardiac cell differentiation | 0.0123852030744534 |
| GO:0001658 | ureteric bud branching | 0.0137995202431396 |
| GO:0030278 | regulation of ossification | 0.0160967928574096 |
| GO:0030282 | bone mineralization | 0.0160967928574096 |
| GO:0001649 | osteoblast differentiation | 0.0163769478384945 |
| GO:0030509 | BMP signaling pathway | 0.0163769478384945 |
| GO:0046850 | regulation of bone remodeling | 0.0163769478384945 |
| GO:0001657 | ureteric bud development | 0.0167337812634476 |
| GO:0042475 | odontogenesis of dentine-containing teeth | 0.0167337812634476 |
| GO:0042476 | odontogenesis | 0.0167337812634476 |
| GO:0010001 | glial cell differentiation | 0.0167337812634476 |
| GO:0048762 | mesenchymal cell differentiation | 0.0167337812634476 |
| GO:0014031 | mesenchymal cell development | 0.0167337812634476 |
| GO:0042063 | gliogenesis | 0.0169143837043772 |
| GO:0001656 | metanephros development | 0.0170116307788382 |
| GO:0045597 | positive regulation of cell differentiation | 0.0170116307788382 |
| GO:0007179 | transforming growth factor beta receptor signaling pathway | 0.0170116307788382 |
| GO:0051216 | cartilage development | 0.0171586166958898 |
| GO:0048754 | branching morphogenesis of a tube | 0.0200590078487712 |
| GO:0001763 | morphogenesis of a branching structure | 0.0211044547701272 |
| GO:0051094 | positive regulation of developmental process | 0.0224102760419235 |
| GO:0001822 | kidney development | 0.0230095602216914 |
| GO:0001655 | urogenital system development | 0.0235135084794501 |
| GO:0007178 | transmembrane receptor protein serine/threonine kinase signaling pathway | 0.0235135084794501 |
| GO:0001503 | ossification | 0.02649465235916 |
| GO:0031214 | biomineral formation | 0.02649465235916 |
| GO:0045165 | cell fate commitment | 0.0274585620368124 |
| GO:0046849 | bone remodeling | 0.0275729885512682 |
| GO:0051240 | positive regulation of multicellular organismal process | 0.0300718626747224 |
| GO:0008285 | negative regulation of cell proliferation | 0.0300718626747224 |
| GO:0048771 | tissue remodeling | 0.0301167926939151 |
| GO:0035239 | tube morphogenesis | 0.0354104308655744 |
| GO:0008083 | growth factor activity | 0.0354104308655744 |
| GO:0045595 | regulation of cell differentiation | 0.0355666753409223 |
| GO:0007507 | heart development | 0.0386596207918497 |
| GO:0001501 | skeletal development | 0.0400698994370635 |
| GO:0035295 | tube development | 0.0438062238145681 |
| GO:0006954 | inflammatory response | 0.0444166115299627 |
| GO:0005125 | cytokine activity | 0.0447944175979461 |
| GO:0007417 | central nervous system development | 0.0474007754684157 |
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 |
|---|---|---|
| brush border epithelial cell | 4.95e-10 | 6 |
| gut absorptive cell | 4.95e-10 | 6 |
| absorptive cell | 4.95e-10 | 6 |
| enterocyte | 4.95e-10 | 6 |
| intestinal epithelial cell | 2.03e-08 | 9 |
| epithelial cell of alimentary canal | 2.03e-08 | 9 |
| columnar/cuboidal epithelial cell | 2.03e-08 | 7 |
| Ontology term | p-value | n |
|---|---|---|
| intestine | 1.22e-24 | 31 |
| gastrointestinal system | 8.72e-19 | 47 |
| mucosa | 4.09e-16 | 15 |
| intestinal mucosa | 2.13e-13 | 13 |
| anatomical wall | 2.13e-13 | 13 |
| wall of intestine | 2.13e-13 | 13 |
| gastrointestinal system mucosa | 2.13e-13 | 13 |
| organ component layer | 6.20e-13 | 24 |
| endoderm-derived structure | 1.87e-11 | 118 |
| endoderm | 1.87e-11 | 118 |
| presumptive endoderm | 1.87e-11 | 118 |
| digestive system | 5.42e-11 | 116 |
| digestive tract | 5.42e-11 | 116 |
| primitive gut | 5.42e-11 | 116 |
| subdivision of digestive tract | 1.40e-09 | 114 |
| epithelium of mucosa | 2.03e-08 | 9 |
| gastrointestinal system epithelium | 2.03e-08 | 9 |
| intestinal epithelium | 2.03e-08 | 9 |
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 | 0.730824 |
| MA0004.1 | 0.536396 |
| MA0006.1 | 0.359699 |
| MA0007.1 | 0.52077 |
| MA0009.1 | 0.987341 |
| MA0014.1 | 1.71935 |
| 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 | 0.457338 |
| MA0042.1 | 0.443591 |
| MA0043.1 | 1.08567 |
| MA0046.1 | 2.3347 |
| MA0048.1 | 0.943003 |
| MA0050.1 | 0.57678 |
| MA0051.1 | 0.695779 |
| MA0052.1 | 1.00829 |
| MA0055.1 | 0.0585191 |
| MA0056.1 | 0 |
| MA0057.1 | 0.457693 |
| MA0058.1 | 0.436487 |
| MA0059.1 | 0.449345 |
| MA0060.1 | 0.275911 |
| MA0061.1 | 3.16246 |
| 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 | 0.575909 |
| MA0072.1 | 0.990133 |
| MA0073.1 | 0.000157319 |
| MA0074.1 | 0.638014 |
| MA0076.1 | 0.407465 |
| 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 | 0.111145 |
| MA0089.1 | 0 |
| MA0090.1 | 0.500693 |
| MA0091.1 | 0.55008 |
| MA0092.1 | 0.501022 |
| MA0093.1 | 0.379257 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.626021 |
| MA0101.1 | 1.16089 |
| MA0103.1 | 0.398766 |
| MA0105.1 | 2.43957 |
| MA0106.1 | 0.737893 |
| MA0107.1 | 1.79828 |
| MA0108.2 | 0.824407 |
| MA0109.1 | 0 |
| MA0111.1 | 0.515457 |
| MA0113.1 | 0.708789 |
| MA0114.1 | 0.822296 |
| MA0115.1 | 1.08851 |
| MA0116.1 | 0.359483 |
| MA0117.1 | 1.05576 |
| MA0119.1 | 0.459301 |
| 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 | 0.243463 |
| MA0140.1 | 0.625902 |
| MA0141.1 | 0.419361 |
| MA0142.1 | 0.876028 |
| MA0143.1 | 0.725672 |
| MA0144.1 | 1.502 |
| MA0145.1 | 0.119202 |
| MA0146.1 | 0.153598 |
| MA0147.1 | 0.320675 |
| MA0148.1 | 0.553294 |
| MA0149.1 | 0.464445 |
| MA0062.2 | 0.204999 |
| MA0035.2 | 0.630778 |
| MA0039.2 | 0.525037 |
| MA0138.2 | 0.788113 |
| MA0002.2 | 0.246463 |
| MA0137.2 | 1.06926 |
| MA0104.2 | 0.261255 |
| MA0047.2 | 0.685741 |
| MA0112.2 | 0.119197 |
| MA0065.2 | 0.763394 |
| MA0150.1 | 0.520653 |
| MA0151.1 | 0 |
| MA0152.1 | 0.685852 |
| MA0153.1 | 1.13945 |
| MA0154.1 | 0.480757 |
| MA0155.1 | 0.414701 |
| MA0156.1 | 0.406559 |
| MA0157.1 | 0.843181 |
| MA0158.1 | 0 |
| MA0159.1 | 0.331229 |
| MA0160.1 | 0.556423 |
| MA0161.1 | 0 |
| MA0162.1 | 0.0465447 |
| MA0163.1 | 0.0423021 |
| MA0164.1 | 0.658997 |
| MA0080.2 | 0.393257 |
| MA0018.2 | 0.669032 |
| MA0099.2 | 0.781628 |
| MA0079.2 | 0.0520572 |
| MA0102.2 | 1.7182 |
| MA0258.1 | 0.290587 |
| MA0259.1 | 0.309517 |
| MA0442.1 | 0 |
