MCL coexpression mm9:2203: Difference between revisions
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{{MCL_coexpression_mm9| | 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transmembrane transporter activity;0.00164356544129732;224674!GO:0015794;glycerol-3-phosphate transport;0.00164356544129732;224674!GO:0015793;glycerol transport;0.00164356544129732;224674!GO:0015169;glycerol-3-phosphate transmembrane transporter activity;0.00164356544129732;224674!GO:0015168;glycerol transmembrane transporter activity;0.00164356544129732;224674!GO:0015166;polyol transmembrane transporter activity;0.00164356544129732;224674!GO:0006127;glycerophosphate shuttle;0.00164356544129732;224674!GO:0002065;columnar/cuboidal epithelial cell differentiation;0.00230092858385784;27428!GO:0015791;polyol transport;0.00230092858385784;224674!GO:0002066;columnar/cuboidal epithelial cell development;0.00230092858385784;27428!GO:0006072;glycerol-3-phosphate metabolic process;0.00627457213097509;224674!GO:0002064;epithelial cell development;0.00671012245769187;27428!GO:0006071;glycerol metabolic process;0.0164270998043318;224674!GO:0019751;polyol metabolic process;0.0164270998043318;224674!GO:0030855;epithelial cell differentiation;0.0233848781821928;27428!GO:0005351;sugar:hydrogen ion symporter activity;0.0233848781821928;224674!GO:0051119;sugar transmembrane transporter activity;0.0233848781821928;224674!GO:0015144;carbohydrate transmembrane transporter activity;0.0233848781821928;224674!GO:0001843;neural tube closure;0.0233848781821928;27428!GO:0014020;primary neural tube formation;0.0233848781821928;27428!GO:0022603;regulation of anatomical structure morphogenesis;0.0233848781821928;27428!GO:0008360;regulation of cell shape;0.0233848781821928;27428!GO:0022604;regulation of cell morphogenesis;0.0233848781821928;27428!GO:0016324;apical plasma membrane;0.0233848781821928;27428!GO:0001841;neural tube formation;0.0233848781821928;27428!GO:0001839;neural plate morphogenesis;0.0233848781821928;27428!GO:0001840;neural plate development;0.0233848781821928;27428!GO:0001838;embryonic epithelial tube formation;0.0233848781821928;27428!GO:0005912;adherens junction;0.0237371809789831;27428!GO:0008643;carbohydrate transport;0.0237371809789831;224674!GO:0021915;neural tube development;0.0240810054663014;27428!GO:0016331;morphogenesis of embryonic epithelium;0.0261939190023719;27428!GO:0045177;apical part of cell;0.0267890120980656;27428!GO:0043296;apical junction complex;0.0295120490852277;27428!GO:0016327;apicolateral plasma membrane;0.0295120490852277;27428!GO:0002009;morphogenesis of an epithelium;0.0391772335293738;27428!GO:0015293;symporter activity;0.0412061163507711;224674!GO:0035239;tube morphogenesis;0.0440692222694824;27428!GO:0005911;intercellular junction;0.0440692222694824;27428!GO:0030036;actin cytoskeleton organization and biogenesis;0.0441084378769543;27428!GO:0030029;actin filament-based process;0.0460924290274504;27428!GO:0015291;secondary active transmembrane transporter activity;0.0479801284305496;224674!|ontology_enrichment_celltype=|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0005409!7.41e-16!47;UBERON:0000160!4.66e-15!31;UBERON:0000344!7.60e-10!15;UBERON:0001242!8.26e-09!13;UBERON:0000060!8.26e-09!13;UBERON:0001262!8.26e-09!13;UBERON:0004786!8.26e-09!13;UBERON:0000464!3.56e-07!57;UBERON:0004923!5.50e-07!24|tfbs_overrepresentation_for_novel_motifs=0.641384,0.402508,0.612053,0.688265,0.483253,0.704257,0.803568,0.370124,0.381467,2.89376,0.755749,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,0.928768,0.24402,0.570433,1.08884,0.815872,2.09942,0.620553,0.846564,0.342316,0.727368,0.535752,0.790816,0.711848,1.12823,0.471365,0.318879,2.17158,0.623685,1.16474,0.786577,0.434783,0.40068,0.478558,0.717547,0.185353,0.504971,0.325217,0.675898,0.938241,1.7626,0.49007,0.539131,1.0041,0.875451,0.282443,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,2.35691,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,0.205546,1.32691,0.323563,0.834514,0.318792,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,0.758875,0.129654,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,0.938512,1.34553,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,1.42067,0.57247,0.633483,1.25851,0.576517,3.00206,1.51002,1.1991,0.442329,4.0351,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.569254,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.293812,0.184289,1.27621,0.416214,0.838313,3.01453,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,2.58747,0.993294,0.830321,1.16191,0.788782,0.992915|tfbs_overrepresentation_jaspar=MA0003.1;4.15047,MA0004.1;0.6888,MA0006.1;0.497533,MA0007.1;0.672186,MA0009.1;1.15569,MA0014.1;1.46333,MA0017.1;0.528196,MA0019.1;0.964875,MA0024.1;1.11019,MA0025.1;1.39562,MA0027.1;2.81824,MA0028.1;0.509589,MA0029.1;1.08753,MA0030.1;1.09438,MA0031.1;1.05719,MA0038.1;0.846479,MA0040.1;1.16866,MA0041.1;0.604221,MA0042.1;1.4388,MA0043.1;1.25564,MA0046.1;1.1929,MA0048.1;0.266382,MA0050.1;0.731539,MA0051.1;1.99205,MA0052.1;1.17701,MA0055.1;0.125758,MA0056.1;0,MA0057.1;0.251896,MA0058.1;0.581673,MA0059.1;0.59559,MA0060.1;1.83511,MA0061.1;0.438628,MA0063.1;0,MA0066.1;0.834648,MA0067.1;1.50873,MA0068.1;0.256913,MA0069.1;1.17737,MA0070.1;1.16732,MA0071.1;0.73062,MA0072.1;1.15853,MA0073.1;0.00221226,MA0074.1;0.795862,MA0076.1;0.550092,MA0077.1;1.13603,MA0078.1;0.891476,MA0081.1;0.621611,MA0083.1;1.25482,MA0084.1;1.84013,MA0087.1;1.21037,MA0088.1;0.582815,MA0089.1;0,MA0090.1;0.650768,MA0091.1;0.703314,MA0092.1;0.651119,MA0093.1;0.519148,MA0095.1;0,MA0098.1;0,MA0100.1;0.783305,MA0101.1;0.605676,MA0103.1;1.33576,MA0105.1;0.313353,MA0106.1;0.899777,MA0107.1;0.533522,MA0108.2;0.989014,MA0109.1;0,MA0111.1;0.666525,MA0113.1;0.869608,MA0114.1;0.43587,MA0115.1;1.25852,MA0116.1;2.15201,MA0117.1;1.22527,MA0119.1;0.606338,MA0122.1;1.24573,MA0124.1;1.45461,MA0125.1;1.37907,MA0130.1;0,MA0131.1;2.20468,MA0132.1;0,MA0133.1;0,MA0135.1;1.29308,MA0136.1;0.817395,MA0139.1;0.365453,MA0140.1;0.78318,MA0141.1;0.563066,MA0142.1;1.04199,MA0143.1;0.887119,MA0144.1;1.11951,MA0145.1;0.21199,MA0146.1;0.0944145,MA0147.1;0.453952,MA0148.1;0.706718,MA0149.1;0.611881,MA0062.2;0.319836,MA0035.2;0.788288,MA0039.2;0.0959929,MA0138.2;0.951653,MA0002.2;0.368961,MA0137.2;0.559766,MA0104.2;0.386166,MA0047.2;0.845655,MA0112.2;0.211985,MA0065.2;0.212467,MA0150.1;0.67206,MA0151.1;0,MA0152.1;0.84577,MA0153.1;1.31015,MA0154.1;0.728853,MA0155.1;2.6534,MA0156.1;0.549102,MA0157.1;1.0083,MA0158.1;0,MA0159.1;0.465802,MA0160.1;0.71003,MA0161.1;0,MA0162.1;1.70461,MA0163.1;0.327769,MA0164.1;0.817786,MA0080.2;0.534538,MA0018.2;0.828253,MA0099.2;0.944966,MA0079.2;0.0553806,MA0102.2;1.8929,MA0258.1;0.419871,MA0259.1;1.12353,MA0442.1;0}} | ||
Latest revision as of 18:09, 17 September 2013
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Mm9::chr17:31433667..31433739,+ | p2@Slc37a1 |
| Mm9::chr17:31433741..31433761,+ | p3@Slc37a1 |
| Mm9::chr5:93238358..93238397,+ | p2@Shroom3 |
| Mm9::chr5:93238398..93238462,+ | p1@Shroom3 |
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:0015665 | alcohol transmembrane transporter activity | 0.00164356544129732 |
| GO:0015794 | glycerol-3-phosphate transport | 0.00164356544129732 |
| GO:0015793 | glycerol transport | 0.00164356544129732 |
| GO:0015169 | glycerol-3-phosphate transmembrane transporter activity | 0.00164356544129732 |
| GO:0015168 | glycerol transmembrane transporter activity | 0.00164356544129732 |
| GO:0015166 | polyol transmembrane transporter activity | 0.00164356544129732 |
| GO:0006127 | glycerophosphate shuttle | 0.00164356544129732 |
| GO:0002065 | columnar/cuboidal epithelial cell differentiation | 0.00230092858385784 |
| GO:0015791 | polyol transport | 0.00230092858385784 |
| GO:0002066 | columnar/cuboidal epithelial cell development | 0.00230092858385784 |
| GO:0006072 | glycerol-3-phosphate metabolic process | 0.00627457213097509 |
| GO:0002064 | epithelial cell development | 0.00671012245769187 |
| GO:0006071 | glycerol metabolic process | 0.0164270998043318 |
| GO:0019751 | polyol metabolic process | 0.0164270998043318 |
| GO:0030855 | epithelial cell differentiation | 0.0233848781821928 |
| GO:0005351 | sugar:hydrogen ion symporter activity | 0.0233848781821928 |
| GO:0051119 | sugar transmembrane transporter activity | 0.0233848781821928 |
| GO:0015144 | carbohydrate transmembrane transporter activity | 0.0233848781821928 |
| GO:0001843 | neural tube closure | 0.0233848781821928 |
| GO:0014020 | primary neural tube formation | 0.0233848781821928 |
| GO:0022603 | regulation of anatomical structure morphogenesis | 0.0233848781821928 |
| GO:0008360 | regulation of cell shape | 0.0233848781821928 |
| GO:0022604 | regulation of cell morphogenesis | 0.0233848781821928 |
| GO:0016324 | apical plasma membrane | 0.0233848781821928 |
| GO:0001841 | neural tube formation | 0.0233848781821928 |
| GO:0001839 | neural plate morphogenesis | 0.0233848781821928 |
| GO:0001840 | neural plate development | 0.0233848781821928 |
| GO:0001838 | embryonic epithelial tube formation | 0.0233848781821928 |
| GO:0005912 | adherens junction | 0.0237371809789831 |
| GO:0008643 | carbohydrate transport | 0.0237371809789831 |
| GO:0021915 | neural tube development | 0.0240810054663014 |
| GO:0016331 | morphogenesis of embryonic epithelium | 0.0261939190023719 |
| GO:0045177 | apical part of cell | 0.0267890120980656 |
| GO:0043296 | apical junction complex | 0.0295120490852277 |
| GO:0016327 | apicolateral plasma membrane | 0.0295120490852277 |
| GO:0002009 | morphogenesis of an epithelium | 0.0391772335293738 |
| GO:0015293 | symporter activity | 0.0412061163507711 |
| GO:0035239 | tube morphogenesis | 0.0440692222694824 |
| GO:0005911 | intercellular junction | 0.0440692222694824 |
| GO:0030036 | actin cytoskeleton organization and biogenesis | 0.0441084378769543 |
| GO:0030029 | actin filament-based process | 0.0460924290274504 |
| GO:0015291 | secondary active transmembrane transporter activity | 0.0479801284305496 |
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 |
|---|---|---|
| gastrointestinal system | 7.41e-16 | 47 |
| intestine | 4.66e-15 | 31 |
| mucosa | 7.60e-10 | 15 |
| intestinal mucosa | 8.26e-09 | 13 |
| anatomical wall | 8.26e-09 | 13 |
| wall of intestine | 8.26e-09 | 13 |
| gastrointestinal system mucosa | 8.26e-09 | 13 |
| anatomical space | 3.56e-07 | 57 |
| organ component layer | 5.50e-07 | 24 |
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 | 4.15047 |
| MA0004.1 | 0.6888 |
| MA0006.1 | 0.497533 |
| MA0007.1 | 0.672186 |
| MA0009.1 | 1.15569 |
| MA0014.1 | 1.46333 |
| MA0017.1 | 0.528196 |
| MA0019.1 | 0.964875 |
| MA0024.1 | 1.11019 |
| MA0025.1 | 1.39562 |
| MA0027.1 | 2.81824 |
| MA0028.1 | 0.509589 |
| MA0029.1 | 1.08753 |
| MA0030.1 | 1.09438 |
| MA0031.1 | 1.05719 |
| MA0038.1 | 0.846479 |
| MA0040.1 | 1.16866 |
| MA0041.1 | 0.604221 |
| MA0042.1 | 1.4388 |
| MA0043.1 | 1.25564 |
| MA0046.1 | 1.1929 |
| MA0048.1 | 0.266382 |
| MA0050.1 | 0.731539 |
| MA0051.1 | 1.99205 |
| MA0052.1 | 1.17701 |
| MA0055.1 | 0.125758 |
| MA0056.1 | 0 |
| MA0057.1 | 0.251896 |
| MA0058.1 | 0.581673 |
| MA0059.1 | 0.59559 |
| MA0060.1 | 1.83511 |
| MA0061.1 | 0.438628 |
| MA0063.1 | 0 |
| MA0066.1 | 0.834648 |
| MA0067.1 | 1.50873 |
| MA0068.1 | 0.256913 |
| MA0069.1 | 1.17737 |
| MA0070.1 | 1.16732 |
| MA0071.1 | 0.73062 |
| MA0072.1 | 1.15853 |
| MA0073.1 | 0.00221226 |
| MA0074.1 | 0.795862 |
| MA0076.1 | 0.550092 |
| MA0077.1 | 1.13603 |
| MA0078.1 | 0.891476 |
| MA0081.1 | 0.621611 |
| MA0083.1 | 1.25482 |
| MA0084.1 | 1.84013 |
| MA0087.1 | 1.21037 |
| MA0088.1 | 0.582815 |
| MA0089.1 | 0 |
| MA0090.1 | 0.650768 |
| MA0091.1 | 0.703314 |
| MA0092.1 | 0.651119 |
| MA0093.1 | 0.519148 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.783305 |
| MA0101.1 | 0.605676 |
| MA0103.1 | 1.33576 |
| MA0105.1 | 0.313353 |
| MA0106.1 | 0.899777 |
| MA0107.1 | 0.533522 |
| MA0108.2 | 0.989014 |
| MA0109.1 | 0 |
| MA0111.1 | 0.666525 |
| MA0113.1 | 0.869608 |
| MA0114.1 | 0.43587 |
| MA0115.1 | 1.25852 |
| MA0116.1 | 2.15201 |
| MA0117.1 | 1.22527 |
| MA0119.1 | 0.606338 |
| MA0122.1 | 1.24573 |
| MA0124.1 | 1.45461 |
| MA0125.1 | 1.37907 |
| MA0130.1 | 0 |
| MA0131.1 | 2.20468 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.29308 |
| MA0136.1 | 0.817395 |
| MA0139.1 | 0.365453 |
| MA0140.1 | 0.78318 |
| MA0141.1 | 0.563066 |
| MA0142.1 | 1.04199 |
| MA0143.1 | 0.887119 |
| MA0144.1 | 1.11951 |
| MA0145.1 | 0.21199 |
| MA0146.1 | 0.0944145 |
| MA0147.1 | 0.453952 |
| MA0148.1 | 0.706718 |
| MA0149.1 | 0.611881 |
| MA0062.2 | 0.319836 |
| MA0035.2 | 0.788288 |
| MA0039.2 | 0.0959929 |
| MA0138.2 | 0.951653 |
| MA0002.2 | 0.368961 |
| MA0137.2 | 0.559766 |
| MA0104.2 | 0.386166 |
| MA0047.2 | 0.845655 |
| MA0112.2 | 0.211985 |
| MA0065.2 | 0.212467 |
| MA0150.1 | 0.67206 |
| MA0151.1 | 0 |
| MA0152.1 | 0.84577 |
| MA0153.1 | 1.31015 |
| MA0154.1 | 0.728853 |
| MA0155.1 | 2.6534 |
| MA0156.1 | 0.549102 |
| MA0157.1 | 1.0083 |
| MA0158.1 | 0 |
| MA0159.1 | 0.465802 |
| MA0160.1 | 0.71003 |
| MA0161.1 | 0 |
| MA0162.1 | 1.70461 |
| MA0163.1 | 0.327769 |
| MA0164.1 | 0.817786 |
| MA0080.2 | 0.534538 |
| MA0018.2 | 0.828253 |
| MA0099.2 | 0.944966 |
| MA0079.2 | 0.0553806 |
| MA0102.2 | 1.8929 |
| MA0258.1 | 0.419871 |
| MA0259.1 | 1.12353 |
| MA0442.1 | 0 |
