MCL coexpression mm9:24: Difference between revisions
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|ontology_enrichment_uberon=UBERON:0000160!3.88e-30!31;UBERON:0005409!2.16e-28!47;UBERON:0000344!3.38e-18!15;UBERON:0001242!5.47e-16!13;UBERON:0000060!5.47e-16!13;UBERON:0001262!5.47e-16!13;UBERON:0004786!5.47e-16!13;UBERON:0004923!1.20e-13!24;UBERON:0004119!6.61e-12!118;UBERON:0000925!6.61e-12!118;UBERON:0006595!6.61e-12!118;UBERON:0003350!2.60e-11!9;UBERON:0004808!2.60e-11!9;UBERON:0001277!2.60e-11!9;UBERON:0001007!6.04e-11!116;UBERON:0001555!6.04e-11!116;UBERON:0007026!6.04e-11!116;UBERON:0004921!1.05e-09!114;UBERON:0000485!9.04e-09!11 | |ontology_enrichment_uberon=UBERON:0000160!3.88e-30!31;UBERON:0005409!2.16e-28!47;UBERON:0000344!3.38e-18!15;UBERON:0001242!5.47e-16!13;UBERON:0000060!5.47e-16!13;UBERON:0001262!5.47e-16!13;UBERON:0004786!5.47e-16!13;UBERON:0004923!1.20e-13!24;UBERON:0004119!6.61e-12!118;UBERON:0000925!6.61e-12!118;UBERON:0006595!6.61e-12!118;UBERON:0003350!2.60e-11!9;UBERON:0004808!2.60e-11!9;UBERON:0001277!2.60e-11!9;UBERON:0001007!6.04e-11!116;UBERON:0001555!6.04e-11!116;UBERON:0007026!6.04e-11!116;UBERON:0004921!1.05e-09!114;UBERON:0000485!9.04e-09!11 | ||
|tfbs_overrepresentation_for_novel_motifs=1.52403,11.1459,1.88546,0.18187,0.0207873,0.0892364,1.23749,0.0773138,0.600548,7.28511,0.542489,0.208348,1.59316,2.15882,0.0461278,0,0.779638,0.0247566,2.11306,2.05786,0.00181357,4.23169,0.675898,0.0191642,1.07262,0.930938,0.12681,0.611833,3.37615,5.93925,1.1505,0.322095,0.617232,1.31206,4.16353,0.0752543,3.09275,0.913304,0.334372,3.19017,0.00181915,0.839657,0.201941,0.305276,12.2463,1.49843,1.71857,1.00379,0.0894185,2.9286,1.80687,0.104993,1.11637,1.43101,0.427347,1.00973,0.0267444,1.55217,1.92329,0.509119,0.632736,1.90537,2.02474,1.06665,1.13126,0.859942,0.313332,0.0392813,0.609006,0.573802,5.13667,0.0143959,8.84319,0.0754304,8.08212,3.34644,1.78275,0.224907,0.0145465,0.0837844,0.0119109,0.735503,0.0561599,0.000436256,1.2299,22.3486,9.24504e-06,0.280465,1.78117,0.301629,0.291329,0.818561,0.0636656,0.0152536,3.95195,0.00074442,0.0978098,2.01996,0.441151,1.48913,0.000892896,0.321234,0.468544,0.671519,0.166573,1.3622,1.08276,0.108488,1.0693,6.7007,0.0482996,0.134306,0.138787,0.490426,0.303868,0.843081,13.7489,0.517698,0.506741,0.00160539,0.0355749,0.024077,0.130669,0.000775127,0.110603,1.52401,0.029295,0.340951,0.480175,0.193316,0.567111,0.0237386,0.810287,0.152982,0.191009,0.00010358,0.102286,0.160773,0.885601,0.794805,0.567357,0.0114444,0.0217615,0.106251,0.102766,0.00508593,0.273723,0.265697,0.0149444,3.29753,4.30797,15.6073,0.0179956,1.46422,0.261449,0.0174808,0.0304798,0.520446,0.0087741,8.27789,0.0640745,0.216532,0.0996097,1.94699,0.0621058,0.0440462,1.62356,0.487577,22.0377 | |tfbs_overrepresentation_for_novel_motifs=1.52403,11.1459,1.88546,0.18187,0.0207873,0.0892364,1.23749,0.0773138,0.600548,7.28511,0.542489,0.208348,1.59316,2.15882,0.0461278,0,0.779638,0.0247566,2.11306,2.05786,0.00181357,4.23169,0.675898,0.0191642,1.07262,0.930938,0.12681,0.611833,3.37615,5.93925,1.1505,0.322095,0.617232,1.31206,4.16353,0.0752543,3.09275,0.913304,0.334372,3.19017,0.00181915,0.839657,0.201941,0.305276,12.2463,1.49843,1.71857,1.00379,0.0894185,2.9286,1.80687,0.104993,1.11637,1.43101,0.427347,1.00973,0.0267444,1.55217,1.92329,0.509119,0.632736,1.90537,2.02474,1.06665,1.13126,0.859942,0.313332,0.0392813,0.609006,0.573802,5.13667,0.0143959,8.84319,0.0754304,8.08212,3.34644,1.78275,0.224907,0.0145465,0.0837844,0.0119109,0.735503,0.0561599,0.000436256,1.2299,22.3486,9.24504e-06,0.280465,1.78117,0.301629,0.291329,0.818561,0.0636656,0.0152536,3.95195,0.00074442,0.0978098,2.01996,0.441151,1.48913,0.000892896,0.321234,0.468544,0.671519,0.166573,1.3622,1.08276,0.108488,1.0693,6.7007,0.0482996,0.134306,0.138787,0.490426,0.303868,0.843081,13.7489,0.517698,0.506741,0.00160539,0.0355749,0.024077,0.130669,0.000775127,0.110603,1.52401,0.029295,0.340951,0.480175,0.193316,0.567111,0.0237386,0.810287,0.152982,0.191009,0.00010358,0.102286,0.160773,0.885601,0.794805,0.567357,0.0114444,0.0217615,0.106251,0.102766,0.00508593,0.273723,0.265697,0.0149444,3.29753,4.30797,15.6073,0.0179956,1.46422,0.261449,0.0174808,0.0304798,0.520446,0.0087741,8.27789,0.0640745,0.216532,0.0996097,1.94699,0.0621058,0.0440462,1.62356,0.487577,22.0377 | ||
|tfbs_overrepresentation_jaspar=MA0003.1;45.5379,MA0004.1;0.344911,MA0006.1;0.906908,MA0007.1;0.257241,MA0009.1;0.548132,MA0014.1;37.5711,MA0017.1;10.4122,MA0019.1;0.0217314,MA0024.1;0.271324,MA0025.1;0.0674169,MA0027.1;0.694955,MA0028.1;2.40216,MA0029.1;0.0140543,MA0030.1;0.0158494,MA0031.1;0.0988965,MA0038.1;0.0615923,MA0040.1;0.00982563,MA0041.1;0.000187447,MA0042.1;7.77851e-05,MA0043.1;0.214643,MA0046.1;1.62946,MA0048.1;3.9757,MA0050.1;0.385559,MA0051.1;0.333813,MA0052.1;0.0543814,MA0055.1;0.968227,MA0056.1;0,MA0057.1;0.242297,MA0058.1;0.158067,MA0059.1;0.0897657,MA0060.1;8.64992,MA0061.1;0.0680434,MA0063.1;0,MA0066.1;0.701789,MA0067.1;0.30158,MA0068.1;0.00517506,MA0069.1;0.643041,MA0070.1;0.145731,MA0071.1;0.0882694,MA0072.1;0.0203289,MA0073.1;1.30405,MA0074.1;3.65911,MA0076.1;1.14496,MA0077.1;0.0592231,MA0078.1;0.0958266,MA0081.1;0.0829427,MA0083.1;0.0339194,MA0084.1;0.197199,MA0087.1;0.0419761,MA0088.1;6.53059,MA0089.1;0,MA0090.1;0.516198,MA0091.1;0.00516403,MA0092.1;0.443065,MA0093.1;0.266419,MA0095.1;0,MA0098.1;0,MA0100.1;0.034734,MA0101.1;0.271484,MA0103.1;2.79467,MA0105.1;0.208053,MA0106.1;2.10403,MA0107.1;0.126922,MA0108.2;0.0579465,MA0109.1;0,MA0111.1;0.0647203,MA0113.1;0.24256,MA0114.1;22.4823,MA0115.1;1.89838,MA0116.1;0.815356,MA0117.1;1.34917,MA0119.1;2.08527,MA0122.1;0.301195,MA0124.1;0.046572,MA0125.1;1.23951,MA0130.1;0,MA0131.1;0.340433,MA0132.1;0,MA0133.1;0,MA0135.1;0.105342,MA0136.1;0.0206346,MA0139.1;5.99593,MA0140.1;1.47182,MA0141.1;1.9131,MA0142.1;0.0478489,MA0143.1;0.0595695,MA0144.1;0.153229,MA0145.1;6.24931,MA0146.1;24.1005,MA0147.1;0.742205,MA0148.1;0.0235512,MA0149.1;2.16272e-09,MA0062.2;2.88522,MA0035.2;0.580317,MA0039.2;49.8897,MA0138.2;0.506312,MA0002.2;0.199332,MA0137.2;0.0100286,MA0104.2;2.34071,MA0047.2;0.169535,MA0112.2;4.16202,MA0065.2;7.14811,MA0150.1;0.0391653,MA0151.1;0,MA0152.1;0.00834484,MA0153.1;0.876638,MA0154.1;3.93012,MA0155.1;6.45677,MA0156.1;0.062884,MA0157.1;0.014066,MA0158.1;0,MA0159.1;0.930057,MA0160.1;1.1277,MA0161.1;0,MA0162.1;22.7584,MA0163.1;5.52427,MA0164.1;0.0332529,MA0080.2;0.0103067,MA0018.2;0.225302,MA0099.2;0.285347,MA0079.2;20.5803,MA0102.2;0.244961,MA0258.1;1.34473,MA0259.1;1.02953,MA0442.1;0 | |||
}} | }} |
Revision as of 11:01, 23 January 2013
Phase1 CAGE Peaks
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:0016772 | transferase activity, transferring phosphorus-containing groups | 3.18393666258914e-11 |
GO:0016301 | kinase activity | 3.83385590066357e-10 |
GO:0016773 | phosphotransferase activity, alcohol group as acceptor | 7.29617956849574e-10 |
GO:0016740 | transferase activity | 1.93606534477229e-07 |
GO:0030554 | adenyl nucleotide binding | 4.35837918735243e-06 |
GO:0017076 | purine nucleotide binding | 1.24548531794828e-05 |
GO:0005524 | ATP binding | 1.62471015649466e-05 |
GO:0004672 | protein kinase activity | 2.01317461134265e-05 |
GO:0032559 | adenyl ribonucleotide binding | 2.01317461134265e-05 |
GO:0044255 | cellular lipid metabolic process | 3.34041685311341e-05 |
GO:0006629 | lipid metabolic process | 3.74200370554098e-05 |
GO:0016310 | phosphorylation | 3.75285570263213e-05 |
GO:0032555 | purine ribonucleotide binding | 3.75285570263213e-05 |
GO:0032553 | ribonucleotide binding | 3.75285570263213e-05 |
GO:0006796 | phosphate metabolic process | 3.79242153056696e-05 |
GO:0006793 | phosphorus metabolic process | 3.79242153056696e-05 |
GO:0045177 | apical part of cell | 0.000202435693490853 |
GO:0000166 | nucleotide binding | 0.000205027026493053 |
GO:0006468 | protein amino acid phosphorylation | 0.000205027026493053 |
GO:0022804 | active transmembrane transporter activity | 0.000401439797198388 |
GO:0006644 | phospholipid metabolic process | 0.000632258490155949 |
GO:0006643 | membrane lipid metabolic process | 0.00104807510089611 |
GO:0043412 | biopolymer modification | 0.00256867991165046 |
GO:0006814 | sodium ion transport | 0.00256867991165046 |
GO:0015291 | secondary active transmembrane transporter activity | 0.00372867326153453 |
GO:0016324 | apical plasma membrane | 0.00436699001051122 |
GO:0005911 | intercellular junction | 0.00436699001051122 |
GO:0046467 | membrane lipid biosynthetic process | 0.00480409937001548 |
GO:0006810 | transport | 0.00530716691774796 |
GO:0004674 | protein serine/threonine kinase activity | 0.00560069708993291 |
GO:0051234 | establishment of localization | 0.00560069708993291 |
GO:0015293 | symporter activity | 0.0074031820532731 |
GO:0007242 | intracellular signaling cascade | 0.0077495635934293 |
GO:0008654 | phospholipid biosynthetic process | 0.00869779459730678 |
GO:0046470 | phosphatidylcholine metabolic process | 0.00997102104173765 |
GO:0043296 | apical junction complex | 0.0128776529142037 |
GO:0022857 | transmembrane transporter activity | 0.0128776529142037 |
GO:0030035 | microspike biogenesis | 0.0131483476552754 |
GO:0015672 | monovalent inorganic cation transport | 0.0134088392890971 |
GO:0016327 | apicolateral plasma membrane | 0.0136303471133843 |
GO:0008092 | cytoskeletal protein binding | 0.0174342509352524 |
GO:0004713 | protein-tyrosine kinase activity | 0.0195187866394327 |
GO:0006464 | protein modification process | 0.0195187866394327 |
GO:0005923 | tight junction | 0.0195187866394327 |
GO:0042974 | retinoic acid receptor binding | 0.01987039789268 |
GO:0046965 | retinoid X receptor binding | 0.01987039789268 |
GO:0005737 | cytoplasm | 0.01987039789268 |
GO:0005743 | mitochondrial inner membrane | 0.01987039789268 |
GO:0051179 | localization | 0.020071071590494 |
GO:0004428 | inositol or phosphatidylinositol kinase activity | 0.0209735896479744 |
GO:0006869 | lipid transport | 0.0226869491790622 |
GO:0016020 | membrane | 0.0229255380144995 |
GO:0019866 | organelle inner membrane | 0.0245824970938637 |
GO:0015294 | solute:cation symporter activity | 0.0272810505761443 |
GO:0005089 | Rho guanyl-nucleotide exchange factor activity | 0.0292888051030089 |
GO:0000287 | magnesium ion binding | 0.0298817571237263 |
GO:0007266 | Rho protein signal transduction | 0.0310166071897277 |
GO:0031966 | mitochondrial membrane | 0.0311592122847732 |
GO:0004126 | cytidine deaminase activity | 0.0311592122847732 |
GO:0004385 | guanylate kinase activity | 0.0311592122847732 |
GO:0035023 | regulation of Rho protein signal transduction | 0.0343302583358113 |
GO:0006066 | alcohol metabolic process | 0.0361328081487294 |
GO:0046943 | carboxylic acid transmembrane transporter activity | 0.0361328081487294 |
GO:0005342 | organic acid transmembrane transporter activity | 0.037997378150427 |
GO:0006650 | glycerophospholipid metabolic process | 0.037997378150427 |
GO:0043687 | post-translational protein modification | 0.038103648765621 |
GO:0016820 | hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances | 0.0384490843888335 |
GO:0005088 | Ras guanyl-nucleotide exchange factor activity | 0.0393991972574956 |
GO:0007265 | Ras protein signal transduction | 0.0394931671683211 |
GO:0022892 | substrate-specific transporter activity | 0.0398257311416847 |
GO:0046942 | carboxylic acid transport | 0.0398257311416847 |
GO:0015849 | organic acid transport | 0.0398257311416847 |
GO:0042995 | cell projection | 0.0398257311416847 |
GO:0044238 | primary metabolic process | 0.0398257311416847 |
GO:0015908 | fatty acid transport | 0.0421281114542623 |
GO:0044237 | cellular metabolic process | 0.045247987991557 |
GO:0005740 | mitochondrial envelope | 0.045247987991557 |
GO:0004715 | non-membrane spanning protein tyrosine kinase activity | 0.045247987991557 |
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 |
---|---|---|
intestinal epithelial cell | 2.60e-11 | 9 |
epithelial cell of alimentary canal | 2.60e-11 | 9 |
brush border epithelial cell | 1.01e-08 | 6 |
gut absorptive cell | 1.01e-08 | 6 |
absorptive cell | 1.01e-08 | 6 |
enterocyte | 1.01e-08 | 6 |
columnar/cuboidal epithelial cell | 2.88e-07 | 7 |
Ontology term | p-value | n |
---|---|---|
intestine | 3.88e-30 | 31 |
gastrointestinal system | 2.16e-28 | 47 |
mucosa | 3.38e-18 | 15 |
intestinal mucosa | 5.47e-16 | 13 |
anatomical wall | 5.47e-16 | 13 |
wall of intestine | 5.47e-16 | 13 |
gastrointestinal system mucosa | 5.47e-16 | 13 |
organ component layer | 1.20e-13 | 24 |
endoderm-derived structure | 6.61e-12 | 118 |
endoderm | 6.61e-12 | 118 |
presumptive endoderm | 6.61e-12 | 118 |
epithelium of mucosa | 2.60e-11 | 9 |
gastrointestinal system epithelium | 2.60e-11 | 9 |
intestinal epithelium | 2.60e-11 | 9 |
digestive system | 6.04e-11 | 116 |
digestive tract | 6.04e-11 | 116 |
primitive gut | 6.04e-11 | 116 |
subdivision of digestive tract | 1.05e-09 | 114 |
simple columnar epithelium | 9.04e-09 | 11 |
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 | 45.5379 |
MA0004.1 | 0.344911 |
MA0006.1 | 0.906908 |
MA0007.1 | 0.257241 |
MA0009.1 | 0.548132 |
MA0014.1 | 37.5711 |
MA0017.1 | 10.4122 |
MA0019.1 | 0.0217314 |
MA0024.1 | 0.271324 |
MA0025.1 | 0.0674169 |
MA0027.1 | 0.694955 |
MA0028.1 | 2.40216 |
MA0029.1 | 0.0140543 |
MA0030.1 | 0.0158494 |
MA0031.1 | 0.0988965 |
MA0038.1 | 0.0615923 |
MA0040.1 | 0.00982563 |
MA0041.1 | 0.000187447 |
MA0042.1 | 7.77851e-05 |
MA0043.1 | 0.214643 |
MA0046.1 | 1.62946 |
MA0048.1 | 3.9757 |
MA0050.1 | 0.385559 |
MA0051.1 | 0.333813 |
MA0052.1 | 0.0543814 |
MA0055.1 | 0.968227 |
MA0056.1 | 0 |
MA0057.1 | 0.242297 |
MA0058.1 | 0.158067 |
MA0059.1 | 0.0897657 |
MA0060.1 | 8.64992 |
MA0061.1 | 0.0680434 |
MA0063.1 | 0 |
MA0066.1 | 0.701789 |
MA0067.1 | 0.30158 |
MA0068.1 | 0.00517506 |
MA0069.1 | 0.643041 |
MA0070.1 | 0.145731 |
MA0071.1 | 0.0882694 |
MA0072.1 | 0.0203289 |
MA0073.1 | 1.30405 |
MA0074.1 | 3.65911 |
MA0076.1 | 1.14496 |
MA0077.1 | 0.0592231 |
MA0078.1 | 0.0958266 |
MA0081.1 | 0.0829427 |
MA0083.1 | 0.0339194 |
MA0084.1 | 0.197199 |
MA0087.1 | 0.0419761 |
MA0088.1 | 6.53059 |
MA0089.1 | 0 |
MA0090.1 | 0.516198 |
MA0091.1 | 0.00516403 |
MA0092.1 | 0.443065 |
MA0093.1 | 0.266419 |
MA0095.1 | 0 |
MA0098.1 | 0 |
MA0100.1 | 0.034734 |
MA0101.1 | 0.271484 |
MA0103.1 | 2.79467 |
MA0105.1 | 0.208053 |
MA0106.1 | 2.10403 |
MA0107.1 | 0.126922 |
MA0108.2 | 0.0579465 |
MA0109.1 | 0 |
MA0111.1 | 0.0647203 |
MA0113.1 | 0.24256 |
MA0114.1 | 22.4823 |
MA0115.1 | 1.89838 |
MA0116.1 | 0.815356 |
MA0117.1 | 1.34917 |
MA0119.1 | 2.08527 |
MA0122.1 | 0.301195 |
MA0124.1 | 0.046572 |
MA0125.1 | 1.23951 |
MA0130.1 | 0 |
MA0131.1 | 0.340433 |
MA0132.1 | 0 |
MA0133.1 | 0 |
MA0135.1 | 0.105342 |
MA0136.1 | 0.0206346 |
MA0139.1 | 5.99593 |
MA0140.1 | 1.47182 |
MA0141.1 | 1.9131 |
MA0142.1 | 0.0478489 |
MA0143.1 | 0.0595695 |
MA0144.1 | 0.153229 |
MA0145.1 | 6.24931 |
MA0146.1 | 24.1005 |
MA0147.1 | 0.742205 |
MA0148.1 | 0.0235512 |
MA0149.1 | 2.16272e-09 |
MA0062.2 | 2.88522 |
MA0035.2 | 0.580317 |
MA0039.2 | 49.8897 |
MA0138.2 | 0.506312 |
MA0002.2 | 0.199332 |
MA0137.2 | 0.0100286 |
MA0104.2 | 2.34071 |
MA0047.2 | 0.169535 |
MA0112.2 | 4.16202 |
MA0065.2 | 7.14811 |
MA0150.1 | 0.0391653 |
MA0151.1 | 0 |
MA0152.1 | 0.00834484 |
MA0153.1 | 0.876638 |
MA0154.1 | 3.93012 |
MA0155.1 | 6.45677 |
MA0156.1 | 0.062884 |
MA0157.1 | 0.014066 |
MA0158.1 | 0 |
MA0159.1 | 0.930057 |
MA0160.1 | 1.1277 |
MA0161.1 | 0 |
MA0162.1 | 22.7584 |
MA0163.1 | 5.52427 |
MA0164.1 | 0.0332529 |
MA0080.2 | 0.0103067 |
MA0018.2 | 0.225302 |
MA0099.2 | 0.285347 |
MA0079.2 | 20.5803 |
MA0102.2 | 0.244961 |
MA0258.1 | 1.34473 |
MA0259.1 | 1.02953 |
MA0442.1 | 0 |