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MCL coexpression mm9:1025: Difference between revisions

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{{MCL_coexpression_mm9
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of epithelial cell polarity;0.0176214447361656;15227!GO:0030859;polarized epithelial cell differentiation;0.0176214447361656;15227!GO:0035089;establishment of apical/basal cell polarity;0.0176214447361656;15227!GO:0045197;establishment and/or maintenance of epithelial cell polarity;0.0176214447361656;15227!GO:0035088;establishment and/or maintenance of apical/basal cell polarity;0.0176214447361656;15227!GO:0001738;morphogenesis of a polarized epithelium;0.0176214447361656;15227!GO:0030010;establishment of cell polarity;0.0176214447361656;15227!GO:0048566;embryonic gut development;0.0176214447361656;15227!GO:0048565;gut development;0.0216849603820765;15227!GO:0007163;establishment and/or maintenance of cell polarity;0.0260176733532009;15227!GO:0001570;vasculogenesis;0.0285761028610465;15227!GO:0030855;epithelial cell differentiation;0.0308432971942609;15227!GO:0048568;embryonic organ development;0.0308432971942609;15227!GO:0007179;transforming growth factor beta receptor signaling pathway;0.0325006961650463;12160!GO:0048513;organ development;0.0325006961650463;15227,12160!GO:0051216;cartilage development;0.0325006961650463;12160!GO:0030198;extracellular matrix organization and biogenesis;0.0363153402358759;15227!GO:0030324;lung development;0.0370449151759794;15227!GO:0030323;respiratory tube development;0.0370449151759794;15227!GO:0048731;system development;0.0371793008965218;15227,12160!GO:0048869;cellular developmental process;0.0371793008965218;15227,12160!GO:0030154;cell differentiation;0.0371793008965218;15227,12160!GO:0007178;transmembrane receptor protein serine/threonine kinase signaling pathway;0.0371793008965218;12160!GO:0001503;ossification;0.0397919222532879;12160!GO:0031214;biomineral formation;0.0397919222532879;12160!GO:0043062;extracellular structure organization and biogenesis;0.0397919222532879;15227!GO:0048856;anatomical structure development;0.0397919222532879;15227,12160!GO:0046849;bone remodeling;0.0397919222532879;12160!GO:0048771;tissue remodeling;0.043510276184561;12160!GO:0002009;morphogenesis of an epithelium;0.043510276184561;15227!GO:0007275;multicellular organismal 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|gostat_on_MCL_coexpression=GO:0045198;establishment of epithelial cell polarity;0.0176214447361656;15227!GO:0030859;polarized epithelial cell differentiation;0.0176214447361656;15227!GO:0035089;establishment of apical/basal cell polarity;0.0176214447361656;15227!GO:0045197;establishment and/or maintenance of epithelial cell polarity;0.0176214447361656;15227!GO:0035088;establishment and/or maintenance of apical/basal cell polarity;0.0176214447361656;15227!GO:0001738;morphogenesis of a polarized epithelium;0.0176214447361656;15227!GO:0030010;establishment of cell polarity;0.0176214447361656;15227!GO:0048566;embryonic gut development;0.0176214447361656;15227!GO:0048565;gut development;0.0216849603820765;15227!GO:0007163;establishment and/or maintenance of cell polarity;0.0260176733532009;15227!GO:0001570;vasculogenesis;0.0285761028610465;15227!GO:0030855;epithelial cell differentiation;0.0308432971942609;15227!GO:0048568;embryonic organ development;0.0308432971942609;15227!GO:0007179;transforming growth factor beta receptor signaling pathway;0.0325006961650463;12160!GO:0048513;organ development;0.0325006961650463;15227,12160!GO:0051216;cartilage development;0.0325006961650463;12160!GO:0030198;extracellular matrix organization and biogenesis;0.0363153402358759;15227!GO:0030324;lung development;0.0370449151759794;15227!GO:0030323;respiratory tube development;0.0370449151759794;15227!GO:0048731;system development;0.0371793008965218;15227,12160!GO:0048869;cellular developmental process;0.0371793008965218;15227,12160!GO:0030154;cell differentiation;0.0371793008965218;15227,12160!GO:0007178;transmembrane receptor protein serine/threonine kinase signaling pathway;0.0371793008965218;12160!GO:0001503;ossification;0.0397919222532879;12160!GO:0031214;biomineral formation;0.0397919222532879;12160!GO:0043062;extracellular structure organization and biogenesis;0.0397919222532879;15227!GO:0048856;anatomical structure development;0.0397919222532879;15227,12160!GO:0046849;bone remodeling;0.0397919222532879;12160!GO:0048771;tissue remodeling;0.043510276184561;12160!GO:0002009;morphogenesis of an epithelium;0.043510276184561;15227!GO:0007275;multicellular organismal development;0.043510276184561;15227,12160!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005177!1.20e-11!79;UBERON:0002048!4.13e-11!14;UBERON:0000117!4.13e-11!14;UBERON:0000171!4.13e-11!14;UBERON:0000170!4.13e-11!14;UBERON:0005597!4.13e-11!14;UBERON:0000118!4.13e-11!14;UBERON:0004921!6.11e-11!114;UBERON:0004119!1.04e-10!118;UBERON:0000925!1.04e-10!118;UBERON:0006595!1.04e-10!118;UBERON:0001007!2.69e-10!116;UBERON:0001555!2.69e-10!116;UBERON:0007026!2.69e-10!116;UBERON:0009569!3.50e-10!66;UBERON:0000466!3.64e-10!79;UBERON:0005178!6.99e-09!17;UBERON:0005181!6.99e-09!17;UBERON:0002224!6.99e-09!17;UBERON:0000915!6.99e-09!17;UBERON:0008947!6.99e-09!17;UBERON:0003258!6.99e-09!17;UBERON:0002100!8.83e-09!90;UBERON:0005153!2.09e-08!17;UBERON:0000468!2.35e-08!333;UBERON:0005409!6.16e-08!47
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.369498,0.411716,0.480627,0.810002,0.495263,0.587291,0.206208,0.215218,0.0609112,1.34037,0.575086,1.12363,0.599731,0.315771,0,0.795315,0.792229,0.561256,0.731589,0.374752,0.27937,0.598814,0.29769,1.07577,0.62766,0.542568,0.516511,0.344372,0.145661,0.50223,0.897561,0.289148,0.166577,0.316253,2.47396,0.279977,0.57142,0.258564,1.21701,0.295233,0.507468,0.0742755,0.317766,0.515031,0.469348,0.714592,0.532496,0.478447,0.917701,0.777641,0.654933,0.431711,1.04034,1.0579,0.606984,0.356236,0.56214,0.176152,0.604914,0.877332,0.664501,0.226529,1.80715,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.21183,1.02583,1.09164,0.97874,0.936963,0.963958,0.703064,0.859987,0.378988,0.212973,0.812889,0.663039,0.200155,0.975495,0.613286,0.374181,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.237542,0.589174,0.913319,0.71485,1.29592,0.280055,0.897279,1.02279,0.778243,0.777175,1.26443,0.837607,0.528416,0.383871,1.74385,0.430942,1.02459,0.380122,0.547992,1.27206,0.796976,0.735764,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.829907,1.00568,0.473246,1.16374,0.620831,1.29374,0.275843,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,1.47713,0.452587,0.256263,1.04192,0.243291,0.619892,1.12411,0.655955,0.327731,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.278874,0.573477,0.433127
}}

Latest revision as of 16:16, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:51310245..51310270,-p1@Fam162b
Mm9::chr10:51310279..51310303,-p2@Fam162b
Mm9::chr11:8403889..8403913,-p@chr11:8403889..8403913
-
Mm9::chr8:123606985..123607053,-p1@1110050K14Rik
Mm9::chr8:123607738..123607759,+p@chr8:123607738..123607759
+
Mm9::chr8:123608252..123608268,+p1@Foxf1a
Mm9::chr9:75623162..75623185,+p1@Bmp5


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 IDGO nameFDR corrected p-value
GO:0045198establishment of epithelial cell polarity0.0176214447361656
GO:0030859polarized epithelial cell differentiation0.0176214447361656
GO:0035089establishment of apical/basal cell polarity0.0176214447361656
GO:0045197establishment and/or maintenance of epithelial cell polarity0.0176214447361656
GO:0035088establishment and/or maintenance of apical/basal cell polarity0.0176214447361656
GO:0001738morphogenesis of a polarized epithelium0.0176214447361656
GO:0030010establishment of cell polarity0.0176214447361656
GO:0048566embryonic gut development0.0176214447361656
GO:0048565gut development0.0216849603820765
GO:0007163establishment and/or maintenance of cell polarity0.0260176733532009
GO:0001570vasculogenesis0.0285761028610465
GO:0030855epithelial cell differentiation0.0308432971942609
GO:0048568embryonic organ development0.0308432971942609
GO:0007179transforming growth factor beta receptor signaling pathway0.0325006961650463
GO:0048513organ development0.0325006961650463
GO:0051216cartilage development0.0325006961650463
GO:0030198extracellular matrix organization and biogenesis0.0363153402358759
GO:0030324lung development0.0370449151759794
GO:0030323respiratory tube development0.0370449151759794
GO:0048731system development0.0371793008965218
GO:0048869cellular developmental process0.0371793008965218
GO:0030154cell differentiation0.0371793008965218
GO:0007178transmembrane receptor protein serine/threonine kinase signaling pathway0.0371793008965218
GO:0001503ossification0.0397919222532879
GO:0031214biomineral formation0.0397919222532879
GO:0043062extracellular structure organization and biogenesis0.0397919222532879
GO:0048856anatomical structure development0.0397919222532879
GO:0046849bone remodeling0.0397919222532879
GO:0048771tissue remodeling0.043510276184561
GO:0002009morphogenesis of an epithelium0.043510276184561
GO:0007275multicellular organismal development0.043510276184561



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>


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)
MA0003.11.08574
MA0004.10.481116
MA0006.10.837454
MA0007.10.465969
MA0009.10.92425
MA0014.11.02494
MA0017.10.337808
MA0019.10.740036
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.10.321735
MA0029.10.858105
MA0030.10.864739
MA0031.10.828781
MA0038.10.62758
MA0040.10.936879
MA0041.10.404721
MA0042.10.391504
MA0043.11.02178
MA0046.10.960497
MA0048.10.40238
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.648475
MA0056.10
MA0057.10.376102
MA0058.10.384683
MA0059.10.397033
MA0060.10.232592
MA0061.10.261749
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.771749
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.10.152496
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.11.49527
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.10.446857
MA0093.10.329976
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.10.348572
MA0105.10.162418
MA0106.10.677988
MA0107.10.342432
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.719313
MA0115.11.0246
MA0116.10.311187
MA0117.10.992087
MA0119.11.04809
MA0122.11.01209
MA0124.11.21735
MA0125.11.14291
MA0130.10
MA0131.10.735438
MA0132.10
MA0133.10
MA0135.11.05845
MA0136.10.600242
MA0139.10.202522
MA0140.10.568252
MA0141.10.964041
MA0142.10.814115
MA0143.10.665982
MA0144.10.72625
MA0145.10.0910975
MA0146.11.57153
MA0147.10.274511
MA0148.11.24416
MA0149.10.411562
MA0062.20.167299
MA0035.20.573016
MA0039.20.219063
MA0138.20.727395
MA0002.20.205289
MA0137.20.957645
MA0104.20.218974
MA0047.20.626803
MA0112.20.0910939
MA0065.20.305574
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.397336
MA0155.10.102995
MA0156.11.67246
MA0157.10.781683
MA0158.10
MA0159.10.776527
MA0160.10.50056
MA0161.10
MA0162.11.71182
MA0163.10.82914
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.22.82057
MA0102.21.65195
MA0258.10.246285
MA0259.10.26402
MA0442.10
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