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MCL coexpression mm9:1863: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0042789;mRNA transcription from RNA polymerase II promoter;0.00421848463266313;13198!GO:0009299;mRNA transcription;0.00421848463266313;13198!GO:0030503;regulation of cell redox homeostasis;0.00562449209387472;13198!GO:0006983;ER overload response;0.0126537204641331;13198!GO:0030968;unfolded protein response;0.0202426245496088;13198!GO:0033554;cellular response to stress;0.0210814447488924;13198!GO:0006984;ER-nuclear signaling pathway;0.0210814447488924;13198!GO:0051716;cellular response to stimulus;0.0210814447488924;13198!GO:0006986;response to unfolded protein;0.0261331101426934;13198!GO:0051789;response to protein stimulus;0.0261331101426934;13198!GO:0045454;cell redox homeostasis;0.031600499200135;13198!GO:0007050;cell cycle arrest;0.031600499200135;13198!}}
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transcription from RNA polymerase II promoter;0.00421848463266313;13198!GO:0009299;mRNA transcription;0.00421848463266313;13198!GO:0030503;regulation of cell redox homeostasis;0.00562449209387472;13198!GO:0006983;ER overload response;0.0126537204641331;13198!GO:0030968;unfolded protein response;0.0202426245496088;13198!GO:0033554;cellular response to stress;0.0210814447488924;13198!GO:0006984;ER-nuclear signaling pathway;0.0210814447488924;13198!GO:0051716;cellular response to stimulus;0.0210814447488924;13198!GO:0006986;response to unfolded protein;0.0261331101426934;13198!GO:0051789;response to protein stimulus;0.0261331101426934;13198!GO:0045454;cell redox homeostasis;0.031600499200135;13198!GO:0007050;cell cycle arrest;0.031600499200135;13198!|ontology_enrichment_celltype=CL:0002320!4.10e-11!46;CL:0000134!4.10e-11!46;CL:0000988!2.57e-10!32;CL:0002032!2.57e-10!32;CL:0000037!2.57e-10!32;CL:0000566!2.57e-10!32;CL:0000837!2.57e-10!32;CL:0000219!4.18e-09!54;CL:0002031!2.12e-07!25|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0002204!1.63e-11!32;UBERON:0002193!2.72e-11!48;UBERON:0002405!2.72e-11!48;UBERON:0002384!4.10e-11!46;UBERON:0002390!1.49e-10!45;UBERON:0003061!1.49e-10!45;UBERON:0003081!3.17e-10!87;UBERON:0004119!7.18e-09!118;UBERON:0000925!7.18e-09!118;UBERON:0006595!7.18e-09!118;UBERON:0001007!4.41e-08!116;UBERON:0001555!4.41e-08!116;UBERON:0007026!4.41e-08!116;UBERON:0004921!9.01e-08!114;UBERON:0000926!1.74e-07!120;UBERON:0004120!1.74e-07!120;UBERON:0006603!1.74e-07!120;UBERON:0002371!2.72e-07!16;UBERON:0001474!6.21e-07!22;UBERON:0004765!6.21e-07!22;UBERON:0001434!6.21e-07!22|tfbs_overrepresentation_for_novel_motifs=0.641384,0.128156,0.612053,1.64561,0.483253,0.704257,0.803568,0.370124,0.381467,1.51468,0.755749,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,0.928768,1.2676,0.570433,0.197567,0.815872,0.481455,0.620553,0.846564,0.342316,0.727368,1.32554,1.44018,0.711848,1.12823,0.471365,0.854272,0.503207,0.623685,0.460474,0.786577,0.434783,1.03515,0.478558,0.717547,0.544696,1.26006,0.66772,0.675898,0.938241,0.744678,0.49007,0.539131,1.0041,0.875451,0.771943,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.98374,0.593145,1.32691,0.323563,0.310084,0.318792,0.926147,1.08947,0.575233,0.986898,1.04072,0.884013,4.5362,1.20828,0.11855,0.129654,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,2.29566,1.00361,0.717061,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,0.442329,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,28.2915,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.293812,0.542121,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,0.0824127|tfbs_overrepresentation_jaspar=MA0003.1;0.0356887,MA0004.1;0.6888,MA0006.1;0.497533,MA0007.1;0.672186,MA0009.1;1.15569,MA0014.1;0.0809287,MA0017.1;0.528196,MA0019.1;0.964875,MA0024.1;1.11019,MA0025.1;1.39562,MA0027.1;2.81824,MA0028.1;1.26991,MA0029.1;2.46391,MA0030.1;2.47781,MA0031.1;1.05719,MA0038.1;0.846479,MA0040.1;2.62831,MA0041.1;0.604221,MA0042.1;1.4388,MA0043.1;2.80412,MA0046.1;1.1929,MA0048.1;0.266382,MA0050.1;0.731539,MA0051.1;0.856094,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;0.403071,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;0.0471131,MA0074.1;0.795862,MA0076.1;0.550092,MA0077.1;1.13603,MA0078.1;0.891476,MA0081.1;0.621611,MA0083.1;8.31216,MA0084.1;1.84013,MA0087.1;1.21037,MA0088.1;0.201215,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;0.540576,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;0.497293,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;0.960068,MA0132.1;0,MA0133.1;0,MA0135.1;1.29308,MA0136.1;0.817395,MA0139.1;0.365453,MA0140.1;1.84211,MA0141.1;0.563066,MA0142.1;1.04199,MA0143.1;0.887119,MA0144.1;0.439506,MA0145.1;1.14526,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;0.238019,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;0.263609,MA0155.1;0.230016,MA0156.1;0.549102,MA0157.1;1.0083,MA0158.1;0,MA0159.1;0.465802,MA0160.1;0.71003,MA0161.1;0,MA0162.1;0.346529,MA0163.1;0.327769,MA0164.1;0.817786,MA0080.2;0.534538,MA0018.2;3.21174,MA0099.2;0.944966,MA0079.2;0.440842,MA0102.2;1.8929,MA0258.1;0.419871,MA0259.1;0.441366,MA0442.1;0}}

Latest revision as of 17:37, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:111434155..111434168,-p3@Glipr1
Mm9::chr10:111434204..111434212,-p5@Glipr1
Mm9::chr10:111434222..111434258,-p1@Glipr1
Mm9::chr10:126727842..126727859,+p1@Ddit3


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:0042789mRNA transcription from RNA polymerase II promoter0.00421848463266313
GO:0009299mRNA transcription0.00421848463266313
GO:0030503regulation of cell redox homeostasis0.00562449209387472
GO:0006983ER overload response0.0126537204641331
GO:0030968unfolded protein response0.0202426245496088
GO:0033554cellular response to stress0.0210814447488924
GO:0006984ER-nuclear signaling pathway0.0210814447488924
GO:0051716cellular response to stimulus0.0210814447488924
GO:0006986response to unfolded protein0.0261331101426934
GO:0051789response to protein stimulus0.0261331101426934
GO:0045454cell redox homeostasis0.031600499200135
GO:0007050cell cycle arrest0.031600499200135



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>

Uber Anatomy
Ontology termp-valuen
musculoskeletal system1.63e-1132
hemolymphoid system2.72e-1148
immune system2.72e-1148
connective tissue4.10e-1146
hematopoietic system1.49e-1045
blood island1.49e-1045
lateral plate mesoderm3.17e-1087
endoderm-derived structure7.18e-09118
endoderm7.18e-09118
presumptive endoderm7.18e-09118
digestive system4.41e-08116
digestive tract4.41e-08116
primitive gut4.41e-08116
subdivision of digestive tract9.01e-08114
mesoderm1.74e-07120
mesoderm-derived structure1.74e-07120
presumptive mesoderm1.74e-07120
bone marrow2.72e-0716
bone element6.21e-0722
skeletal element6.21e-0722
skeletal system6.21e-0722


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)
MA0003.10.0356887
MA0004.10.6888
MA0006.10.497533
MA0007.10.672186
MA0009.11.15569
MA0014.10.0809287
MA0017.10.528196
MA0019.10.964875
MA0024.11.11019
MA0025.11.39562
MA0027.12.81824
MA0028.11.26991
MA0029.12.46391
MA0030.12.47781
MA0031.11.05719
MA0038.10.846479
MA0040.12.62831
MA0041.10.604221
MA0042.11.4388
MA0043.12.80412
MA0046.11.1929
MA0048.10.266382
MA0050.10.731539
MA0051.10.856094
MA0052.11.17701
MA0055.10.125758
MA0056.10
MA0057.10.251896
MA0058.10.581673
MA0059.10.59559
MA0060.10.403071
MA0061.10.438628
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.10.256913
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.10.0471131
MA0074.10.795862
MA0076.10.550092
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.18.31216
MA0084.11.84013
MA0087.11.21037
MA0088.10.201215
MA0089.10
MA0090.10.650768
MA0091.10.703314
MA0092.10.651119
MA0093.10.519148
MA0095.10
MA0098.10
MA0100.10.783305
MA0101.10.605676
MA0103.10.540576
MA0105.10.313353
MA0106.10.899777
MA0107.10.533522
MA0108.20.989014
MA0109.10
MA0111.10.666525
MA0113.10.869608
MA0114.10.43587
MA0115.11.25852
MA0116.10.497293
MA0117.11.22527
MA0119.10.606338
MA0122.11.24573
MA0124.11.45461
MA0125.11.37907
MA0130.10
MA0131.10.960068
MA0132.10
MA0133.10
MA0135.11.29308
MA0136.10.817395
MA0139.10.365453
MA0140.11.84211
MA0141.10.563066
MA0142.11.04199
MA0143.10.887119
MA0144.10.439506
MA0145.11.14526
MA0146.10.0944145
MA0147.10.453952
MA0148.10.706718
MA0149.10.611881
MA0062.20.319836
MA0035.20.788288
MA0039.20.238019
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.20.386166
MA0047.20.845655
MA0112.20.211985
MA0065.20.212467
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.10.263609
MA0155.10.230016
MA0156.10.549102
MA0157.11.0083
MA0158.10
MA0159.10.465802
MA0160.10.71003
MA0161.10
MA0162.10.346529
MA0163.10.327769
MA0164.10.817786
MA0080.20.534538
MA0018.23.21174
MA0099.20.944966
MA0079.20.440842
MA0102.21.8929
MA0258.10.419871
MA0259.10.441366
MA0442.10
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