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MCL coexpression mm9:2068: Difference between revisions

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{{MCL_coexpression_mm9
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reticulum;0.00347010480930672;53421,67437,107513!GO:0005784;translocon complex;0.0111744080782777;67437!GO:0005791;rough endoplasmic reticulum;0.0111744080782777;67437!GO:0030867;rough endoplasmic reticulum membrane;0.0111744080782777;67437!GO:0006886;intracellular protein transport;0.0159407093075002;53421,67437!GO:0015450;P-P-bond-hydrolysis-driven protein transmembrane transporter activity;0.0159407093075002;53421!GO:0022884;macromolecule transmembrane transporter activity;0.0159407093075002;53421!GO:0046907;intracellular transport;0.0159407093075002;53421,67437!GO:0008320;protein transmembrane transporter activity;0.0159407093075002;53421!GO:0006613;cotranslational protein targeting to membrane;0.0159407093075002;67437!GO:0030176;integral to endoplasmic reticulum membrane;0.0159407093075002;67437!GO:0015031;protein transport;0.0159407093075002;53421,67437!GO:0031227;intrinsic to endoplasmic reticulum membrane;0.0159407093075002;67437!GO:0045184;establishment of protein 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|gostat_on_MCL_coexpression=GO:0005783;endoplasmic reticulum;0.00347010480930672;53421,67437,107513!GO:0005784;translocon complex;0.0111744080782777;67437!GO:0005791;rough endoplasmic reticulum;0.0111744080782777;67437!GO:0030867;rough endoplasmic reticulum membrane;0.0111744080782777;67437!GO:0006886;intracellular protein transport;0.0159407093075002;53421,67437!GO:0015450;P-P-bond-hydrolysis-driven protein transmembrane transporter activity;0.0159407093075002;53421!GO:0022884;macromolecule transmembrane transporter activity;0.0159407093075002;53421!GO:0046907;intracellular transport;0.0159407093075002;53421,67437!GO:0008320;protein transmembrane transporter activity;0.0159407093075002;53421!GO:0006613;cotranslational protein targeting to membrane;0.0159407093075002;67437!GO:0030176;integral to endoplasmic reticulum membrane;0.0159407093075002;67437!GO:0015031;protein transport;0.0159407093075002;53421,67437!GO:0031227;intrinsic to endoplasmic reticulum membrane;0.0159407093075002;67437!GO:0045184;establishment of protein localization;0.0159407093075002;53421,67437!GO:0008104;protein localization;0.0159407093075002;53421,67437!GO:0051649;establishment of cellular localization;0.0159407093075002;53421,67437!GO:0006612;protein targeting to membrane;0.0159407093075002;67437!GO:0051641;cellular localization;0.0159407093075002;53421,67437!GO:0033036;macromolecule localization;0.0159407093075002;53421,67437!GO:0044444;cytoplasmic part;0.0159407093075002;53421,67437,107513!GO:0009306;protein secretion;0.0159407093075002;53421!GO:0031301;integral to organelle membrane;0.0253324253186313;67437!GO:0065002;intracellular protein transport across a membrane;0.0255365256537682;53421!GO:0031300;intrinsic to organelle membrane;0.0255365256537682;67437!GO:0005789;endoplasmic reticulum membrane;0.0311753307934355;67437!GO:0042175;nuclear envelope-endoplasmic reticulum network;0.0312558327928293;67437!GO:0044432;endoplasmic reticulum part;0.0329716736381077;67437!GO:0015399;primary active transmembrane transporter activity;0.0489871804209735;53421!GO:0015405;P-P-bond-hydrolysis-driven transmembrane transporter activity;0.0489871804209735;53421!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000466!6.57e-15!79;UBERON:0002100!1.03e-12!90;UBERON:0005177!1.07e-12!79;UBERON:0000464!1.05e-10!57;UBERON:0002553!3.02e-10!39;UBERON:0003886!3.38e-10!38;UBERON:0002323!1.20e-09!37;UBERON:0004458!1.20e-09!37;UBERON:0001264!1.83e-08!12;UBERON:0002075!2.10e-07!19;UBERON:0009569!2.28e-07!66
|tfbs_overrepresentation_for_novel_motifs=0.641384,0.402508,0.612053,0.688265,0.483253,0.704257,0.803568,0.370124,0.381467,0.162942,0.755749,0.790506,0.37041,0.81685,1.2551,0,1.02248,1.19379,0.352304,0.24402,0.570433,0.57409,0.815872,0.481455,0.620553,0.846564,0.342316,0.727368,0.535752,0.290745,0.711848,1.12823,0.471365,0.318879,0.503207,0.089443,0.460474,0.786577,0.434783,0.40068,0.478558,0.717547,0.185353,0.504971,0.0986756,0.675898,0.938241,0.744678,0.949442,0.539131,1.0041,0.875451,0.282443,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.98374,0.205546,1.32691,0.323563,0.310084,0.854076,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,1.69489,1.20828,0.11855,0.129654,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,1.05366,0.367176,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,0.143825,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.293812,0.184289,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,0.280875
|tfbs_overrepresentation_jaspar=MA0003.1;0.0356887,MA0004.1;0.6888,MA0006.1;0.497533,MA0007.1;1.61215,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;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;0.589368,MA0043.1;1.25564,MA0046.1;1.1929,MA0048.1;0.266382,MA0050.1;0.731539,MA0051.1;0.856094,MA0052.1;1.17701,MA0055.1;0.396346,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;2.83575,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;1.1032,MA0089.1;0,MA0090.1;0.650768,MA0091.1;0.703314,MA0092.1;2.65214,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;0.78318,MA0141.1;0.563066,MA0142.1;1.04199,MA0143.1;0.887119,MA0144.1;1.11951,MA0145.1;0.21199,MA0146.1;0.313734,MA0147.1;0.453952,MA0148.1;0.706718,MA0149.1;0.611881,MA0062.2;0.319836,MA0035.2;0.788288,MA0039.2;0.0220513,MA0138.2;0.951653,MA0002.2;0.368961,MA0137.2;0.559766,MA0104.2;0.386166,MA0047.2;0.845655,MA0112.2;0.608441,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;0.10667,MA0163.1;0.0996272,MA0164.1;0.817786,MA0080.2;0.534538,MA0018.2;0.828253,MA0099.2;0.944966,MA0079.2;0.00774881,MA0102.2;1.8929,MA0258.1;1.07695,MA0259.1;0.441366,MA0442.1;0
}}

Latest revision as of 17:57, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:38071380..38071398,-p@chr13:38071380..38071398
-
Mm9::chr3:65185318..65185322,-p@chr3:65185318..65185322
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Mm9::chr6:28838574..28838577,+p@chr6:28838574..28838577
+
Mm9::chr6:88454974..88454978,-p@chr6:88454974..88454978
-


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:0005783endoplasmic reticulum0.00347010480930672
GO:0005784translocon complex0.0111744080782777
GO:0005791rough endoplasmic reticulum0.0111744080782777
GO:0030867rough endoplasmic reticulum membrane0.0111744080782777
GO:0006886intracellular protein transport0.0159407093075002
GO:0015450P-P-bond-hydrolysis-driven protein transmembrane transporter activity0.0159407093075002
GO:0022884macromolecule transmembrane transporter activity0.0159407093075002
GO:0046907intracellular transport0.0159407093075002
GO:0008320protein transmembrane transporter activity0.0159407093075002
GO:0006613cotranslational protein targeting to membrane0.0159407093075002
GO:0030176integral to endoplasmic reticulum membrane0.0159407093075002
GO:0015031protein transport0.0159407093075002
GO:0031227intrinsic to endoplasmic reticulum membrane0.0159407093075002
GO:0045184establishment of protein localization0.0159407093075002
GO:0008104protein localization0.0159407093075002
GO:0051649establishment of cellular localization0.0159407093075002
GO:0006612protein targeting to membrane0.0159407093075002
GO:0051641cellular localization0.0159407093075002
GO:0033036macromolecule localization0.0159407093075002
GO:0044444cytoplasmic part0.0159407093075002
GO:0009306protein secretion0.0159407093075002
GO:0031301integral to organelle membrane0.0253324253186313
GO:0065002intracellular protein transport across a membrane0.0255365256537682
GO:0031300intrinsic to organelle membrane0.0255365256537682
GO:0005789endoplasmic reticulum membrane0.0311753307934355
GO:0042175nuclear envelope-endoplasmic reticulum network0.0312558327928293
GO:0044432endoplasmic reticulum part0.0329716736381077
GO:0015399primary active transmembrane transporter activity0.0489871804209735
GO:0015405P-P-bond-hydrolysis-driven transmembrane transporter activity0.0489871804209735



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>

Uber Anatomy
Ontology termp-valuen
immaterial anatomical entity6.57e-1579
trunk1.03e-1290
trunk region element1.07e-1279
anatomical space1.05e-1057
anatomical cavity3.02e-1039
body cavity precursor3.38e-1038
body cavity1.20e-0937
body cavity or lining1.20e-0937
pancreas1.83e-0812
viscus2.10e-0719
subdivision of trunk2.28e-0766


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
MA0007.11.61215
MA0009.11.15569
MA0014.10.0809287
MA0017.10.528196
MA0019.10.964875
MA0024.11.11019
MA0025.11.39562
MA0027.12.81824
MA0028.10.509589
MA0029.11.08753
MA0030.11.09438
MA0031.11.05719
MA0038.10.846479
MA0040.11.16866
MA0041.10.604221
MA0042.10.589368
MA0043.11.25564
MA0046.11.1929
MA0048.10.266382
MA0050.10.731539
MA0051.10.856094
MA0052.11.17701
MA0055.10.396346
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
MA0068.12.83575
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.10.00221226
MA0074.10.795862
MA0076.10.550092
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.11.1032
MA0089.10
MA0090.10.650768
MA0091.10.703314
MA0092.12.65214
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
MA0140.10.78318
MA0141.10.563066
MA0142.11.04199
MA0143.10.887119
MA0144.11.11951
MA0145.10.21199
MA0146.10.313734
MA0147.10.453952
MA0148.10.706718
MA0149.10.611881
MA0062.20.319836
MA0035.20.788288
MA0039.20.0220513
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.20.386166
MA0047.20.845655
MA0112.20.608441
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
MA0162.10.10667
MA0163.10.0996272
MA0164.10.817786
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.20.00774881
MA0102.21.8929
MA0258.11.07695
MA0259.10.441366
MA0442.10
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