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MCL coexpression mm9:191: Difference between revisions

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{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0,1.22712182217855,1.26728648445014,0.776225572617656,0.796185150816745,0.576234596046205,0.6907407246269,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.25038304456037,1.3283784181531,1.24658190581998,1.0545474806307,1.08265214419717,0.502952869011992,0.420811032427087,0.698200551674405,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.526695425314275,0,0,0,0.107511441879825,0,0,0,0,0,0,0,0,0,0,0.314943337730996,0,0,0,0,0,0,0,0,0.372236665520211,0,0,0,0,0,0,0,0,0.534592197574126,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.922733113900944,0.930827846122658,0,0,0,0.205488721231012,0.4257815014932,0.551037261538165,0.80974306344921,0.911371521737087,0.876825103122052,0.848919674365828,0.796643395005908,0.739896326177542,0.638369155937494,0.577806444086236,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.10536076625968,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.383439311973697,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.832808412473544,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0445418537893845,0,0.15737368738825,0,0.034489466458534,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.034796599340108,0.081359932135904,0,0,0.0310911785760183,0.0750453505157095,0.0567146198773073,0.0523284672130554,0.0472245945615809,0,0.0476191773904887,0.0766073954291401,0,0.0596387295197733,0.128033729919821,0.0709519923534245,0.092873634605593,0.0589368614163519,0.0438474322863328,0.0678996586311492,0.0729583017401753,0.0882975200408346,0.101328897466453,0.0255370399853546,0.0486884105045233,0.0408018333703219,0,0.0625582350728301,0.0766064454112358,0,0.0462298993288061,0.155257708002722,0,0,0
|gostat_on_MCL_coexpression=GO:0009203;ribonucleoside triphosphate catabolic process;0.038325164999839;93685!GO:0030300;regulation of cholesterol absorption;0.038325164999839;11808!GO:0030299;cholesterol absorption;0.038325164999839;11808!GO:0044241;lipid digestion;0.038325164999839;11808!GO:0009191;ribonucleoside diphosphate catabolic process;0.038325164999839;93685!GO:0009143;nucleoside triphosphate catabolic process;0.038325164999839;93685!GO:0009185;ribonucleoside diphosphate metabolic process;0.038325164999839;93685!GO:0009134;nucleoside diphosphate catabolic process;0.038325164999839;93685!GO:0042627;chylomicron;0.038325164999839;11808!GO:0009261;ribonucleotide catabolic process;0.038325164999839;93685!GO:0050892;intestinal absorption;0.0447711166420025;11808!GO:0017110;nucleoside-diphosphatase activity;0.0455877250377747;93685!
|ontology_enrichment_celltype=CL:0000239!3.68e-10!6;CL:0000677!3.68e-10!6;CL:0000212!3.68e-10!6;CL:0000584!3.68e-10!6;CL:0000075!1.51e-08!7
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000160!1.17e-25!31;UBERON:0005409!2.01e-18!47;UBERON:0000344!2.78e-14!15;UBERON:0001242!2.80e-11!13;UBERON:0000060!2.80e-11!13;UBERON:0001262!2.80e-11!13;UBERON:0004786!2.80e-11!13;UBERON:0004923!4.48e-09!24;UBERON:0002108!8.44e-07!4
|tfbs_overrepresentation_for_novel_motifs=0.0151974,4.70741,0.0563333,0.241985,0.381291,0.02557,0.0497618,1.47522,0.775985,0.189148,0.036867,0.0460055,0.522741,1.17237,0.265421,0,0.138669,2.06445,0.0566521,2.34101,0.927215,0.0230533,0.0534624,0.117592,0.0602981,0.491579,4.1144,1.24817,0.184769,3.16412,0.113518,0.197802,0.106965,0.321863,0.00325416,0.364985,0.00173006,0.0449101,0.602498,6.30708,0.0482466,0.522308,0.0316412,1.2208,0.122523,0.225947,0.0987896,0.0342152,0.263633,0.543949,0.129394,1.38945,0.309693,0.293909,0.306656,0.0561765,0.0321014,1.03012,0.698515,0.448551,0.1854,0.0773893,1.10861,0.123566,0.0600525,0.14508,0.411886,0.714043,0.182553,0.582319,0.464965,0.752464,1.84947e-05,0.331647,0.000100674,0.0615039,4.54211,0.311609,0.175032,0.0410536,2.99212,0.14818,0.0768051,0.00959939,0.248509,8.91763e-05,0.502107,0.020023,0.101055,0.864265,0.469,1.29724,0.205896,0.602622,0.0010377,0.0542217,0.226963,0.207688,0.325838,0.0548246,1.25852,0.197626,0.281356,0.129705,1.89792,0.281409,0.16203,1.3034,0.121528,0.040029,0.175173,0.282632,0.117682,0.0382686,0.47488,0.216574,0.000432918,0.100565,0.139372,0.0920176,0.33573,0.363366,0.495139,1.07052,3.2843,0.177244,0.431286,1.73479,0.410666,0.0565327,0.269307,0.0211704,0.387083,0.478509,0.493018,0.462947,0.195082,0.118581,0.451982,1.21737,0.834426,0.415684,0.0685509,1.11572,0.12579,0.117838,0.329381,1.1788,0.946961,0.0518572,0.0212097,4.39023e-07,0.295048,3.52603,0.0606174,0.356288,1.39355,0.070795,1.24061,0.0164778,0.459848,0.247923,0.525668,1.59561,0.124089,0.211126,0.0387817,0.173366,0.553966
|tfbs_overrepresentation_jaspar=MA0003.1;3.46736e-07,MA0004.1;0.0226833,MA0006.1;0.00300774,MA0007.1;0.0198299,MA0009.1;0.214658,MA0014.1;0.000125913,MA0017.1;1.03437,MA0019.1;0.110663,MA0024.1;0.187051,MA0025.1;0.383522,MA0027.1;1.70825,MA0028.1;0.00354928,MA0029.1;0.516916,MA0030.1;0.177847,MA0031.1;0.157022,MA0038.1;0.226796,MA0040.1;0.222824,MA0041.1;0.0106718,MA0042.1;0.129556,MA0043.1;0.280639,MA0046.1;0.238407,MA0048.1;0.252422,MA0050.1;0.127551,MA0051.1;0.236374,MA0052.1;0.228144,MA0055.1;8.94103,MA0056.1;0,MA0057.1;0.418675,MA0058.1;0.00844533,MA0059.1;0.732375,MA0060.1;0.00475879,MA0061.1;0.155117,MA0063.1;0,MA0066.1;0.0594129,MA0067.1;0.473816,MA0068.1;0.0861753,MA0069.1;0.228369,MA0070.1;0.221972,MA0071.1;0.126877,MA0072.1;0.216436,MA0073.1;0.000670544,MA0074.1;0.712384,MA0076.1;0.00591694,MA0077.1;0.202534,MA0078.1;0.273203,MA0081.1;0.162164,MA0083.1;0.280072,MA0084.1;0.763469,MA0087.1;0.249896,MA0088.1;0.000105629,MA0089.1;0,MA0090.1;0.628492,MA0091.1;1.14721,MA0092.1;0.380534,MA0093.1;0.00402865,MA0095.1;0,MA0098.1;0,MA0100.1;0.0440101,MA0101.1;0.295268,MA0103.1;3.16741,MA0105.1;0.0119277,MA0106.1;0.0828885,MA0107.1;0.181682,MA0108.2;0.386694,MA0109.1;0,MA0111.1;0.0189154,MA0113.1;0.0714693,MA0114.1;3.8113,MA0115.1;1.41067,MA0116.1;0.0182401,MA0117.1;0.259864,MA0119.1;0.770704,MA0122.1;2.94743,MA0124.1;0.429916,MA0125.1;0.3708,MA0130.1;0,MA0131.1;0.108468,MA0132.1;0,MA0133.1;0,MA0135.1;1.49908,MA0136.1;0.439893,MA0139.1;0.501553,MA0140.1;0.382356,MA0141.1;1.58019,MA0142.1;0.148854,MA0143.1;0.268535,MA0144.1;1.76005,MA0145.1;0.103346,MA0146.1;0.00239899,MA0147.1;0.0104379,MA0148.1;0.110009,MA0149.1;0.0115146,MA0062.2;0.000862111,MA0035.2;2.57519,MA0039.2;4.27212e-06,MA0138.2;0.341255,MA0002.2;0.231171,MA0137.2;2.39745,MA0104.2;0.0143078,MA0047.2;0.0630718,MA0112.2;0.0164966,MA0065.2;2.37175,MA0150.1;0.221082,MA0151.1;0,MA0152.1;0.226097,MA0153.1;0.319381,MA0154.1;2.35288,MA0155.1;2.40062,MA0156.1;2.76651,MA0157.1;0.131489,MA0158.1;0,MA0159.1;2.81372,MA0160.1;2.07308,MA0161.1;0,MA0162.1;1.07638e-09,MA0163.1;0.0069236,MA0164.1;0.0540521,MA0080.2;0.0833902,MA0018.2;0.458858,MA0099.2;0.101721,MA0079.2;3.66396e-05,MA0102.2;0.812014,MA0258.1;0.229807,MA0259.1;0.629938,MA0442.1;0
}}

Latest revision as of 14:51, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:39245914..39245917,-p@chr10:39245914..39245917
-
Mm9::chr11:70318816..70318834,+p2@Tm4sf5
Mm9::chr11:70323193..70323295,+p3@Tm4sf5
Mm9::chr11:70323747..70323757,+p6@Tm4sf5
Mm9::chr11:70324670..70324684,-p@chr11:70324670..70324684
-
Mm9::chr13:34020263..34020267,-p@chr13:34020263..34020267
-
Mm9::chr15:58184283..58184304,-p@chr15:58184283..58184304
-
Mm9::chr15:75693658..75693668,+p@chr15:75693658..75693668
+
Mm9::chr15:75693673..75693697,+p@chr15:75693673..75693697
+
Mm9::chr15:75693709..75693724,+p@chr15:75693709..75693724
+
Mm9::chr19:11049139..11049152,-p2@Ms4a10
Mm9::chr19:11049154..11049200,-p1@Ms4a10
Mm9::chr19:43785907..43785950,+p5@Entpd7
Mm9::chr2:68259263..68259293,+p@chr2:68259263..68259293
+
Mm9::chr4:133899547..133899595,+p1@Slc30a2
Mm9::chr5:31252419..31252506,+p1@Abhd1
Mm9::chr5:31252508..31252520,+p1@ENSMUST00000006814
Mm9::chr6:129050956..129050965,-p2@Clec2e
Mm9::chr7:20536078..20536097,-p1@2210010C17Rik
Mm9::chr7:50890020..50890033,+p2@Ceacam18
Mm9::chr7:99968402..99968425,+p2@Rab30
Mm9::chr9:107493255..107493276,+p@chr9:107493255..107493276
+
Mm9::chr9:107493277..107493307,+p@chr9:107493277..107493307
+
Mm9::chr9:40128499..40128534,-p@chr9:40128499..40128534
-
Mm9::chr9:46049135..46049151,+p1@Apoa4
Mm9::chr9:46049553..46049572,+p@chr9:46049553..46049572
+
Mm9::chr9:46049587..46049613,+p@chr9:46049587..46049613
+
Mm9::chr9:46049601..46049682,-p@chr9:46049601..46049682
-
Mm9::chr9:46049631..46049643,+p@chr9:46049631..46049643
+
Mm9::chr9:46050350..46050364,+p@chr9:46050350..46050364
+
Mm9::chr9:46050368..46050461,+p@chr9:46050368..46050461
+
Mm9::chr9:46050406..46050418,-p@chr9:46050406..46050418
-
Mm9::chr9:46050472..46050525,+p@chr9:46050472..46050525
+
Mm9::chr9:46050527..46050532,+p@chr9:46050527..46050532
+
Mm9::chr9:46050533..46050543,+p@chr9:46050533..46050543
+
Mm9::chr9:46050554..46050575,+p@chr9:46050554..46050575
+
Mm9::chr9:46050577..46050605,+p@chr9:46050577..46050605
+
Mm9::chr9:46050606..46050626,+p@chr9:46050606..46050626
+
Mm9::chr9:46050633..46050670,+p@chr9:46050633..46050670
+
Mm9::chr9:46050688..46050713,+p@chr9:46050688..46050713
+
Mm9::chr9:46050715..46050725,+p@chr9:46050715..46050725
+
Mm9::chr9:46050739..46050748,+p@chr9:46050739..46050748
+
Mm9::chr9:46050805..46050816,+p@chr9:46050805..46050816
+
Mm9::chr9:46050877..46050884,+p@chr9:46050877..46050884
+
Mm9::chr9:46050983..46050990,+p@chr9:46050983..46050990
+
Mm9::chr9:46050996..46051001,+p@chr9:46050996..46051001
+
Mm9::chr9:46051084..46051095,+p@chr9:46051084..46051095
+
Mm9::chr9:46051114..46051123,+p@chr9:46051114..46051123
+
Mm9::chr9:46051125..46051130,+p@chr9:46051125..46051130
+
Mm9::chr9:46051188..46051198,+p@chr9:46051188..46051198
+
Mm9::chr9:46051225..46051236,+p@chr9:46051225..46051236
+
Mm9::chr9:46051523..46051542,-p1@ENSMUST00000156612
p1@uc009phe.1


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:0009203ribonucleoside triphosphate catabolic process0.038325164999839
GO:0030300regulation of cholesterol absorption0.038325164999839
GO:0030299cholesterol absorption0.038325164999839
GO:0044241lipid digestion0.038325164999839
GO:0009191ribonucleoside diphosphate catabolic process0.038325164999839
GO:0009143nucleoside triphosphate catabolic process0.038325164999839
GO:0009185ribonucleoside diphosphate metabolic process0.038325164999839
GO:0009134nucleoside diphosphate catabolic process0.038325164999839
GO:0042627chylomicron0.038325164999839
GO:0009261ribonucleotide catabolic process0.038325164999839
GO:0050892intestinal absorption0.0447711166420025
GO:0017110nucleoside-diphosphatase activity0.0455877250377747



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>

Cell Type
Ontology termp-valuen
brush border epithelial cell3.68e-106
gut absorptive cell3.68e-106
absorptive cell3.68e-106
enterocyte3.68e-106
columnar/cuboidal epithelial cell1.51e-087

Uber Anatomy
Ontology termp-valuen
intestine1.17e-2531
gastrointestinal system2.01e-1847
mucosa2.78e-1415
intestinal mucosa2.80e-1113
anatomical wall2.80e-1113
wall of intestine2.80e-1113
gastrointestinal system mucosa2.80e-1113
organ component layer4.48e-0924
small intestine8.44e-074


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)
MA0003.13.46736e-07
MA0004.10.0226833
MA0006.10.00300774
MA0007.10.0198299
MA0009.10.214658
MA0014.10.000125913
MA0017.11.03437
MA0019.10.110663
MA0024.10.187051
MA0025.10.383522
MA0027.11.70825
MA0028.10.00354928
MA0029.10.516916
MA0030.10.177847
MA0031.10.157022
MA0038.10.226796
MA0040.10.222824
MA0041.10.0106718
MA0042.10.129556
MA0043.10.280639
MA0046.10.238407
MA0048.10.252422
MA0050.10.127551
MA0051.10.236374
MA0052.10.228144
MA0055.18.94103
MA0056.10
MA0057.10.418675
MA0058.10.00844533
MA0059.10.732375
MA0060.10.00475879
MA0061.10.155117
MA0063.10
MA0066.10.0594129
MA0067.10.473816
MA0068.10.0861753
MA0069.10.228369
MA0070.10.221972
MA0071.10.126877
MA0072.10.216436
MA0073.10.000670544
MA0074.10.712384
MA0076.10.00591694
MA0077.10.202534
MA0078.10.273203
MA0081.10.162164
MA0083.10.280072
MA0084.10.763469
MA0087.10.249896
MA0088.10.000105629
MA0089.10
MA0090.10.628492
MA0091.11.14721
MA0092.10.380534
MA0093.10.00402865
MA0095.10
MA0098.10
MA0100.10.0440101
MA0101.10.295268
MA0103.13.16741
MA0105.10.0119277
MA0106.10.0828885
MA0107.10.181682
MA0108.20.386694
MA0109.10
MA0111.10.0189154
MA0113.10.0714693
MA0114.13.8113
MA0115.11.41067
MA0116.10.0182401
MA0117.10.259864
MA0119.10.770704
MA0122.12.94743
MA0124.10.429916
MA0125.10.3708
MA0130.10
MA0131.10.108468
MA0132.10
MA0133.10
MA0135.11.49908
MA0136.10.439893
MA0139.10.501553
MA0140.10.382356
MA0141.11.58019
MA0142.10.148854
MA0143.10.268535
MA0144.11.76005
MA0145.10.103346
MA0146.10.00239899
MA0147.10.0104379
MA0148.10.110009
MA0149.10.0115146
MA0062.20.000862111
MA0035.22.57519
MA0039.24.27212e-06
MA0138.20.341255
MA0002.20.231171
MA0137.22.39745
MA0104.20.0143078
MA0047.20.0630718
MA0112.20.0164966
MA0065.22.37175
MA0150.10.221082
MA0151.10
MA0152.10.226097
MA0153.10.319381
MA0154.12.35288
MA0155.12.40062
MA0156.12.76651
MA0157.10.131489
MA0158.10
MA0159.12.81372
MA0160.12.07308
MA0161.10
MA0162.11.07638e-09
MA0163.10.0069236
MA0164.10.0540521
MA0080.20.0833902
MA0018.20.458858
MA0099.20.101721
MA0079.23.66396e-05
MA0102.20.812014
MA0258.10.229807
MA0259.10.629938
MA0442.10
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