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MCL coexpression mm9:161: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0000349!2.21e-20!3;CL:0000351!2.21e-20!3
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000358!2.21e-20!3;UBERON:0000307!2.21e-20!3;UBERON:0007010!2.21e-20!3;UBERON:0005631!2.57e-20!3;UBERON:0000478!2.57e-20!3;UBERON:0000158!2.57e-20!3;UBERON:0005795!2.38e-15!4;UBERON:0000995!2.38e-15!4;UBERON:0001987!2.90e-14!2;UBERON:0003124!2.90e-14!2;UBERON:0004340!2.90e-14!2;UBERON:0003975!2.13e-12!5;UBERON:0003133!2.71e-09!24;UBERON:0005156!1.49e-08!26;UBERON:0000990!1.49e-08!26;UBERON:0003134!6.04e-08!8;UBERON:0000305!9.86e-08!1;UBERON:0006834!1.14e-07!1;UBERON:0004175!4.09e-07!9;UBERON:0000474!4.09e-07!9
|tfbs_overrepresentation_for_novel_motifs=0.550881,0.73628,0.154907,0.0453708,0.174234,0.493604,0.255143,0.220346,0.873763,1.15619,0.940138,0.238231,0.327282,1.60372,0.0544662,0,0.296236,0.576766,0.267091,0.560097,0.211526,0.265314,0.271606,0.171213,0.0740578,2.81536,0.341601,0.835905,0.158237,0.769282,0.780918,0.135777,0.154812,1.00558,1.21009,0.058071,0.361243,0.443162,0.180561,0.0661574,0.275753,0.15481,0.147961,0.343535,1.09016,0.424323,0.8013,0.183603,0.584169,0.16305,0.276376,0.358322,1.50126,0.62368,1.21345,0.283562,0.305768,0.220896,0.418678,0.280511,0.125514,0.374137,0.0287964,0.947648,0.300477,0.0930137,0.32505,0.611288,0.779476,0.484899,1.84017,1.30073,0.0460867,0.252042,0.18476,0.443868,0.639183,0.440711,0.373725,0.367758,0.243169,0.316558,0.163008,0.200835,0.178777,0.0529932,0.0827423,0.172474,0.215447,0.757302,0.378015,1.02577,0.439074,0.0171375,0.0974399,1.32365,0.444604,0.442858,0.461928,0.168107,0.521621,0.135631,0.207371,0.0810325,0.580331,0.0573212,0.106502,0.178739,0.816441,0.0466808,0.0828215,0.208492,0.115357,0.0174626,1.7679,0.412018,0.0418495,0.714242,0.29774,0.347998,0.25571,0.517962,0.579007,0.198544,0.426467,0.118828,0.266912,0.138939,0.323926,0.88769,0.196823,0.249421,0.302288,0.128584,0.400489,1.53315,0.367053,0.314065,0.362159,1.10499,0.728176,0.328549,0.954774,0.435937,1.43435,0.312218,0.213666,1.06682,0.372874,0.441454,0.117054,0.0065424,0.219435,0.506615,0.127866,0.27426,0.645345,0.553077,0.542589,0.0323265,0.369481,0.178272,0.761095,0.178681,0.0767232,0.0296284,1.77327,0.447724,0.182671
}}

Latest revision as of 14:48, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:79390075..79390115,+p2@Arid3a
Mm9::chr10:79390120..79390129,+p4@Arid3a
Mm9::chr11:104469314..104469326,+p3@Itgb3
Mm9::chr11:107408246..107408290,+p@chr11:107408246..107408290
+
Mm9::chr11:57646181..57646192,-p@chr11:57646181..57646192
-
Mm9::chr11:97459817..97459838,+p1@2410003L11Rik
Mm9::chr12:18394291..18394302,+p1@ENSMUST00000080502
Mm9::chr13:33119401..33119416,+p1@Serpinb9b
Mm9::chr13:33250231..33250243,-p2@Serpinb9c
Mm9::chr13:33284821..33284833,+p1@Serpinb9d
Mm9::chr14:70723590..70723605,-p4@Slc39a14
Mm9::chr16:17233653..17233683,+p1@Hic2
Mm9::chr16:33985120..33985122,+p@chr16:33985120..33985122
+
Mm9::chr17:45709444..45709455,-p16@Hsp90ab1
Mm9::chr17:56562125..56562160,-p@chr17:56562125..56562160
-
Mm9::chr1:135069525..135069528,+p@chr1:135069525..135069528
+
Mm9::chr2:10292892..10292915,+p@chr2:10292892..10292915
+
Mm9::chr2:104689622..104689640,-p2@Prrg4
Mm9::chr2:172371173..172371185,+p@chr2:172371173..172371185
+
Mm9::chr2:172375136..172375149,+p2@Tfap2c
Mm9::chr2:172376261..172376267,+p4@Tfap2c
Mm9::chr2:172376528..172376543,+p3@Tfap2c
Mm9::chr2:172377022..172377035,+p@chr2:172377022..172377035
+
Mm9::chr3:41359645..41359667,+p3@Phf17
Mm9::chr4:127007791..127007870,-p1@Gjb3
Mm9::chr4:127035368..127035431,-p1@Gjb5
Mm9::chr4:127035439..127035452,-p3@Gjb5
Mm9::chr4:129852357..129852382,-p2@Tinagl1
Mm9::chr5:109985549..109985572,-p@chr5:109985549..109985572
-
Mm9::chr5:120998338..120998349,-p@chr5:120998338..120998349
-
Mm9::chr5:30062377..30062390,+p4@Dnajb6
Mm9::chr6:4708451..4708464,+p@chr6:4708451..4708464
+
Mm9::chr6:4710113..4710124,+p@chr6:4710113..4710124
+
Mm9::chr7:134891681..134891691,+p9@Fbxl19
Mm9::chr7:135073489..135073494,-p3@Prss8
Mm9::chr7:147123950..147123998,+p@chr7:147123950..147123998
+
Mm9::chr7:150688420..150688437,-p1@Phlda2
Mm9::chr7:29478031..29478040,+p8@Fbxo27
Mm9::chr7:29922648..29922661,+p@chr7:29922648..29922661
+
Mm9::chr7:3169086..3169093,-p3@AU018091
Mm9::chr7:49994357..49994363,-p@chr7:49994357..49994363
-
Mm9::chr7:50333422..50333437,+p@chr7:50333422..50333437
+
Mm9::chr9:100498105..100498143,+p7@Stag1
Mm9::chr9:100498372..100498421,+p6@Stag1
Mm9::chr9:14419741..14419753,-p12@Amotl1
Mm9::chr9:14419862..14419869,-p17@Amotl1
Mm9::chr9:62659233..62659283,-p4@Fem1b
Mm9::chr9:97176146..97176173,+p@chr9:97176146..97176173
+
Mm9::chrX:136596834..136596879,-p4@Nup62cl
Mm9::chrX:136596987..136596999,-p3@Nup62cl
Mm9::chrX:136597089..136597122,-p2@Nup62cl
Mm9::chrX:136597123..136597144,-p1@Nup62cl
Mm9::chrX:136597258..136597265,-p5@Nup62cl
Mm9::chrX:34750993..34751005,-p1@Gm9
Mm9::chrX:35929343..35929364,-p7@Cul4b
Mm9::chrX:35929366..35929381,-p4@Cul4b
Mm9::chrX:50467569..50467589,-p1@Plac1
Mm9::chrX:61426720..61426733,+p1@3830417A13Rik
Mm9::chrX:69058113..69058134,+p@chrX:69058113..69058134
+
Mm9::chrX:69058139..69058146,+p@chrX:69058139..69058146
+
Mm9::chrX:69058149..69058160,+p@chrX:69058149..69058160
+
Mm9::chrX:70884737..70884749,+p2@Dusp9
Mm9::chrX:70884753..70884775,+p1@Dusp9
Mm9::chrX:70884778..70884781,+p4@Dusp9
Mm9::chrX:70885456..70885468,+p@chrX:70885456..70885468
+
Mm9::chrX:70885500..70885511,+p@chrX:70885500..70885511
+
Mm9::chrX:70886090..70886121,+p@chrX:70886090..70886121
+
Mm9::chrX:91395970..91395977,-p@chrX:91395970..91395977
-


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:0022829wide pore channel activity0.0205594866160349
GO:0005243gap junction channel activity0.0205594866160349
GO:0005922connexon complex0.0205594866160349
GO:0004867serine-type endopeptidase inhibitor activity0.0205594866160349
GO:0005921gap junction0.0235609285926919
GO:0001890placenta development0.0235609285926919
GO:0004866endopeptidase inhibitor activity0.0288628581844393
GO:0030414protease inhibitor activity0.0288628581844393
GO:0005911intercellular junction0.0288628581844393
GO:0015093ferrous iron transmembrane transporter activity0.030055333369857
GO:0014704intercalated disc0.0356811463156563



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
extraembryonic cell2.21e-203
trophoblast cell2.21e-203

Uber Anatomy
Ontology termp-valuen
blastocyst2.21e-203
blastula2.21e-203
cleaving embryo2.21e-203
extraembryonic membrane2.57e-203
extraembryonic structure2.57e-203
membranous layer2.57e-203
embryonic uterus2.38e-154
uterus2.38e-154
placenta2.90e-142
chorion2.90e-142
allantois2.90e-142
internal female genitalia2.13e-125
reproductive organ2.71e-0924
reproductive structure1.49e-0826
reproductive system1.49e-0826
female reproductive organ6.04e-088
amnion9.86e-081
uterus or analog1.14e-071
internal genitalia4.09e-079
female reproductive system4.09e-079


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)
MA0003.10.979071
MA0004.10.455252
MA0006.10.0190027
MA0007.10.237087
MA0009.10.149897
MA0014.11.3137
MA0017.12.06804
MA0019.10.508551
MA0024.11.29472
MA0025.10.299033
MA0027.11.59306
MA0028.10.356159
MA0029.10.747963
MA0030.10.119321
MA0031.10.102488
MA0038.10.574274
MA0040.10.156803
MA0041.11.94429
MA0042.10.854935
MA0043.10.206742
MA0046.10.170091
MA0048.10.248033
MA0050.10.336282
MA0051.10.140991
MA0052.10.161323
MA0055.10.315297
MA0056.10
MA0057.10.275308
MA0058.10.0513007
MA0059.10.135744
MA0060.12.8577
MA0061.11.5835
MA0063.10
MA0066.10.547234
MA0067.10.382513
MA0068.10.213247
MA0069.10.161515
MA0070.10.15608
MA0071.10.847612
MA0072.11.44607
MA0073.11.03558
MA0074.10.462514
MA0076.10.685272
MA0077.10.139722
MA0078.10.169181
MA0081.10.0242635
MA0083.10.206245
MA0084.10.659146
MA0087.10.179974
MA0088.10.477754
MA0089.10
MA0090.10.841082
MA0091.10.0103231
MA0092.10.367789
MA0093.10.240778
MA0095.10
MA0098.10
MA0100.10.43643
MA0101.10.147313
MA0103.10.286056
MA0105.10.338932
MA0106.11.53211
MA0107.11.75241
MA0108.20.0751434
MA0109.10
MA0111.10.40249
MA0113.10.038551
MA0114.13.34072
MA0115.11.13169
MA0116.10.109241
MA0117.10.552547
MA0119.10.669324
MA0122.10.200745
MA0124.10.341692
MA0125.10.287434
MA0130.10
MA0131.10.499912
MA0132.10
MA0133.10
MA0135.10.230079
MA0136.10.273678
MA0139.10.208358
MA0140.10.436174
MA0141.11.00036
MA0142.10.655046
MA0143.11.97111
MA0144.14.26965
MA0145.10.259404
MA0146.10.103806
MA0147.10.34148
MA0148.10.0106709
MA0149.10.0218927
MA0062.21.7248
MA0035.20.0947456
MA0039.22.16027
MA0138.20.0621398
MA0002.20.452505
MA0137.21.9702
MA0104.20.100688
MA0047.20.0329327
MA0112.20.0323037
MA0065.23.49382
MA0150.10.415319
MA0151.10
MA0152.12.25744
MA0153.10.241059
MA0154.11.48711
MA0155.10.130021
MA0156.11.52963
MA0157.10.0824096
MA0158.10
MA0159.10.969919
MA0160.10.508282
MA0161.10
MA0162.10.223656
MA0163.10.519238
MA0164.10.814807
MA0080.20.428202
MA0018.20.532845
MA0099.20.216885
MA0079.20.891731
MA0102.20.706336
MA0258.10.153154
MA0259.10.44718
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:161&oldid=3072160"