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MCL coexpression mm9:209: Difference between revisions

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{{MCL_coexpression_mm9
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of synaptic transmission, cholinergic;0.0332000219142059;16773!GO:0047045;testosterone 17-beta-dehydrogenase (NADP+) activity;0.0332000219142059;15487!GO:0032224;positive regulation of synaptic transmission, cholinergic;0.0332000219142059;16773!GO:0003708;retinoic acid receptor activity;0.0398138396827877;19401!GO:0033327;Leydig cell differentiation;0.0398138396827877;13363!GO:0016539;intein-mediated protein splicing;0.0398138396827877;13363!GO:0030908;protein splicing;0.0398138396827877;13363!GO:0051971;positive regulation of transmission of nerve impulse;0.0398138396827877;16773!GO:0050806;positive regulation of synaptic transmission;0.0398138396827877;16773!GO:0031646;positive regulation of neurological process;0.0398138396827877;16773!GO:0005606;laminin-1 complex;0.0452330855396336;16773!GO:0055012;ventricular cardiac muscle cell differentiation;0.0497345914387747;19401!GO:0045995;regulation of embryonic development;0.0497345914387747;16773!GO:0043256;laminin 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|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000991!3.79e-54!18;UBERON:0005564!3.79e-54!18;UBERON:0000473!2.57e-50!14;UBERON:0004176!6.44e-49!17;UBERON:0009196!6.44e-49!17;UBERON:0009117!6.44e-49!17;UBERON:0003135!6.86e-47!15;UBERON:0003101!6.83e-44!16;UBERON:0000079!6.83e-44!16;UBERON:0003133!2.70e-40!24;UBERON:0005156!4.28e-37!26;UBERON:0000990!4.28e-37!26;UBERON:0002323!1.16e-25!37;UBERON:0004458!1.16e-25!37;UBERON:0003886!5.98e-25!38;UBERON:0002553!2.83e-24!39;UBERON:0000464!3.82e-16!57;UBERON:0000466!3.28e-11!79;UBERON:0000926!4.29e-08!120;UBERON:0004120!4.29e-08!120;UBERON:0006603!4.29e-08!120
|tfbs_overrepresentation_for_novel_motifs=0.495452,0.271481,0.0900774,0.335188,0.351047,0.646369,0.0718138,1.03584,0.843934,0.0506675,0.20331,0.511208,1.64436,0.265233,0.225204,0,0.176334,0.329859,0.690214,0.835314,0.34538,0.820435,0.0764323,0.0885618,0.236835,0.619784,0.64021,0.177214,0.0498912,0.406379,0.163695,0.678623,0.0266111,0.528641,0.106652,0.0022893,0.0235712,0.2336,0.862031,0.0380874,1.42448,0.168596,0.552711,0.228917,0.770007,0.134478,0.409098,0.428539,1.43181,0.286874,0.165852,0.101004,0.154505,0.91327,0.358841,0.2736,1.89899,0.223599,1.30871,0.078937,0.646878,0.105528,0.302626,0.159231,0.286837,0.183542,0.469298,0.779659,0.22516,0.645209,0.0169719,0.820833,0.0195685,0.385253,0.0122692,0.673127,0.947923,0.124708,0.62,0.180201,0.412471,0.187017,0.341652,0.125815,0.296819,0.000210738,2.8068,0.172237,0.41582,0.932016,0.528571,0.300486,0.250717,0.579797,0.124972,0.739012,1.01683,0.25267,0.130864,1.80749,2.06002,0.241691,0.331962,0.166205,0.16558,0.168176,0.202468,0.188857,0.0155042,0.0674785,0.103893,0.333321,0.0696149,0.0571943,0.534653,1.41104,0.000827764,0.0373393,0.177127,1.28221,0.389556,0.14722,1.04381,0.784165,0.581865,0.219311,0.0751141,0.246028,0.468027,0.0336037,0.854779,0.137799,1.12798,0.0856656,1.3629,3.24765,0.027755,0.684179,0.510949,1.28785,0.901817,6.56864,0.315088,0.69537,0.487049,0.169029,0.819982,1.24909,0.282602,0.005597,1.00553,0.00127415,0.346528,0.356373,1.50581,2.785,0.680878,1.29491,0.261535,0.115631,0.519098,0.29619,1.17469,0.250896,0.159827,0.587532,0.161463,0.235842,0.0132001
|tfbs_overrepresentation_jaspar=MA0003.1;0.000579246,MA0004.1;0.144622,MA0006.1;0.101746,MA0007.1;0.567443,MA0009.1;0.260251,MA0014.1;4.6029e-05,MA0017.1;0.129813,MA0019.1;0.144464,MA0024.1;0.230104,MA0025.1;5.09679,MA0027.1;1.78014,MA0028.1;0.00747391,MA0029.1;0.215644,MA0030.1;0.219976,MA0031.1;0.196896,MA0038.1;0.297921,MA0040.1;0.741478,MA0041.1;0.413962,MA0042.1;0.383143,MA0043.1;0.881833,MA0046.1;0.285948,MA0048.1;0.20449,MA0050.1;1.55665,MA0051.1;1.57613,MA0052.1;0.274867,MA0055.1;0.345744,MA0056.1;0,MA0057.1;0.0992152,MA0058.1;0.0723945,MA0059.1;0.395928,MA0060.1;0.0392157,MA0061.1;1.87379,MA0063.1;0,MA0066.1;0.0837834,MA0067.1;0.533552,MA0068.1;0.0574526,MA0069.1;0.27511,MA0070.1;0.268186,MA0071.1;0.714064,MA0072.1;1.33542,MA0073.1;2.28008,MA0074.1;0.521239,MA0076.1;0.0115448,MA0077.1;0.247052,MA0078.1;0.712087,MA0081.1;1.47206,MA0083.1;0.330594,MA0084.1;0.829882,MA0087.1;0.807952,MA0088.1;0.275995,MA0089.1;0,MA0090.1;0.27877,MA0091.1;0.156491,MA0092.1;0.517784,MA0093.1;0.121134,MA0095.1;0,MA0098.1;0,MA0100.1;0.0645544,MA0101.1;0.682443,MA0103.1;0.289464,MA0105.1;0.131702,MA0106.1;0.112066,MA0107.1;1.39135,MA0108.2;0.157468,MA0109.1;0,MA0111.1;0.877264,MA0113.1;0.324571,MA0114.1;0.0175858,MA0115.1;0.333331,MA0116.1;0.216774,MA0117.1;0.832079,MA0119.1;1.39346,MA0122.1;0.323899,MA0124.1;0.488052,MA0125.1;0.426393,MA0130.1;0,MA0131.1;0.141936,MA0132.1;0,MA0133.1;0,MA0135.1;0.359267,MA0136.1;0.265819,MA0139.1;0.231732,MA0140.1;1.29339,MA0141.1;5.3491,MA0142.1;0.550541,MA0143.1;0.345382,MA0144.1;0.421754,MA0145.1;0.144474,MA0146.1;0.024967,MA0147.1;0.15457,MA0148.1;0.364643,MA0149.1;0.0203741,MA0062.2;0.00274296,MA0035.2;0.870209,MA0039.2;0.000343349,MA0138.2;1.96706,MA0002.2;1.9796,MA0137.2;0.324882,MA0104.2;0.0797526,MA0047.2;0.296989,MA0112.2;0.22277,MA0065.2;0.0231909,MA0150.1;1.28896,MA0151.1;0,MA0152.1;0.297119,MA0153.1;0.372306,MA0154.1;0.781281,MA0155.1;0.0343506,MA0156.1;0.01143,MA0157.1;0.168226,MA0158.1;0,MA0159.1;0.0767394,MA0160.1;1.45823,MA0161.1;0,MA0162.1;0.00104847,MA0163.1;0.0317133,MA0164.1;0.953974,MA0080.2;0.136094,MA0018.2;0.0812385,MA0099.2;0.827507,MA0079.2;5.12975e-08,MA0102.2;0.879116,MA0258.1;0.557032,MA0259.1;0.138577,MA0442.1;0
}}

Latest revision as of 14:53, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:27336825..27336853,-p4@Lama2
Mm9::chr10:80266026..80266037,+p@chr10:80266026..80266037
+
Mm9::chr10:80268873..80268886,+p@chr10:80268873..80268886
+
Mm9::chr11:98826125..98826141,+p12@Rara
Mm9::chr12:15613141..15613159,+p@chr12:15613141..15613159
+
Mm9::chr12:15613173..15613196,+p@chr12:15613173..15613196
+
Mm9::chr13:64185792..64185799,-p@chr13:64185792..64185799
-
Mm9::chr13:64190453..64190472,-p2@Hsd17b3
Mm9::chr13:64190487..64190500,-p3@Hsd17b3
Mm9::chr13:64190505..64190516,-p4@Hsd17b3
Mm9::chr13:64190530..64190544,-p1@Hsd17b3
Mm9::chr13:64190565..64190575,-p5@Hsd17b3
Mm9::chr13:64190682..64190702,-p6@Hsd17b3
Mm9::chr13:64190730..64190737,-p8@Hsd17b3
Mm9::chr14:52854959..52854970,-p@chr14:52854959..52854970
-
Mm9::chr15:25584890..25584921,+p@chr15:25584890..25584921
+
Mm9::chr15:98728914..98728989,-p1@Dhh
Mm9::chr17:24610840..24610867,+p1@9930021D14Rik
Mm9::chr17:26343369..26343379,-p@chr17:26343369..26343379
-
Mm9::chr17:26343389..26343398,-p@chr17:26343389..26343398
-
Mm9::chr19:45151174..45151192,+p@chr19:45151174..45151192
+
Mm9::chr19:45151197..45151217,+p@chr19:45151197..45151217
+
Mm9::chr1:75503214..75503225,-p11@Obsl1
Mm9::chr2:152757674..152757681,+p@chr2:152757674..152757681
+
Mm9::chr3:87804937..87804965,-p@chr3:87804937..87804965
-
Mm9::chr3:9028360..9028371,+p@chr3:9028360..9028371
+
Mm9::chr5:104863543..104863571,+p@chr5:104863543..104863571
+
Mm9::chr5:114411821..114411827,-p@chr5:114411821..114411827
-
Mm9::chr5:117768747..117768768,+p@chr5:117768747..117768768
+
Mm9::chr5:123229458..123229472,-p2@Camkk2
Mm9::chr6:113343056..113343076,+p4@Ttll3
Mm9::chr6:52911717..52911733,-p@chr6:52911717..52911733
-
Mm9::chr6:83138985..83138996,+p10@Dctn1
Mm9::chr6:92777628..92777657,+p2@ENSMUST00000133858
Mm9::chr6:92777666..92777679,+p3@ENSMUST00000133858
Mm9::chr7:104599777..104599780,+p5@Kctd14
Mm9::chr7:122456428..122456433,-p@chr7:122456428..122456433
-
Mm9::chr7:151449983..151449996,+p@chr7:151449983..151449996
+
Mm9::chr7:151450010..151450017,+p@chr7:151450010..151450017
+
Mm9::chr8:97519604..97519648,+p@chr8:97519604..97519648
+
Mm9::chr8:97519650..97519661,+p@chr8:97519650..97519661
+
Mm9::chr9:62620734..62620748,+p@chr9:62620734..62620748
+
Mm9::chr9:83143732..83143739,-p@chr9:83143732..83143739
-
Mm9::chr9:83143828..83143845,-p@chr9:83143828..83143845
-


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:0032222regulation of synaptic transmission, cholinergic0.0332000219142059
GO:0047045testosterone 17-beta-dehydrogenase (NADP+) activity0.0332000219142059
GO:0032224positive regulation of synaptic transmission, cholinergic0.0332000219142059
GO:0003708retinoic acid receptor activity0.0398138396827877
GO:0033327Leydig cell differentiation0.0398138396827877
GO:0016539intein-mediated protein splicing0.0398138396827877
GO:0030908protein splicing0.0398138396827877
GO:0051971positive regulation of transmission of nerve impulse0.0398138396827877
GO:0050806positive regulation of synaptic transmission0.0398138396827877
GO:0031646positive regulation of neurological process0.0398138396827877
GO:0005606laminin-1 complex0.0452330855396336
GO:0055012ventricular cardiac muscle cell differentiation0.0497345914387747
GO:0045995regulation of embryonic development0.0497345914387747
GO:0043256laminin complex0.0497345914387747



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)
MA0003.10.000579246
MA0004.10.144622
MA0006.10.101746
MA0007.10.567443
MA0009.10.260251
MA0014.14.6029e-05
MA0017.10.129813
MA0019.10.144464
MA0024.10.230104
MA0025.15.09679
MA0027.11.78014
MA0028.10.00747391
MA0029.10.215644
MA0030.10.219976
MA0031.10.196896
MA0038.10.297921
MA0040.10.741478
MA0041.10.413962
MA0042.10.383143
MA0043.10.881833
MA0046.10.285948
MA0048.10.20449
MA0050.11.55665
MA0051.11.57613
MA0052.10.274867
MA0055.10.345744
MA0056.10
MA0057.10.0992152
MA0058.10.0723945
MA0059.10.395928
MA0060.10.0392157
MA0061.11.87379
MA0063.10
MA0066.10.0837834
MA0067.10.533552
MA0068.10.0574526
MA0069.10.27511
MA0070.10.268186
MA0071.10.714064
MA0072.11.33542
MA0073.12.28008
MA0074.10.521239
MA0076.10.0115448
MA0077.10.247052
MA0078.10.712087
MA0081.11.47206
MA0083.10.330594
MA0084.10.829882
MA0087.10.807952
MA0088.10.275995
MA0089.10
MA0090.10.27877
MA0091.10.156491
MA0092.10.517784
MA0093.10.121134
MA0095.10
MA0098.10
MA0100.10.0645544
MA0101.10.682443
MA0103.10.289464
MA0105.10.131702
MA0106.10.112066
MA0107.11.39135
MA0108.20.157468
MA0109.10
MA0111.10.877264
MA0113.10.324571
MA0114.10.0175858
MA0115.10.333331
MA0116.10.216774
MA0117.10.832079
MA0119.11.39346
MA0122.10.323899
MA0124.10.488052
MA0125.10.426393
MA0130.10
MA0131.10.141936
MA0132.10
MA0133.10
MA0135.10.359267
MA0136.10.265819
MA0139.10.231732
MA0140.11.29339
MA0141.15.3491
MA0142.10.550541
MA0143.10.345382
MA0144.10.421754
MA0145.10.144474
MA0146.10.024967
MA0147.10.15457
MA0148.10.364643
MA0149.10.0203741
MA0062.20.00274296
MA0035.20.870209
MA0039.20.000343349
MA0138.21.96706
MA0002.21.9796
MA0137.20.324882
MA0104.20.0797526
MA0047.20.296989
MA0112.20.22277
MA0065.20.0231909
MA0150.11.28896
MA0151.10
MA0152.10.297119
MA0153.10.372306
MA0154.10.781281
MA0155.10.0343506
MA0156.10.01143
MA0157.10.168226
MA0158.10
MA0159.10.0767394
MA0160.11.45823
MA0161.10
MA0162.10.00104847
MA0163.10.0317133
MA0164.10.953974
MA0080.20.136094
MA0018.20.0812385
MA0099.20.827507
MA0079.25.12975e-08
MA0102.20.879116
MA0258.10.557032
MA0259.10.138577
MA0442.10
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