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MCL coexpression mm9:340: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000945!2.77e-14!16;UBERON:0010039!2.77e-14!16;UBERON:0000014!8.78e-07!5;UBERON:0001003!8.78e-07!5;UBERON:0002097!8.78e-07!5;UBERON:0002199!8.78e-07!5;UBERON:0007029!8.78e-07!5;UBERON:0007376!8.78e-07!5;UBERON:0002416!8.78e-07!5;UBERON:0007383!8.78e-07!5
|tfbs_overrepresentation_for_novel_motifs=0.110832,0.0067908,0.0967691,0.831798,0.701412,0.442517,0.203465,1.77639,0.699778,0.0166489,0.173735,0.568323,0.0181895,0.212045,0.195204,0,0.359959,0.674982,0.0702244,0.272746,2.58909,0.880744,0.211409,2.02582,0.330779,0.23172,0.169642,0.156999,0.0645727,0.629469,0.148148,0.444875,1.03558,0.285662,0.19578,0.0718753,0.0394039,0.19269,0.131332,0.25408,0.687976,0.151372,0.793004,0.437292,0.158204,0.128506,0.296243,0.167123,1.11123,0.504749,0.345732,0.251452,0.378342,0.569522,0.585246,0.217101,0.525548,0.186482,0.155641,0.215654,0.427748,0.258489,0.464178,0.33663,0.22505,0.96703,0.710311,1.04299,0.423773,0.901202,0.0871308,0.418659,0.0106533,0.615662,0.0108504,0.267317,3.81785,0.287424,0.413185,1.45829,1.01841,0.374245,0.25741,0.197096,0.512157,0.000115462,0.000180154,0.403279,0.300065,1.20106,0.775527,0.516553,2.01401,0.72126,0.0311482,1.16319,0.394469,0.458317,0.803726,0.0823725,0.637194,0.444635,0.553884,0.915262,0.34536,0.151097,0.394568,0.49385,0.0827779,0.0792537,0.106955,0.555481,0.0809652,0.177151,0.78216,1.49568,0.00248467,0.426065,0.361025,0.346862,0.620583,0.319864,0.658005,1.42556,0.833329,0.416312,0.209158,0.450055,0.7089,0.415597,0.53872,0.130779,0.68148,0.226858,0.802533,0.159824,0.745293,0.152256,0.75625,1.56412,1.1699,0.714696,0.241832,0.45388,0.340119,0.151656,0.298675,1.52485,0.373295,0.0469598,0.0389106,0.000969399,0.570933,0.115918,0.226192,0.645175,0.70255,0.459789,0.353936,0.11537,0.765175,1.27377,0.416689,0.344026,0.895778,0.220885,0.633271,0.194075,0.0576766
|tfbs_overrepresentation_jaspar=MA0003.1;0.000126699,MA0004.1;0.135415,MA0006.1;0.0509523,MA0007.1;0.39838,MA0009.1;0.467692,MA0014.1;0.00392691,MA0017.1;0.061744,MA0019.1;0.315968,MA0024.1;0.430047,MA0025.1;0.677312,MA0027.1;2.06014,MA0028.1;0.055063,MA0029.1;0.411611,MA0030.1;0.417163,MA0031.1;0.387282,MA0038.1;0.65478,MA0040.1;0.478574,MA0041.1;0.0931678,MA0042.1;0.292213,MA0043.1;0.552986,MA0046.1;0.499059,MA0048.1;0.0277501,MA0050.1;0.159414,MA0051.1;0.238165,MA0052.1;0.485607,MA0055.1;0.168072,MA0056.1;0,MA0057.1;0.00389221,MA0058.1;0.0831725,MA0059.1;0.0892761,MA0060.1;0.0247719,MA0061.1;0.134639,MA0063.1;0,MA0066.1;0.223752,MA0067.1;0.78096,MA0068.1;0.16743,MA0069.1;1.21932,MA0070.1;0.477443,MA0071.1;0.932447,MA0072.1;1.18537,MA0073.1;3.76843e-08,MA0074.1;0.19855,MA0076.1;0.0701228,MA0077.1;1.14504,MA0078.1;0.726633,MA0081.1;0.101252,MA0083.1;1.36054,MA0084.1;1.09535,MA0087.1;0.513946,MA0088.1;0.0859682,MA0089.1;0,MA0090.1;0.369798,MA0091.1;1.39746,MA0092.1;1.2227,MA0093.1;0.212413,MA0095.1;0,MA0098.1;0,MA0100.1;0.190641,MA0101.1;0.644769,MA0103.1;0.507674,MA0105.1;0.0482315,MA0106.1;0.268507,MA0107.1;0.227901,MA0108.2;2.41831,MA0109.1;0,MA0111.1;0.123589,MA0113.1;0.691468,MA0114.1;0.569427,MA0115.1;0.555491,MA0116.1;0.422589,MA0117.1;0.526724,MA0119.1;0.0941347,MA0122.1;0.544387,MA0124.1;0.731064,MA0125.1;0.662359,MA0130.1;0,MA0131.1;0.312378,MA0132.1;0,MA0133.1;0,MA0135.1;0.585739,MA0136.1;0.609426,MA0139.1;0.078666,MA0140.1;0.557269,MA0141.1;0.940272,MA0142.1;0.375247,MA0143.1;0.259584,MA0144.1;0.0336011,MA0145.1;0.0410716,MA0146.1;0.00198396,MA0147.1;0.0375422,MA0148.1;0.445966,MA0149.1;0.0966891,MA0062.2;0.0103676,MA0035.2;0.193764,MA0039.2;0.00467971,MA0138.2;0.306125,MA0002.2;0.20637,MA0137.2;0.0740003,MA0104.2;0.0212101,MA0047.2;0.653482,MA0112.2;0.509613,MA0065.2;0.333255,MA0150.1;0.39821,MA0151.1;0,MA0152.1;1.21903,MA0153.1;0.600798,MA0154.1;0.178898,MA0155.1;0.0533867,MA0156.1;0.0697319,MA0157.1;0.348973,MA0158.1;0,MA0159.1;0.0409628,MA0160.1;0.450623,MA0161.1;0,MA0162.1;6.78264e-05,MA0163.1;0.00247972,MA0164.1;0.212655,MA0080.2;0.495494,MA0018.2;0.219518,MA0099.2;1.47794,MA0079.2;4.56197e-09,MA0102.2;1.14642,MA0258.1;0.284909,MA0259.1;0.0340942,MA0442.1;0
}}

Latest revision as of 15:08, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:80580869..80580904,+p4@Map2k2
Mm9::chr11:121463007..121463024,+p6@Tbcd
Mm9::chr15:59626509..59626514,-p1@Gm19510
Mm9::chr15:74564722..74564729,-p2@Lypd2
Mm9::chr18:20220073..20220091,-p@chr18:20220073..20220091
-
Mm9::chr18:20220148..20220153,-p@chr18:20220148..20220153
-
Mm9::chr2:127570249..127570296,-p2@Nphp1
Mm9::chr2:30049671..30049687,-p3@Ccbl1
Mm9::chr3:125681557..125681568,-p@chr3:125681557..125681568
-
Mm9::chr3:92222001..92222010,+p1@Sprr2j-ps
Mm9::chr3:92222042..92222055,+p2@Sprr2j-ps
Mm9::chr3:92236500..92236507,+p1@Sprr2k
Mm9::chr3:92260735..92260763,+p@chr3:92260735..92260763
+
Mm9::chr3:92261115..92261125,-p@chr3:92261115..92261125
-
Mm9::chr3:92261163..92261174,-p@chr3:92261163..92261174
-
Mm9::chr3:92261211..92261222,-p@chr3:92261211..92261222
-
Mm9::chr3:92261253..92261263,-p@chr3:92261253..92261263
-
Mm9::chr3:92262637..92262652,-p1@Sprr3
Mm9::chr3:93201855..93201866,+p@chr3:93201855..93201866
+
Mm9::chr3:93202135..93202148,+p@chr3:93202135..93202148
+
Mm9::chr6:55434602..55434607,+p@chr6:55434602..55434607
+
Mm9::chr7:26152711..26152722,-p@chr7:26152711..26152722
-
Mm9::chr7:26154731..26154749,-p1@Cnfn


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:0001533cornified envelope5.77541237792595e-06
GO:0031424keratinization7.39858915949517e-06
GO:0009913epidermal cell differentiation1.1018611209622e-05
GO:0048730epidermis morphogenesis2.31959133667652e-05
GO:0048729tissue morphogenesis6.76484108271804e-05
GO:0008544epidermis development0.000118616180189891
GO:0007398ectoderm development0.000118616180189891
GO:0009888tissue development0.00219537389489957
GO:0047316glutamine-phenylpyruvate transaminase activity0.00448023764738825
GO:0047804cysteine-S-conjugate beta-lyase activity0.00806288133218585
GO:0016212kynurenine-oxoglutarate transaminase activity0.010992729869998
GO:00168471-aminocyclopropane-1-carboxylate synthase activity0.0134329824711121
GO:0016846carbon-sulfur lyase activity0.0278725354145116
GO:0005856cytoskeleton0.0319885563879413



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
stomach2.77e-1416
food storage organ2.77e-1416
zone of skin8.78e-075
skin epidermis8.78e-075
skin of body8.78e-075
integument8.78e-075
surface8.78e-075
outer epithelium8.78e-075
integumental system8.78e-075
enveloping layer of ectoderm8.78e-075


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)
MA0003.10.000126699
MA0004.10.135415
MA0006.10.0509523
MA0007.10.39838
MA0009.10.467692
MA0014.10.00392691
MA0017.10.061744
MA0019.10.315968
MA0024.10.430047
MA0025.10.677312
MA0027.12.06014
MA0028.10.055063
MA0029.10.411611
MA0030.10.417163
MA0031.10.387282
MA0038.10.65478
MA0040.10.478574
MA0041.10.0931678
MA0042.10.292213
MA0043.10.552986
MA0046.10.499059
MA0048.10.0277501
MA0050.10.159414
MA0051.10.238165
MA0052.10.485607
MA0055.10.168072
MA0056.10
MA0057.10.00389221
MA0058.10.0831725
MA0059.10.0892761
MA0060.10.0247719
MA0061.10.134639
MA0063.10
MA0066.10.223752
MA0067.10.78096
MA0068.10.16743
MA0069.11.21932
MA0070.10.477443
MA0071.10.932447
MA0072.11.18537
MA0073.13.76843e-08
MA0074.10.19855
MA0076.10.0701228
MA0077.11.14504
MA0078.10.726633
MA0081.10.101252
MA0083.11.36054
MA0084.11.09535
MA0087.10.513946
MA0088.10.0859682
MA0089.10
MA0090.10.369798
MA0091.11.39746
MA0092.11.2227
MA0093.10.212413
MA0095.10
MA0098.10
MA0100.10.190641
MA0101.10.644769
MA0103.10.507674
MA0105.10.0482315
MA0106.10.268507
MA0107.10.227901
MA0108.22.41831
MA0109.10
MA0111.10.123589
MA0113.10.691468
MA0114.10.569427
MA0115.10.555491
MA0116.10.422589
MA0117.10.526724
MA0119.10.0941347
MA0122.10.544387
MA0124.10.731064
MA0125.10.662359
MA0130.10
MA0131.10.312378
MA0132.10
MA0133.10
MA0135.10.585739
MA0136.10.609426
MA0139.10.078666
MA0140.10.557269
MA0141.10.940272
MA0142.10.375247
MA0143.10.259584
MA0144.10.0336011
MA0145.10.0410716
MA0146.10.00198396
MA0147.10.0375422
MA0148.10.445966
MA0149.10.0966891
MA0062.20.0103676
MA0035.20.193764
MA0039.20.00467971
MA0138.20.306125
MA0002.20.20637
MA0137.20.0740003
MA0104.20.0212101
MA0047.20.653482
MA0112.20.509613
MA0065.20.333255
MA0150.10.39821
MA0151.10
MA0152.11.21903
MA0153.10.600798
MA0154.10.178898
MA0155.10.0533867
MA0156.10.0697319
MA0157.10.348973
MA0158.10
MA0159.10.0409628
MA0160.10.450623
MA0161.10
MA0162.16.78264e-05
MA0163.10.00247972
MA0164.10.212655
MA0080.20.495494
MA0018.20.219518
MA0099.21.47794
MA0079.24.56197e-09
MA0102.21.14642
MA0258.10.284909
MA0259.10.0340942
MA0442.10
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