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MCL coexpression mm9:182: Difference between revisions

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{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.153880826611225,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0617533076901792,0,0,0,0,0,0.117729217788871,0,0,0,0,0,0.0438795366937978,0,0,0,0,0,0,0,0,0,0,0.0469568706916304,0.0201240793641256,0.112901225419538,0.0207607123523015,0,0.0206030317439609,0.114425913041783,0.148506588447784,0.0514097768499148,0.174463933976285,0.110319863569628,0,0.0651189800845078,0.158869788505911,0,0,0.0385665907204561,0.0669668960965366,0,0,0,0,0.0606187686764715,0,0,0.0696031033168343,0.0458432280665598,0.0819907263755358,0.0652962901395099,0.0805105854221362,0.0509235292940968,0.0926821660500116,0.00998563100978843,0,0,0,0.0609639314262262,0.055406237837571,0.0523528812100954,0.0215502939106758,0.128773541986592,0,0,0,0,0.0215640332643444,0.0209547445151271,0.0812688455295622,0,0,0,0,0,0.0915002620172692,0.0719048481885784,0.0453231997000282,0.0926606817691936,0.116785086449131,0.165857749845381,0.103212884397651,0.166448281439834,0.127300564333298,0.364239413353659,0.237950519184841,0.23829705210096,0.221413475632559,0.186624607472909,0,0.0425379529581421,0,0,0.011005690177518,0.0129920886107978,0,0,0.00535500813108725,0,0,0.0662136857075299,0.0834657004726295,0.00689854303922023,0.0558839010423019,0,0.0849828766602549,0.0788703512227347,0,0.0893741091821246,0,0.148387507215387,0.142359732304287,0.173463294671616,0.195658603019455,0.159215297421721,0.211653043078159,0.136781266430475,0.0597086398946045,0,0,0,0,0,0,0,0.172137356316638,0.10536076625968,0.725343592025448,0.137398724818722,0.210606173730573,0.17199550242317,0.0716601710131013,0.170978156452844,0.531707688093908,0,0.0495622797347119,0.0799826606478215,0.193034057987777,0.125485336951101,0.234043989592131,0.582161400428896,0.506084336604706,0.680201872303073,0.653984380441187,0.905586642068648,0.825075366789607,0.812690421248762,0,0,0,0.0535006778525544,0.0646640766951323,0.0481354699899057,0,0.0977676536600382,0,0,0,0,0,0,0,0,0,0,0.0576433181427177,0,0.060487198139331,0.0663147875126409,0,0,0,0,0,0,0.0443776375478306,0,0.0236025764468866,0.119268019631849,0,0,0,0,0,0,0,0.0636690261430045,0.0385741412904134,0,0.167123311310189,0.153407546465022,0,0.0662835200988411,0.0650059127791652,0.0494606362651129,0,0,0.111087966368681,0.0738741926906438,0,0,0.136843881272943,0.0857271995061012,0.055643654597214,0.0894734883806707,0,0,0,0,0,0,0.0445418537893845,0.0824580172145032,0.0857765460992942,0.0805698793017906,0.0703440807961409,0.0618374048633924,0.100105043383282,0,0,0,0,0,0,0.0677982110636083,0.0915665403705771,0.0531569878936061,0.0433069931089932,0.03346092271514,0.0348767343276367,0,0,0.0424616899933645,0,0,0,0,0,0,0.00109315305376106,0,0,0,0,0.0887491219977394,0,0,0,0,0.138417952808354,0.1176914972494,0.0124455767696781,0,0,0,0,0.0688732037536692,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0455176435646802,0.0371532349352818,0.0145301236673661,0.0531827301773239,0.0293468760001098,0.0472245945615809,0,0.0476191773904887,0.0766073954291401,0,0.0596387295197733,0.128033729919821,0.0709519923534245,0.092873634605593,0,0.0225679379736398,0.0352754493378881,0.0729583017401753,0.09562083374215,0.0553034373508932,0,0.000195109906033109,0.0529124198937543,0,0,0,0,0.0142916639059838,0.0827874332789343,0.0760168881589905,0.00669008943816042,0.0300488889835442
|gostat_on_MCL_coexpression=GO:0005529;sugar binding;0.00599056731030821;21824,17064!GO:0030246;carbohydrate binding;0.00608980077054871;21824,17064!GO:0050819;negative regulation of coagulation;0.0127084984748003;21824!GO:0050818;regulation of coagulation;0.0142958856510686;21824!GO:0005509;calcium ion binding;0.0211565737232751;21824,17064!GO:0007565;female pregnancy;0.038075356412911;21824!GO:0007596;blood coagulation;0.038075356412911;21824!GO:0007599;hemostasis;0.038075356412911;21824!GO:0050817;coagulation;0.038075356412911;21824!GO:0050878;regulation of body fluid levels;0.0444017506439279;21824!GO:0042060;wound healing;0.0455437900789349;21824!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0009569!1.99e-11!66;UBERON:0002048!2.00e-09!14;UBERON:0000117!2.00e-09!14;UBERON:0000171!2.00e-09!14;UBERON:0000170!2.00e-09!14;UBERON:0005597!2.00e-09!14;UBERON:0000118!2.00e-09!14;UBERON:0005177!1.61e-08!79;UBERON:0005153!1.06e-07!17;UBERON:0004872!1.68e-07!33;UBERON:0005178!8.83e-07!17;UBERON:0005181!8.83e-07!17;UBERON:0002224!8.83e-07!17;UBERON:0000915!8.83e-07!17;UBERON:0008947!8.83e-07!17;UBERON:0003258!8.83e-07!17
|tfbs_overrepresentation_for_novel_motifs=0.0124732,0.0044206,0.0093248,0.214334,0.194352,0.445211,0.0434608,0.619255,0.00973171,0.0044219,0.129166,0.358416,0.0566897,0.0471364,1.40695,0,0.127048,0.307712,0.0178073,0.04965,0.838751,0.138961,0.0468597,0.325792,0.0507648,0.0560179,0.659694,0.109196,0.00383782,0.0649632,0.0229161,0.183906,0.0880249,0.101208,0.119559,0.000119007,0.0311347,0.0390221,0.525881,0.00327522,0.318713,0.0239541,0.0102986,0.823875,0.217776,0.0170511,0.0891609,0.289491,0.059592,0.0233259,0.118196,0.23311,0.011716,0.277369,0.289834,0.185156,1.36543,0.145026,0.199969,0.0487189,0.171929,0.0690583,0.0790104,0.362277,0.0529378,0.415356,0.393152,0.692274,2.95266,0.561562,0.0390982,0.0268496,0.000329538,0.844008,6.21141e-05,0.0209498,0.0536793,0.0842964,0.48748,0.0988716,0.480545,0.136146,1.85412,1.25296,0.233092,1.22436e-09,29.8142,1.35653,3.4742,0.8417,0.44947,0.665883,1.06576,0.756504,0.000732212,1.65929,0.107284,0.193469,0.0892716,0.0076815,0.629012,0.183736,0.265108,0.377547,0.117967,0.0238645,0.149431,0.118042,0.0356156,0.00603767,0.152325,0.266353,0.0342025,0.032982,0.455276,0.0377407,2.029e-06,0.0196046,0.12772,0.610688,0.318309,0.102664,0.791415,1.0039,0.500504,0.164066,0.174489,1.65647,0.39195,0.356307,0.253351,0.0176887,0.368741,0.198486,0.473194,2.04717,0.338633,0.103728,0.432674,1.19378,0.811996,0.396892,0.826078,0.190296,0.114762,0.103042,0.303157,1.15529,0.575372,0.0122318,0.729219,1.97972e-07,0.278483,0.0466545,0.197568,0.338479,0.234185,0.626146,0.058806,0.0644765,0.440436,0.232522,0.164324,0.0552988,0.113143,0.423602,0.0306293,0.154721,0.340031
}}

Latest revision as of 14:50, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:115747077..115747081,+p@chr10:115747077..115747081
+
Mm9::chr10:115762285..115762289,+p@chr10:115762285..115762289
+
Mm9::chr10:115784442..115784445,+p@chr10:115784442..115784445
+
Mm9::chr10:115802415..115802428,+p@chr10:115802415..115802428
+
Mm9::chr10:115814687..115814688,+p@chr10:115814687..115814688
+
Mm9::chr11:53496800..53496839,-p@chr11:53496800..53496839
-
Mm9::chr16:85494593..85494595,-p@chr16:85494593..85494595
-
Mm9::chr17:87177841..87177845,+p@chr17:87177841..87177845
+
Mm9::chr17:87178069..87178097,+p@chr17:87178069..87178097
+
Mm9::chr17:87178100..87178121,+p@chr17:87178100..87178121
+
Mm9::chr17:87220495..87220499,+p@chr17:87220495..87220499
+
Mm9::chr17:87223030..87223045,+p@chr17:87223030..87223045
+
Mm9::chr17:87223095..87223117,+p@chr17:87223095..87223117
+
Mm9::chr17:87224988..87225003,+p@chr17:87224988..87225003
+
Mm9::chr17:87228733..87228774,+p@chr17:87228733..87228774
+
Mm9::chr17:87230312..87230317,+p@chr17:87230312..87230317
+
Mm9::chr17:87230399..87230413,+p@chr17:87230399..87230413
+
Mm9::chr17:87230456..87230468,+p@chr17:87230456..87230468
+
Mm9::chr17:87230588..87230610,+p@chr17:87230588..87230610
+
Mm9::chr17:87230632..87230639,+p@chr17:87230632..87230639
+
Mm9::chr17:87230653..87230664,+p@chr17:87230653..87230664
+
Mm9::chr17:87230684..87230691,+p@chr17:87230684..87230691
+
Mm9::chr17:87230685..87230709,-p@chr17:87230685..87230709
-
Mm9::chr17:87230694..87230713,+p@chr17:87230694..87230713
+
Mm9::chr17:87230755..87230766,+p@chr17:87230755..87230766
+
Mm9::chr17:87230788..87230808,+p@chr17:87230788..87230808
+
Mm9::chr17:87230813..87230832,+p@chr17:87230813..87230832
+
Mm9::chr17:87230860..87230907,+p@chr17:87230860..87230907
+
Mm9::chr17:87230958..87230961,+p@chr17:87230958..87230961
+
Mm9::chr18:61914577..61914583,-p@chr18:61914577..61914583
-
Mm9::chr1:10988780..10988788,+p@chr1:10988780..10988788
+
Mm9::chr1:10994604..10994606,+p@chr1:10994604..10994606
+
Mm9::chr1:11289533..11289563,+p@chr1:11289533..11289563
+
Mm9::chr1:59872821..59872825,+p@chr1:59872821..59872825
+
Mm9::chr2:148231240..148231243,-p@chr2:148231240..148231243
-
Mm9::chr2:148264176..148264189,-p@chr2:148264176..148264189
-
Mm9::chr2:152894949..152894961,+p@chr2:152894949..152894961
+
Mm9::chr2:84173701..84173715,-p@chr2:84173701..84173715
-
Mm9::chr2:84182702..84182714,-p@chr2:84182702..84182714
-
Mm9::chr2:84182758..84182771,-p@chr2:84182758..84182771
-
Mm9::chr2:84182950..84182961,-p@chr2:84182950..84182961
-
Mm9::chr2:84184050..84184063,-p@chr2:84184050..84184063
-
Mm9::chr2:84196553..84196569,-p@chr2:84196553..84196569
-
Mm9::chr2:84202149..84202153,-p@chr2:84202149..84202153
-
Mm9::chr2:84229855..84229864,-p@chr2:84229855..84229864
-
Mm9::chr2:84252797..84252844,-p@chr2:84252797..84252844
-
Mm9::chr2:84256779..84256790,-p@chr2:84256779..84256790
-
Mm9::chr2:84261546..84261559,-p@chr2:84261546..84261559
-
Mm9::chr2:84264580..84264589,-p@chr2:84264580..84264589
-
Mm9::chr4:123284381..123284386,-p@chr4:123284381..123284386
-
Mm9::chr5:17083638..17083649,+p@chr5:17083638..17083649
+
Mm9::chr6:128088031..128088043,-p@chr6:128088031..128088043
-
Mm9::chr6:128183862..128183869,-p@chr6:128183862..128183869
-
Mm9::chr8:106657720..106657726,+p@chr8:106657720..106657726
+
Mm9::chr8:123594200..123594223,-p@chr8:123594200..123594223
-


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:0005529sugar binding0.00599056731030821
GO:0030246carbohydrate binding0.00608980077054871
GO:0050819negative regulation of coagulation0.0127084984748003
GO:0050818regulation of coagulation0.0142958856510686
GO:0005509calcium ion binding0.0211565737232751
GO:0007565female pregnancy0.038075356412911
GO:0007596blood coagulation0.038075356412911
GO:0007599hemostasis0.038075356412911
GO:0050817coagulation0.038075356412911
GO:0050878regulation of body fluid levels0.0444017506439279
GO:0042060wound healing0.0455437900789349



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
subdivision of trunk1.99e-1166
lung2.00e-0914
respiratory tube2.00e-0914
respiration organ2.00e-0914
pair of lungs2.00e-0914
lung primordium2.00e-0914
lung bud2.00e-0914
trunk region element1.61e-0879
epithelial bud1.06e-0717
splanchnic layer of lateral plate mesoderm1.68e-0733
thoracic cavity element8.83e-0717
thoracic segment organ8.83e-0717
thoracic cavity8.83e-0717
thoracic segment of trunk8.83e-0717
respiratory primordium8.83e-0717
endoderm of foregut8.83e-0717


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)
MA0003.14.61955e-09
MA0004.10.0190227
MA0006.10.0477758
MA0007.10.194981
MA0009.10.20022
MA0014.11.98509e-07
MA0017.10.0652307
MA0019.10.10039
MA0024.10.173522
MA0025.10.365239
MA0027.11.68414
MA0028.10.00268637
MA0029.10.160867
MA0030.10.164647
MA0031.10.144623
MA0038.10.205138
MA0040.10.599308
MA0041.12.13781
MA0042.11.61551
MA0043.10.730688
MA0046.10.223269
MA0048.10.000662842
MA0050.10.271002
MA0051.10.0590598
MA0052.10.611555
MA0055.14.9493e-07
MA0056.10
MA0057.10.964155
MA0058.10.006711
MA0059.10.0408598
MA0060.10.00342128
MA0061.10.00624167
MA0063.10
MA0066.10.0523466
MA0067.10.454225
MA0068.11.7221
MA0069.10.213518
MA0070.10.20731
MA0071.10.0264513
MA0072.10.201943
MA0073.13.18124
MA0074.10.0414112
MA0076.10.0798395
MA0077.11.05282
MA0078.10.532513
MA0081.10.286228
MA0083.10.263855
MA0084.10.741403
MA0087.10.234442
MA0088.10.829093
MA0089.10
MA0090.10.0646221
MA0091.10.233292
MA0092.10.569018
MA0093.10.00307113
MA0095.10
MA0098.10
MA0100.10.150315
MA0101.10.00872398
MA0103.10.486091
MA0105.10.0490525
MA0106.121.5906
MA0107.10.00372721
MA0108.20.111172
MA0109.10
MA0111.10.0726779
MA0113.10.22733
MA0114.10.738175
MA0115.10.266362
MA0116.10.0142784
MA0117.10.244148
MA0119.10.0449563
MA0122.10.257729
MA0124.10.410915
MA0125.10.352733
MA0130.10
MA0131.10.0983113
MA0132.10
MA0133.10
MA0135.10.290227
MA0136.10.710289
MA0139.10.0528351
MA0140.10.976557
MA0141.10.194265
MA0142.10.838998
MA0143.10.244857
MA0144.11.00321
MA0145.10.121939
MA0146.10.00260674
MA0147.10.00112511
MA0148.11.4699
MA0149.11.36767
MA0062.20.0545982
MA0035.22.43015
MA0039.22.56076e-09
MA0138.20.0947272
MA0002.20.00175838
MA0137.20.341931
MA0104.20.000299985
MA0047.20.7838
MA0112.20.262975
MA0065.20.0767997
MA0150.10.0756443
MA0151.10
MA0152.10.784105
MA0153.10.302289
MA0154.10.0729869
MA0155.10.00776058
MA0156.10.175052
MA0157.10.381966
MA0158.10
MA0159.10.083099
MA0160.11.48662
MA0161.10
MA0162.16.09438e-07
MA0163.13.88533e-08
MA0164.10.711289
MA0080.20.468391
MA0018.20.4201
MA0099.20.0919292
MA0079.24.35523e-07
MA0102.20.789692
MA0258.10.661578
MA0259.10.0634865
MA0442.10
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