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MCL coexpression mm9:139: Difference between revisions

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{{MCL_coexpression_mm9
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development;0.00187162462721913;14183,21869,15245!GO:0030323;respiratory tube development;0.00187162462721913;14183,21869,15245!GO:0005515;protein binding;0.00187162462721913;21869,110310,11596,15245,14828,213469,26992,14183,234686,16774,16782,140781!GO:0008543;fibroblast growth factor receptor signaling pathway;0.00417780837550083;14183,15245!GO:0005605;basal lamina;0.0118687760175718;16774,16782!GO:0035295;tube development;0.0233656378188877;14183,21869,15245!GO:0009953;dorsal/ventral pattern formation;0.0233656378188877;21869,15245!GO:0008201;heparin binding;0.0339440635180946;14183,16782!GO:0005201;extracellular matrix structural constituent;0.0339440635180946;16774,16782!GO:0005604;basement membrane;0.0339440635180946;16774,16782!GO:0005539;glycosaminoglycan binding;0.0401738399512;14183,16782!GO:0048732;gland development;0.0401738399512;14183,21869!GO:0030247;polysaccharide binding;0.0418270320754177;14183,16782!GO:0001871;pattern binding;0.0418270320754177;14183,16782!GO:0060045;positive regulation of cardiac muscle cell proliferation;0.0418270320754177;14183!GO:0060043;regulation of cardiac muscle cell proliferation;0.0418270320754177;14183!GO:0044420;extracellular matrix part;0.0418270320754177;16774,16782!GO:0005007;fibroblast growth factor receptor activity;0.0418270320754177;14183!GO:0043022;ribosome binding;0.0418270320754177;14828!GO:0021798;forebrain dorsal/ventral pattern formation;0.0418270320754177;21869!GO:0031526;brush border membrane;0.0418270320754177;225997!GO:0045879;negative regulation of smoothened signaling pathway;0.0418270320754177;15245!GO:0040036;regulation of fibroblast growth factor receptor signaling 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|gostat_on_MCL_coexpression=GO:0030324;lung development;0.00187162462721913;14183,21869,15245!GO:0030323;respiratory tube development;0.00187162462721913;14183,21869,15245!GO:0005515;protein binding;0.00187162462721913;21869,110310,11596,15245,14828,213469,26992,14183,234686,16774,16782,140781!GO:0008543;fibroblast growth factor receptor signaling pathway;0.00417780837550083;14183,15245!GO:0005605;basal lamina;0.0118687760175718;16774,16782!GO:0035295;tube development;0.0233656378188877;14183,21869,15245!GO:0009953;dorsal/ventral pattern formation;0.0233656378188877;21869,15245!GO:0008201;heparin binding;0.0339440635180946;14183,16782!GO:0005201;extracellular matrix structural constituent;0.0339440635180946;16774,16782!GO:0005604;basement membrane;0.0339440635180946;16774,16782!GO:0005539;glycosaminoglycan binding;0.0401738399512;14183,16782!GO:0048732;gland development;0.0401738399512;14183,21869!GO:0030247;polysaccharide binding;0.0418270320754177;14183,16782!GO:0001871;pattern binding;0.0418270320754177;14183,16782!GO:0060045;positive regulation of cardiac muscle cell proliferation;0.0418270320754177;14183!GO:0060043;regulation of cardiac muscle cell proliferation;0.0418270320754177;14183!GO:0044420;extracellular matrix part;0.0418270320754177;16774,16782!GO:0005007;fibroblast growth factor receptor activity;0.0418270320754177;14183!GO:0043022;ribosome binding;0.0418270320754177;14828!GO:0021798;forebrain dorsal/ventral pattern formation;0.0418270320754177;21869!GO:0031526;brush border membrane;0.0418270320754177;225997!GO:0045879;negative regulation of smoothened signaling pathway;0.0418270320754177;15245!GO:0040036;regulation of fibroblast growth factor receptor signaling pathway;0.0418270320754177;15245!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002048!2.04e-27!14;UBERON:0000117!2.04e-27!14;UBERON:0000171!2.04e-27!14;UBERON:0000170!2.04e-27!14;UBERON:0005597!2.04e-27!14;UBERON:0000118!2.04e-27!14;UBERON:0005153!7.03e-22!17;UBERON:0005178!7.03e-22!17;UBERON:0005181!7.03e-22!17;UBERON:0002224!7.03e-22!17;UBERON:0000915!7.03e-22!17;UBERON:0008947!7.03e-22!17;UBERON:0003258!7.03e-22!17;UBERON:0005157!5.21e-18!20;UBERON:0000310!5.75e-12!6;UBERON:0001443!5.75e-12!6;UBERON:0000065!6.58e-07!41
|tfbs_overrepresentation_for_novel_motifs=0.0129687,1.32748,0.439334,0.691127,0.351765,0.174592,0.162381,0.314815,0.485617,0.0832641,0.0415715,0.301935,1.11043,0.348041,0.176942,0,0.807504,0.212597,0.350689,0.171295,0.485406,0.284826,0.175185,0.665352,0.914283,0.0183157,0.548317,0.095175,0.538025,0.616965,0.1843,0.0973909,0.315089,0.540237,0.0508963,0.114976,0.0589263,0.145589,0.0781313,0.0848782,0.33703,0.191781,0.446604,0.181202,1.88824,0.263997,0.599727,0.108611,0.34219,0.0351951,1.63333,0.24469,1.01488,0.973412,0.528965,0.184571,0.0400746,0.734886,2.10942,0.182169,0.298616,1.13346,0.0785283,0.185622,0.0770933,0.224391,0.265564,0.537467,0.0869245,0.415939,0.133798,0.01393,0.0154698,0.198883,0.331244,0.132833,1.91798,0.0328939,0.279369,1.20621,0.34768,0.0644645,0.0244699,0.198728,0.134031,8.71617e-05,0.0316034,0.927894,0.338572,0.679613,0.314844,0.136587,0.336936,0.0426548,0.0163319,0.241933,0.211817,0.104323,0.142191,0.052751,0.563917,0.0972688,0.159036,0.435458,0.433604,0.029302,0.0733118,0.223247,0.021874,0.492379,0.328144,0.160024,0.211005,0.442718,0.319989,0.133015,0.261843,0.16006,0.467903,0.103956,0.202191,0.675358,0.40769,0.132375,0.94676,0.593918,0.340031,0.100038,0.264526,2.41369,0.14976,0.020171,0.2446,0.643099,0.892401,9.26233,0.36909,0.553596,0.300024,1.02228,1.56827,0.268798,0.0908638,0.334147,0.0508189,2.69058,1.3621,2.25442,1.0819,0.0818911,0.0357229,0.00650229,0.16971,0.262225,0.640327,0.218995,0.0998638,0.318721,0.743445,0.0144536,0.30686,0.133593,0.283962,0.711957,0.186556,0.0738327,0.279631,0.299031,0.210774
|tfbs_overrepresentation_jaspar=MA0003.1;0.146739,MA0004.1;0.0220952,MA0006.1;0.095049,MA0007.1;0.423052,MA0009.1;0.109275,MA0014.1;0.0937995,MA0017.1;0.351771,MA0019.1;0.0421173,MA0024.1;0.0899821,MA0025.1;0.241615,MA0027.1;1.50773,MA0028.1;0.0552863,MA0029.1;0.277314,MA0030.1;2.04988,MA0031.1;2.45813,MA0038.1;0.209354,MA0040.1;1.21908,MA0041.1;0.264528,MA0042.1;0.132089,MA0043.1;0.15848,MA0046.1;3.25074,MA0048.1;0.00391057,MA0050.1;0.375116,MA0051.1;1.40347,MA0052.1;0.119003,MA0055.1;0.000387204,MA0056.1;0,MA0057.1;0.70638,MA0058.1;0.00583815,MA0059.1;0.026304,MA0060.1;0.000839638,MA0061.1;0.624859,MA0063.1;0,MA0066.1;0.0760706,MA0067.1;0.319057,MA0068.1;0.753876,MA0069.1;0.761634,MA0070.1;0.367208,MA0071.1;0.373123,MA0072.1;0.110547,MA0073.1;24.0327,MA0074.1;0.311045,MA0076.1;0.0404451,MA0077.1;0.330629,MA0078.1;0.265458,MA0081.1;0.175272,MA0083.1;0.158042,MA0084.1;0.583888,MA0087.1;0.831555,MA0088.1;0.0596989,MA0089.1;0,MA0090.1;2.51811,MA0091.1;0.0256196,MA0092.1;0.048463,MA0093.1;0.00208699,MA0095.1;0,MA0098.1;0,MA0100.1;0.0521274,MA0101.1;0.842172,MA0103.1;0.253715,MA0105.1;0.140484,MA0106.1;0.27655,MA0107.1;3.3105,MA0108.2;0.0486077,MA0109.1;0,MA0111.1;1.15177,MA0113.1;0.0956638,MA0114.1;0.0408629,MA0115.1;0.160031,MA0116.1;1.21242,MA0117.1;0.863805,MA0119.1;0.615103,MA0122.1;2.8002,MA0124.1;0.280977,MA0125.1;1.21832,MA0130.1;0,MA0131.1;0.0408933,MA0132.1;0,MA0133.1;0,MA0135.1;0.179184,MA0136.1;0.583402,MA0139.1;0.297534,MA0140.1;0.0520761,MA0141.1;0.102122,MA0142.1;0.858979,MA0143.1;0.259726,MA0144.1;0.0834447,MA0145.1;0.845654,MA0146.1;1.27011,MA0147.1;0.0247091,MA0148.1;4.64889,MA0149.1;0.161489,MA0062.2;0.0353581,MA0035.2;0.0542043,MA0039.2;4.94126,MA0138.2;0.350898,MA0002.2;0.425091,MA0137.2;0.181869,MA0104.2;0.0167779,MA0047.2;3.89575,MA0112.2;0.0811026,MA0065.2;0.298191,MA0150.1;0.00304263,MA0151.1;0,MA0152.1;0.0820114,MA0153.1;1.05492,MA0154.1;0.178255,MA0155.1;3.12988,MA0156.1;0.0881033,MA0157.1;2.77417,MA0158.1;0,MA0159.1;0.774902,MA0160.1;0.527093,MA0161.1;0,MA0162.1;0.152493,MA0163.1;0.42148,MA0164.1;1.62104,MA0080.2;0.95554,MA0018.2;0.18861,MA0099.2;0.340839,MA0079.2;2.28158,MA0102.2;0.62983,MA0258.1;0.111624,MA0259.1;0.0855984,MA0442.1;0
}}

Latest revision as of 14:46, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:22537591..22537602,+p@chr10:22537591..22537602
+
Mm9::chr11:106887167..106887206,+p@chr11:106887167..106887206
+
Mm9::chr11:30473115..30473144,-p@chr11:30473115..30473144
-
Mm9::chr11:3969929..3969971,+p@chr11:3969929..3969971
+
Mm9::chr11:59457994..59457997,-p@chr11:59457994..59457997
-
Mm9::chr11:8403786..8403797,-p@chr11:8403786..8403797
-
Mm9::chr11:85533239..85533252,-p1@ENSMUST00000146806
p1@ENSMUST00000151652
p1@uc007krv.1
p1@uc007krw.1
Mm9::chr12:113959715..113959741,+p@chr12:113959715..113959741
+
Mm9::chr12:57354175..57354199,+p1@Gm19990
Mm9::chr12:57446779..57446829,-p1@Mbip
Mm9::chr12:57598384..57598417,-p@chr12:57598384..57598417
-
Mm9::chr12:57598537..57598547,-p@chr12:57598537..57598547
-
Mm9::chr12:57598716..57598720,-p@chr12:57598716..57598720
-
Mm9::chr12:57623172..57623185,-p@chr12:57623172..57623185
-
Mm9::chr12:57630364..57630373,-p3@E030019B13Rik
Mm9::chr12:57630383..57630384,-p7@E030019B13Rik
Mm9::chr12:57630397..57630424,-p1@E030019B13Rik
Mm9::chr12:57630433..57630438,-p6@E030019B13Rik
Mm9::chr12:57630443..57630450,-p4@E030019B13Rik
Mm9::chr12:57630487..57630498,-p2@E030019B13Rik
Mm9::chr12:57633887..57633899,-p@chr12:57633887..57633899
-
Mm9::chr12:57634587..57634598,-p@chr12:57634587..57634598
-
Mm9::chr12:57636178..57636194,-p2@Nkx2-1
Mm9::chr12:57636220..57636236,-p3@Nkx2-1
Mm9::chr12:57636240..57636256,-p4@Nkx2-1
Mm9::chr12:57636278..57636289,+p@chr12:57636278..57636289
+
Mm9::chr12:57636911..57636924,-p@chr12:57636911..57636924
-
Mm9::chr12:57636936..57636953,-p@chr12:57636936..57636953
-
Mm9::chr12:57636959..57636976,-p@chr12:57636959..57636976
-
Mm9::chr12:57636985..57637010,-p@chr12:57636985..57637010
-
Mm9::chr12:57637058..57637082,-p@chr12:57637058..57637082
-
Mm9::chr12:57637086..57637109,-p@chr12:57637086..57637109
-
Mm9::chr12:57637595..57637608,-p7@Nkx2-1
Mm9::chr12:57637649..57637665,-p8@Nkx2-1
Mm9::chr12:57637700..57637717,-p9@Nkx2-1
Mm9::chr12:57637732..57637777,-p5@Nkx2-1
Mm9::chr12:57637882..57637924,-p6@Nkx2-1
Mm9::chr12:57638513..57638544,-p@chr12:57638513..57638544
-
Mm9::chr12:77106196..77106236,+p@chr12:77106196..77106236
+
Mm9::chr12:77420044..77420048,+p@chr12:77420044..77420048
+
Mm9::chr13:37574250..37574261,+p@chr13:37574250..37574261
+
Mm9::chr13:73604796..73604797,+p4@Lpcat1
Mm9::chr14:55612574..55612583,-p@chr14:55612574..55612583
-
Mm9::chr14:55612604..55612634,-p@chr14:55612604..55612634
-
Mm9::chr14:67443681..67443691,-p@chr14:67443681..67443691
-
Mm9::chr14:67453090..67453135,-p@chr14:67453090..67453135
-
Mm9::chr14:70930388..70930406,+p7@Lgi3
Mm9::chr14:70930418..70930431,+p5@Lgi3
Mm9::chr14:70930467..70930498,+p6@Lgi3
Mm9::chr14:70931427..70931437,+p@chr14:70931427..70931437
+
Mm9::chr15:101241551..101241569,+p3@Krt7
Mm9::chr16:11447378..11447389,+p4@Snx29
Mm9::chr17:34735097..34735109,+p2@Ager
Mm9::chr17:35786701..35786713,+p3@Sfta2
Mm9::chr17:35786714..35786742,+p2@Sfta2
Mm9::chr17:35786761..35786793,+p1@Sfta2
Mm9::chr18:12492437..12492455,+p3@Lama3
Mm9::chr18:12492462..12492512,+p2@Lama3
Mm9::chr18:12569366..12569383,+p@chr18:12569366..12569383
+
Mm9::chr19:18833097..18833135,+p3@Trpm6
Mm9::chr1:155033255..155033266,-p@chr1:155033255..155033266
-
Mm9::chr1:95065175..95065196,+p@chr1:95065175..95065196
+
Mm9::chr2:84939301..84939342,+p8@Aplnr
Mm9::chr4:107747066..107747081,-p@chr4:107747066..107747081
-
Mm9::chr4:138812977..138812992,+p@chr4:138812977..138812992
+
Mm9::chr4:138812999..138813015,+p@chr4:138812999..138813015
+
Mm9::chr5:104152010..104152026,+p@chr5:104152010..104152026
+
Mm9::chr5:124602799..124602836,-p@chr5:124602799..124602836
-
Mm9::chr5:124602840..124602849,-p@chr5:124602840..124602849
-
Mm9::chr5:144753500..144753517,-p@chr5:144753500..144753517
-
Mm9::chr5:28785482..28785498,-p@chr5:28785482..28785498
-
Mm9::chr5:32655895..32655909,+p6@Plb1
Mm9::chr7:114808281..114808295,+p@chr7:114808281..114808295
+
Mm9::chr7:137407733..137407747,-p3@Fgfr2
Mm9::chr7:51923747..51923760,-p@chr7:51923747..51923760
-
Mm9::chr8:107871785..107871840,-p1@Fhod1
Mm9::chr8:70800702..70800714,+p4@Sh2d4a
Mm9::chr8:82581888..82581916,-p1@Hhip
Mm9::chr8:90885602..90885616,-p@chr8:90885602..90885616
-
Mm9::chr8:90885810..90885824,-p5@Brd7
Mm9::chrX:162984441..162984446,-p@chrX:162984441..162984446
-
Mm9::chrX:21292028..21292064,-p@chrX:21292028..21292064
-
Mm9::chrX:7299393..7299413,+p2@Wdr45


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:0030324lung development0.00187162462721913
GO:0030323respiratory tube development0.00187162462721913
GO:0005515protein binding0.00187162462721913
GO:0008543fibroblast growth factor receptor signaling pathway0.00417780837550083
GO:0005605basal lamina0.0118687760175718
GO:0035295tube development0.0233656378188877
GO:0009953dorsal/ventral pattern formation0.0233656378188877
GO:0008201heparin binding0.0339440635180946
GO:0005201extracellular matrix structural constituent0.0339440635180946
GO:0005604basement membrane0.0339440635180946
GO:0005539glycosaminoglycan binding0.0401738399512
GO:0048732gland development0.0401738399512
GO:0030247polysaccharide binding0.0418270320754177
GO:0001871pattern binding0.0418270320754177
GO:0060045positive regulation of cardiac muscle cell proliferation0.0418270320754177
GO:0060043regulation of cardiac muscle cell proliferation0.0418270320754177
GO:0044420extracellular matrix part0.0418270320754177
GO:0005007fibroblast growth factor receptor activity0.0418270320754177
GO:0043022ribosome binding0.0418270320754177
GO:0021798forebrain dorsal/ventral pattern formation0.0418270320754177
GO:0031526brush border membrane0.0418270320754177
GO:0045879negative regulation of smoothened signaling pathway0.0418270320754177
GO:0040036regulation of fibroblast growth factor receptor signaling pathway0.0418270320754177



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
lung2.04e-2714
respiratory tube2.04e-2714
respiration organ2.04e-2714
pair of lungs2.04e-2714
lung primordium2.04e-2714
lung bud2.04e-2714
epithelial bud7.03e-2217
thoracic cavity element7.03e-2217
thoracic segment organ7.03e-2217
thoracic cavity7.03e-2217
thoracic segment of trunk7.03e-2217
respiratory primordium7.03e-2217
endoderm of foregut7.03e-2217
epithelial fold5.21e-1820
breast5.75e-126
chest5.75e-126
respiratory tract6.58e-0741


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)
MA0003.10.146739
MA0004.10.0220952
MA0006.10.095049
MA0007.10.423052
MA0009.10.109275
MA0014.10.0937995
MA0017.10.351771
MA0019.10.0421173
MA0024.10.0899821
MA0025.10.241615
MA0027.11.50773
MA0028.10.0552863
MA0029.10.277314
MA0030.12.04988
MA0031.12.45813
MA0038.10.209354
MA0040.11.21908
MA0041.10.264528
MA0042.10.132089
MA0043.10.15848
MA0046.13.25074
MA0048.10.00391057
MA0050.10.375116
MA0051.11.40347
MA0052.10.119003
MA0055.10.000387204
MA0056.10
MA0057.10.70638
MA0058.10.00583815
MA0059.10.026304
MA0060.10.000839638
MA0061.10.624859
MA0063.10
MA0066.10.0760706
MA0067.10.319057
MA0068.10.753876
MA0069.10.761634
MA0070.10.367208
MA0071.10.373123
MA0072.10.110547
MA0073.124.0327
MA0074.10.311045
MA0076.10.0404451
MA0077.10.330629
MA0078.10.265458
MA0081.10.175272
MA0083.10.158042
MA0084.10.583888
MA0087.10.831555
MA0088.10.0596989
MA0089.10
MA0090.12.51811
MA0091.10.0256196
MA0092.10.048463
MA0093.10.00208699
MA0095.10
MA0098.10
MA0100.10.0521274
MA0101.10.842172
MA0103.10.253715
MA0105.10.140484
MA0106.10.27655
MA0107.13.3105
MA0108.20.0486077
MA0109.10
MA0111.11.15177
MA0113.10.0956638
MA0114.10.0408629
MA0115.10.160031
MA0116.11.21242
MA0117.10.863805
MA0119.10.615103
MA0122.12.8002
MA0124.10.280977
MA0125.11.21832
MA0130.10
MA0131.10.0408933
MA0132.10
MA0133.10
MA0135.10.179184
MA0136.10.583402
MA0139.10.297534
MA0140.10.0520761
MA0141.10.102122
MA0142.10.858979
MA0143.10.259726
MA0144.10.0834447
MA0145.10.845654
MA0146.11.27011
MA0147.10.0247091
MA0148.14.64889
MA0149.10.161489
MA0062.20.0353581
MA0035.20.0542043
MA0039.24.94126
MA0138.20.350898
MA0002.20.425091
MA0137.20.181869
MA0104.20.0167779
MA0047.23.89575
MA0112.20.0811026
MA0065.20.298191
MA0150.10.00304263
MA0151.10
MA0152.10.0820114
MA0153.11.05492
MA0154.10.178255
MA0155.13.12988
MA0156.10.0881033
MA0157.12.77417
MA0158.10
MA0159.10.774902
MA0160.10.527093
MA0161.10
MA0162.10.152493
MA0163.10.42148
MA0164.11.62104
MA0080.20.95554
MA0018.20.18861
MA0099.20.340839
MA0079.22.28158
MA0102.20.62983
MA0258.10.111624
MA0259.10.0855984
MA0442.10
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