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MCL coexpression mm9:139: Difference between revisions

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|ontology_enrichment_disease=
|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
|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
}}
}}

Revision as of 17:52, 26 November 2012


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)

{{{tfbs_overrepresentation_jaspar}}}

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