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MCL coexpression mm9:181: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005177!3.93e-15!79;UBERON:0009569!4.10e-13!66;UBERON:0002100!1.34e-11!90;UBERON:0000468!2.55e-09!333;UBERON:0005172!2.96e-09!49;UBERON:0005173!2.96e-09!49;UBERON:0002417!2.96e-09!49;UBERON:0000916!2.96e-09!49;UBERON:0005153!2.42e-08!17;UBERON:0003914!2.89e-08!47;UBERON:0002048!4.13e-08!14;UBERON:0000117!4.13e-08!14;UBERON:0000171!4.13e-08!14;UBERON:0000170!4.13e-08!14;UBERON:0005597!4.13e-08!14;UBERON:0000118!4.13e-08!14;UBERON:0000466!1.70e-07!79
|ontology_enrichment_uberon=UBERON:0005177!3.93e-15!79;UBERON:0009569!4.10e-13!66;UBERON:0002100!1.34e-11!90;UBERON:0000468!2.55e-09!333;UBERON:0005172!2.96e-09!49;UBERON:0005173!2.96e-09!49;UBERON:0002417!2.96e-09!49;UBERON:0000916!2.96e-09!49;UBERON:0005153!2.42e-08!17;UBERON:0003914!2.89e-08!47;UBERON:0002048!4.13e-08!14;UBERON:0000117!4.13e-08!14;UBERON:0000171!4.13e-08!14;UBERON:0000170!4.13e-08!14;UBERON:0005597!4.13e-08!14;UBERON:0000118!4.13e-08!14;UBERON:0000466!1.70e-07!79
|tfbs_overrepresentation_for_novel_motifs=0.542449,0.591782,0.269988,0.214334,0.725975,0.0943105,0.379275,0.619255,0.492121,0.592,0.88533,0.156123,0.0566897,0.178347,0.0504479,0,0.796572,0.476649,0.157279,0.04965,0.0322402,0.50191,0.0468597,0.325792,0.487408,1.19854,0.342554,0.265257,1.63541,0.540761,0.0990629,0.183906,0.674469,0.265391,1.09428,0.628189,0.158725,0.152939,0.0222432,0.0841178,0.318713,0.251962,0.825571,0.121472,2.00283,0.950716,0.299449,0.289491,0.592419,0.481828,0.118196,0.864078,0.361346,0.277369,0.289834,0.185156,0.752685,0.954455,0.600114,0.183201,0.98612,1.34205,0.75179,0.732256,0.759959,0.82336,1.0187,0.692274,0.169183,0.561562,0.0390982,0.121304,0.106809,0.314307,0.558022,0.653853,0.707584,0.0842964,0.48748,0.858836,0.480545,0.136146,0.0685124,0.101028,0.233092,0.227862,4.27053,0.541733,0.0912995,0.8417,0.44947,0.665883,0.191734,0.205897,0.0554781,0.284961,0.804782,0.564259,0.299751,0.541683,0.629012,0.540783,0.265108,0.118492,0.37618,0.0238645,0.149431,0.0283987,0.220134,0.584264,0.792243,0.266353,0.379666,0.133363,0.455276,0.484857,0.526153,1.39848,0.401389,0.0294832,0.318309,0.102664,0.0566365,0.285033,0.500504,1.52128,0.174489,0.187574,0.39195,0.543397,0.253351,0.651397,0.368741,0.0537659,0.473194,0.0285225,0.855607,0.768524,0.432674,1.19378,0.811996,1.02688,0.219399,0.190296,0.74184,0.474774,0.628882,1.15529,0.34357,0.335314,0.729219,0.103812,0.278483,0.456584,0.0534603,0.898064,0.0658999,0.626146,0.058806,0.567238,1.12152,0.232522,0.954962,1.10427,0.113143,0.190296,0.0774428,0.154721,5.89138
}}
}}

Revision as of 17:56, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:115738473..115738484,+p4@Ptprb
Mm9::chr10:115738511..115738531,+p1@Ptprb
Mm9::chr10:115738545..115738560,+p2@Ptprb
Mm9::chr10:127684322..127684388,+p2@LOC100504989
p2@Timeless
Mm9::chr11:3831508..3831547,-p@chr11:3831508..3831547
-
Mm9::chr12:118896523..118896537,+p@chr12:118896523..118896537
+
Mm9::chr12:118896549..118896560,+p@chr12:118896549..118896560
+
Mm9::chr13:100623209..100623213,-p@chr13:100623209..100623213
-
Mm9::chr13:4227928..4227973,+p2@Akr1c19
Mm9::chr13:49600143..49600185,+p2@Ecm2
Mm9::chr14:35188703..35188768,+p1@Mmrn2
Mm9::chr15:101055566..101055589,-p1@uc007xst.1
Mm9::chr15:91502663..91502681,+p@chr15:91502663..91502681
+
Mm9::chr15:97550874..97550879,-p@chr15:97550874..97550879
-
Mm9::chr16:18776741..18776774,-p@chr16:18776741..18776774
-
Mm9::chr16:85550398..85550422,-p4@Cyyr1
Mm9::chr17:26602043..26602080,-p@chr17:26602043..26602080
-
Mm9::chr17:31993536..31993558,-p@chr17:31993536..31993558
-
Mm9::chr17:75835203..75835225,+p3@Rasgrp3
Mm9::chr19:5952183..5952220,-p@chr19:5952183..5952220
-
Mm9::chr1:159342389..159342433,-p3@Rasal2
Mm9::chr1:175732842..175732861,-p2@ENSMUST00000155076
Mm9::chr1:175732871..175732891,-p1@ENSMUST00000155076
Mm9::chr1:196446295..196446304,+p5@Plxna2
Mm9::chr1:54035384..54035428,-p@chr1:54035384..54035428
-
Mm9::chr1:59821108..59821130,+p2@Bmpr2
Mm9::chr1:59821148..59821170,+p1@Bmpr2
Mm9::chr2:146337728..146337751,-p2@Ralgapa2
Mm9::chr2:32502159..32502194,+p1@Eng
Mm9::chr3:133863028..133863054,+p1@uc008rku.1
Mm9::chr3:151100854..151100878,+p2@Eltd1
Mm9::chr4:137476787..137476802,+p9@Ece1
Mm9::chr4:137476803..137476835,+p7@Ece1
Mm9::chr4:86520318..86520342,+p1@Acer2
Mm9::chr4:86520893..86520899,+p@chr4:86520893..86520899
+
Mm9::chr4:94406184..94406204,+p1@Tek
Mm9::chr4:94406213..94406228,+p5@Tek
Mm9::chr5:36071671..36071688,-p1@Sh3tc1
Mm9::chr5:36071697..36071727,-p2@Sh3tc1
Mm9::chr6:125263716..125263741,-p2@Ltbr
Mm9::chr6:54922390..54922418,-p2@Nod1
Mm9::chr6:54922422..54922460,-p1@Nod1
Mm9::chr6:91928845..91928907,+p1@Fgd5
Mm9::chr7:91032132..91032155,+p@chr7:91032132..91032155
+
Mm9::chr8:130883224..130883244,+p3@Nrp1
Mm9::chr8:130883258..130883269,+p5@Nrp1
Mm9::chr8:130883285..130883306,+p2@Nrp1
Mm9::chr8:70735928..70735949,-p@chr8:70735928..70735949
-
Mm9::chr8:70735953..70735964,-p@chr8:70735953..70735964
-
Mm9::chr8:74035661..74035677,-p1@Plvap
Mm9::chr9:37209578..37209642,+p1@Robo4
Mm9::chr9:37209651..37209662,+p3@Robo4
Mm9::chr9:42913858..42913876,-p6@Arhgef12
Mm9::chrX:39412707..39412717,+p19@Xiap
Mm9::chrX:39412780..39412841,+p7@Xiap


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:0048646anatomical structure formation0.000497368783731777
GO:0005085guanyl-nucleotide exchange factor activity0.00135038313484387
GO:0001525angiogenesis0.0013876934355548
GO:0005088Ras guanyl-nucleotide exchange factor activity0.002204301449548
GO:0048514blood vessel morphogenesis0.002204301449548
GO:0001568blood vessel development0.00310569406640817
GO:0001944vasculature development0.00310569406640817
GO:0051336regulation of hydrolase activity0.00853382769664921
GO:0030695GTPase regulator activity0.00934428635433393
GO:0051056regulation of small GTPase mediated signal transduction0.0102117062414612
GO:0032502developmental process0.0109839690164534
GO:0009966regulation of signal transduction0.0109839690164534
GO:0007264small GTPase mediated signal transduction0.0109839690164534
GO:0043281regulation of caspase activity0.0109983096970839
GO:0007265Ras protein signal transduction0.0110827496733445
GO:0005083small GTPase regulator activity0.0110827496733445
GO:0009986cell surface0.0187754382056304
GO:0030334regulation of cell migration0.0218211564321479
GO:0005089Rho guanyl-nucleotide exchange factor activity0.0218211564321479
GO:0007275multicellular organismal development0.0218211564321479
GO:0048731system development0.0218211564321479
GO:0035023regulation of Rho protein signal transduction0.0225900197786311
GO:0051270regulation of cell motility0.0225900197786311
GO:0009887organ morphogenesis0.0225900197786311
GO:0016512endothelin-converting enzyme 1 activity0.0225900197786311
GO:0016511endothelin-converting enzyme activity0.0225900197786311
GO:0015889cobalamin transport0.0225900197786311
GO:0040012regulation of locomotion0.0225900197786311
GO:0048513organ development0.0278753591736214
GO:0019199transmembrane receptor protein kinase activity0.0279995574557085
GO:0007167enzyme linked receptor protein signaling pathway0.0279995574557085
GO:0050790regulation of catalytic activity0.0279995574557085
GO:0015087cobalt ion transmembrane transporter activity0.0279995574557085
GO:0016477cell migration0.0284174683586845
GO:0007266Rho protein signal transduction0.028898955822084
GO:0048856anatomical structure development0.0300318473563428
GO:0007242intracellular signaling cascade0.0300318473563428
GO:0006824cobalt ion transport0.0300318473563428
GO:0043154negative regulation of caspase activity0.0300318473563428
GO:0060037pharyngeal system development0.0300318473563428
GO:0051180vitamin transport0.0300318473563428
GO:0005615extracellular space0.0319250026199231
GO:0065009regulation of a molecular function0.0320554163701384
GO:0031419cobalamin binding0.032555283113838
GO:0017154semaphorin receptor activity0.032555283113838
GO:0006928cell motility0.032555283113838
GO:0051674localization of cell0.032555283113838
GO:0046578regulation of Ras protein signal transduction0.032555283113838
GO:0065007biological regulation0.0333028538379638
GO:0044421extracellular region part0.037021189567865
GO:0009653anatomical structure morphogenesis0.0387457327661686
GO:0016486peptide hormone processing0.0398379135829609
GO:0004245neprilysin activity0.0398379135829609
GO:0007413axonal fasciculation0.0398379135829609
GO:0004872receptor activity0.0435159628939011
GO:0030517negative regulation of axon extension0.0438789741123988



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
trunk region element3.93e-1579
subdivision of trunk4.10e-1366
trunk1.34e-1190
multi-cellular organism2.55e-09333
abdomen element2.96e-0949
abdominal segment element2.96e-0949
abdominal segment of trunk2.96e-0949
abdomen2.96e-0949
epithelial bud2.42e-0817
epithelial tube2.89e-0847
lung4.13e-0814
respiratory tube4.13e-0814
respiration organ4.13e-0814
pair of lungs4.13e-0814
lung primordium4.13e-0814
lung bud4.13e-0814
immaterial anatomical entity1.70e-0779


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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