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MCL coexpression mm9:183: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005418!8.91e-10!5;UBERON:0002472!8.91e-10!5;UBERON:0008784!8.91e-10!5;UBERON:0006058!8.91e-10!5;UBERON:0004709!8.91e-10!5;UBERON:0002529!8.91e-10!5;UBERON:0010538!8.91e-10!5;UBERON:0005420!8.91e-10!5;UBERON:0010758!8.91e-10!5;UBERON:0000978!8.91e-10!5;UBERON:0002103!8.91e-10!5;UBERON:0000376!8.91e-10!5;UBERON:0000154!8.91e-10!5;UBERON:0010709!8.91e-10!5;UBERON:0005730!8.91e-10!5;UBERON:0000026!9.56e-09!12;UBERON:0004708!9.56e-09!12;UBERON:0002101!9.56e-09!12;UBERON:0004357!9.56e-09!12;UBERON:0004347!9.56e-09!12;UBERON:0005732!9.56e-09!12;UBERON:0005733!9.56e-09!12;UBERON:0000981!1.09e-08!4;UBERON:0003608!1.09e-08!4;UBERON:0003826!1.09e-08!4;UBERON:0008202!1.09e-08!4;UBERON:0004381!1.09e-08!4;UBERON:0007273!1.09e-08!4;UBERON:0010912!1.09e-08!4;UBERON:0002513!1.09e-08!4;UBERON:0004375!1.09e-08!4;UBERON:0010740!1.09e-08!4;UBERON:0010363!1.09e-08!4;UBERON:0003860!1.09e-08!4;UBERON:0002428!1.09e-08!4;UBERON:0010742!1.09e-08!4;UBERON:0002495!1.09e-08!4;UBERON:0003464!1.09e-08!4;UBERON:0003606!1.09e-08!4;UBERON:0005893!1.09e-08!4;UBERON:0009749!1.09e-08!4;UBERON:0010712!1.09e-08!4;UBERON:0010886!1.09e-08!4;UBERON:0005254!1.09e-08!4;UBERON:0010885!1.09e-08!4;UBERON:0010881!1.09e-08!4;UBERON:0010882!1.09e-08!4;UBERON:0007844!1.09e-08!4;UBERON:0001441!1.09e-08!4;UBERON:0011249!1.09e-08!4;UBERON:0002091!1.09e-08!4;UBERON:0003285!1.09e-08!4;UBERON:0004288!1.09e-08!4;UBERON:0010129!1.09e-08!4;UBERON:0006234!1.09e-08!4;UBERON:0010707!6.07e-08!13
|ontology_enrichment_uberon=UBERON:0005418!8.91e-10!5;UBERON:0002472!8.91e-10!5;UBERON:0008784!8.91e-10!5;UBERON:0006058!8.91e-10!5;UBERON:0004709!8.91e-10!5;UBERON:0002529!8.91e-10!5;UBERON:0010538!8.91e-10!5;UBERON:0005420!8.91e-10!5;UBERON:0010758!8.91e-10!5;UBERON:0000978!8.91e-10!5;UBERON:0002103!8.91e-10!5;UBERON:0000376!8.91e-10!5;UBERON:0000154!8.91e-10!5;UBERON:0010709!8.91e-10!5;UBERON:0005730!8.91e-10!5;UBERON:0000026!9.56e-09!12;UBERON:0004708!9.56e-09!12;UBERON:0002101!9.56e-09!12;UBERON:0004357!9.56e-09!12;UBERON:0004347!9.56e-09!12;UBERON:0005732!9.56e-09!12;UBERON:0005733!9.56e-09!12;UBERON:0000981!1.09e-08!4;UBERON:0003608!1.09e-08!4;UBERON:0003826!1.09e-08!4;UBERON:0008202!1.09e-08!4;UBERON:0004381!1.09e-08!4;UBERON:0007273!1.09e-08!4;UBERON:0010912!1.09e-08!4;UBERON:0002513!1.09e-08!4;UBERON:0004375!1.09e-08!4;UBERON:0010740!1.09e-08!4;UBERON:0010363!1.09e-08!4;UBERON:0003860!1.09e-08!4;UBERON:0002428!1.09e-08!4;UBERON:0010742!1.09e-08!4;UBERON:0002495!1.09e-08!4;UBERON:0003464!1.09e-08!4;UBERON:0003606!1.09e-08!4;UBERON:0005893!1.09e-08!4;UBERON:0009749!1.09e-08!4;UBERON:0010712!1.09e-08!4;UBERON:0010886!1.09e-08!4;UBERON:0005254!1.09e-08!4;UBERON:0010885!1.09e-08!4;UBERON:0010881!1.09e-08!4;UBERON:0010882!1.09e-08!4;UBERON:0007844!1.09e-08!4;UBERON:0001441!1.09e-08!4;UBERON:0011249!1.09e-08!4;UBERON:0002091!1.09e-08!4;UBERON:0003285!1.09e-08!4;UBERON:0004288!1.09e-08!4;UBERON:0010129!1.09e-08!4;UBERON:0006234!1.09e-08!4;UBERON:0010707!6.07e-08!13
|tfbs_overrepresentation_for_novel_motifs=0.160577,1.36726,0.465683,0.214334,0.983476,0.234508,0.379275,0.446256,0.492121,0.0939641,0.129166,0.642881,0.305077,0.401017,0.379834,0,0.399663,0.476649,0.0883663,0.890459,0.0950503,0.203739,0.177495,1.26645,0.284407,0.0560179,0.486792,0.265257,0.0700672,0.708279,0.244402,1.03453,1.20126,0.533746,0.228768,0.155899,0.0311347,0.352244,0.974919,0.158033,0.318713,0.251962,0.159691,0.583765,0.0829169,0.0777425,0.299449,0.289491,0.275059,0.298042,0.376776,0.23311,1.26777,0.277369,0.289834,0.413912,0.0793159,0.145026,2.45565,0.183201,0.171929,0.243268,0.75179,0.112645,0.0529378,0.82336,0.393152,0.692274,0.505319,0.561562,0.413173,0.0622668,0.00120799,0.314307,0.108207,1.05975,1.38553,0.0842964,0.945107,1.17077,1.11829,0.136146,0.518685,0.00688579,0.233092,0.0339042,0.230259,0.541733,0.632638,0.8417,0.44947,0.236414,0.191734,0.347465,0.211684,0.431431,0.434662,0.193469,0.0892716,0.541683,0.433207,0.540783,0.265108,0.377547,0.117967,0.0238645,0.149431,0.524105,0.389508,0.0966612,0.307043,0.266353,0.379666,0.133363,0.455276,0.183328,0.0179395,0.687473,0.401389,0.610688,0.318309,0.102664,0.0566365,0.59671,0.500504,0.164066,0.697584,0.187574,1.01607,0.543397,0.253351,0.651397,0.368741,1.1724,0.473194,1.33237,1.19671,1.12239,0.432674,1.19378,0.811996,0.396892,0.219399,1.06005,0.367821,1.11809,0.628882,1.15529,0.173597,0.335314,0.0053682,0.00012692,0.278483,1.72345,0.764451,0.338479,0.504966,0.13447,0.157674,0.0135836,0.440436,0.656791,0.493371,0.0552988,0.734514,0.423602,0.273286,1.89958,0.0143329
}}
}}

Revision as of 17:56, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:34109780..34109796,+p1@Col10a1
Mm9::chr11:20798688..20798696,-p@chr11:20798688..20798696
-
Mm9::chr11:77624716..77624729,+p26@Myo18a
Mm9::chr11:94426353..94426370,+p1@Chad
Mm9::chr12:82434510..82434539,-p2@Slc8a3
Mm9::chr14:21315951..21315958,-p3@Zmynd17
Mm9::chr15:58649683..58649688,-p@chr15:58649683..58649688
-
Mm9::chr15:71864632..71864654,-p1@Col22a1
Mm9::chr16:27307718..27307736,+p1@Ostn
Mm9::chr16:32400888..32400899,+p2@Tm4sf19
Mm9::chr16:32400907..32400920,+p1@Tm4sf19
Mm9::chr17:34176086..34176098,+p3@Col11a2
Mm9::chr17:34176111..34176127,+p2@Col11a2
Mm9::chr17:34176173..34176200,+p5@Col11a2
Mm9::chr18:78254099..78254110,-p3@Siglec15
Mm9::chr18:78254135..78254146,-p1@Siglec15
Mm9::chr18:78254174..78254185,-p2@Siglec15
Mm9::chr19:42687256..42687271,-p1@Loxl4
Mm9::chr1:162083669..162083681,-p2@Tnn
Mm9::chr1:162083702..162083716,-p1@Tnn
Mm9::chr1:57155729..57155740,-p@chr1:57155729..57155740
-
Mm9::chr1:81163452..81163476,+p@chr1:81163452..81163476
+
Mm9::chr2:164773241..164773248,+p3@Mmp9
Mm9::chr3:131046407..131046426,-p@chr3:131046407..131046426
-
Mm9::chr3:14869216..14869224,+p@chr3:14869216..14869224
+
Mm9::chr3:88188375..88188393,-p1@Bglap
Mm9::chr3:95303195..95303211,+p1@Ctsk
Mm9::chr5:104562996..104562998,-p@chr5:104562996..104562998
-
Mm9::chr5:104631628..104631643,+p1@Dmp1
Mm9::chr5:104728300..104728315,+p1@Ibsp
Mm9::chr5:104738330..104738341,+p@chr5:104738330..104738341
+
Mm9::chr5:104738346..104738365,+p@chr5:104738346..104738365
+
Mm9::chr5:104738384..104738419,+p@chr5:104738384..104738419
+
Mm9::chr5:104739095..104739117,-p@chr5:104739095..104739117
-
Mm9::chr5:104739132..104739155,-p@chr5:104739132..104739155
-
Mm9::chr6:51525785..51525803,+p@chr6:51525785..51525803
+
Mm9::chr6:51525810..51525817,+p@chr6:51525810..51525817
+
Mm9::chr6:51525826..51525838,+p@chr6:51525826..51525838
+
Mm9::chr7:148136135..148136156,-p1@Ifitm5
Mm9::chr7:148136181..148136190,-p2@Ifitm5
Mm9::chr7:3567707..3567718,-p2@Oscar
Mm9::chr7:3567737..3567754,-p1@Oscar
Mm9::chr8:108807113..108807116,-p@chr8:108807113..108807116
-
Mm9::chr8:72411280..72411300,-p1@Cilp2
Mm9::chr8:74049600..74049612,-p2@uc009mdq.1
Mm9::chr8:74049618..74049629,-p1@uc009mdq.1
Mm9::chr9:107814899..107814905,+p@chr9:107814899..107814905
+
Mm9::chr9:110645069..110645080,-p4@Pth1r
Mm9::chr9:110645081..110645095,-p1@Pth1r
Mm9::chr9:21934585..21934591,-p@chr9:21934585..21934591
-
Mm9::chr9:21934647..21934657,-p@chr9:21934647..21934657
-
Mm9::chr9:21935011..21935025,-p1@Acp5
Mm9::chr9:70799951..70799962,-p4@Lipc
Mm9::chr9:7272520..7272537,+p1@Mmp13
Mm9::chrX:153853237..153853250,-p1@Phex


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:0001503ossification9.39167572983397e-08
GO:0031214biomineral formation9.39167572983397e-08
GO:0001501skeletal development9.39167572983397e-08
GO:0046849bone remodeling1.12070436394931e-07
GO:0048771tissue remodeling2.37740323321377e-07
GO:0030282bone mineralization6.39853335032151e-07
GO:0005615extracellular space1.67176511208622e-06
GO:0044421extracellular region part2.94148392710855e-06
GO:0009888tissue development1.97297292138458e-05
GO:0005578proteinaceous extracellular matrix0.000397389940734604
GO:0030500regulation of bone mineralization0.0021230096364638
GO:0030574collagen catabolic process0.0021230096364638
GO:0044259multicellular organismal macromolecule metabolic process0.0021230096364638
GO:0044268multicellular organismal protein metabolic process0.0021230096364638
GO:0044256protein digestion0.0021230096364638
GO:0044254multicellular organismal protein catabolic process0.0021230096364638
GO:0044266multicellular organismal macromolecule catabolic process0.0021230096364638
GO:0044243multicellular organismal catabolic process0.0021230096364638
GO:0032963collagen metabolic process0.00256062945348381
GO:0044236multicellular organismal metabolic process0.00271680136502611
GO:0004222metalloendopeptidase activity0.00290623633204116
GO:0030278regulation of ossification0.00397184911185981
GO:0001649osteoblast differentiation0.00482097140514813
GO:0046850regulation of bone remodeling0.00512279925182716
GO:0030020extracellular matrix structural constituent conferring tensile strength0.00512279925182716
GO:0048513organ development0.0059725965513933
GO:0005581collagen0.00692106639459702
GO:0007586digestion0.00871710445467921
GO:0048856anatomical structure development0.00873828959623076
GO:0004216cathepsin K activity0.00873828959623076
GO:0004991parathyroid hormone receptor activity0.00873828959623076
GO:0004229gelatinase B activity0.00873828959623076
GO:0004175endopeptidase activity0.00993151401688284
GO:0008237metallopeptidase activity0.00993151401688284
GO:0051216cartilage development0.0100263524183424
GO:0048731system development0.0146727669410031
GO:0005201extracellular matrix structural constituent0.0146727669410031
GO:0007275multicellular organismal development0.0146727669410031
GO:0006817phosphate transport0.0173945241819232
GO:0032502developmental process0.0201871413154484
GO:0004232interstitial collagenase activity0.0204368531176428
GO:0002076osteoblast development0.0258985643784834
GO:0022610biological adhesion0.0258985643784834
GO:0007155cell adhesion0.0258985643784834
GO:0044420extracellular matrix part0.0275598544505392
GO:0006508proteolysis0.0275598544505392
GO:0045668negative regulation of osteoblast differentiation0.0290606792893455
GO:0008133collagenase activity0.0290606792893455
GO:0004720protein-lysine 6-oxidase activity0.0341414850662139
GO:0008233peptidase activity0.0347487623026659
GO:0004245neprilysin activity0.0382477051841511



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
hindlimb bud8.91e-105
stylopod8.91e-105
lower limb segment8.91e-105
multi-limb segment region8.91e-105
pelvic appendage8.91e-105
limb segment8.91e-105
paired limb/fin segment8.91e-105
pelvic appendage bud8.91e-105
subdivision of organism along appendicular axis8.91e-105
leg8.91e-105
hindlimb8.91e-105
hindlimb stylopod8.91e-105
posterior region of body8.91e-105
pelvic complex8.91e-105
hindlimb/pelvic fin field8.91e-105
appendage9.56e-0912
paired limb/fin9.56e-0912
limb9.56e-0912
paired limb/fin bud9.56e-0912
limb bud9.56e-0912
limb/fin field9.56e-0912
limb field9.56e-0912
femur1.09e-084
hindlimb long bone1.09e-084
upper leg bone1.09e-084
bone of hip region1.09e-084
skeleton of limb1.09e-084
pelvic appendage skeleton1.09e-084
subdivision of skeleton1.09e-084
endochondral bone1.09e-084
bone of free limb or fin1.09e-084
bone of appendage girdle complex1.09e-084
endochondral element1.09e-084
hindlimb mesenchyme1.09e-084
limb bone1.09e-084
bone of pelvic complex1.09e-084
long bone1.09e-084
hindlimb bone1.09e-084
limb long bone1.09e-084
leg bone1.09e-084
limb mesenchyme1.09e-084
limb skeleton subdivision1.09e-084
hindlimb bone pre-cartilage condensation1.09e-084
upper leg mesenchyme1.09e-084
hindlimb cartilage element1.09e-084
limb cartilage element1.09e-084
limb bone pre-cartilage condensation1.09e-084
cartilage element1.09e-084
hindlimb skeleton1.09e-084
appendicular skeletal system1.09e-084
appendicular skeleton1.09e-084
limb of embryo1.09e-084
skeleton1.09e-084
femur cartilage element1.09e-084
femur pre-cartilage condensation1.09e-084
appendage girdle complex6.07e-0813


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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