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MCL coexpression mm9:225: Difference between revisions

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{{MCL_coexpression_mm9
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extracellular matrix;9.94805947125308e-09;12824,11595,17180,12950,12839,12815,17182!GO:0005201;extracellular matrix structural constituent;9.94805947125308e-09;12824,17180,12839,12815,17182!GO:0022610;biological adhesion;4.72297215510633e-07;213119,12824,12845,11595,12950,12839,12815!GO:0007155;cell adhesion;4.72297215510633e-07;213119,12824,12845,11595,12950,12839,12815!GO:0030198;extracellular matrix organization and biogenesis;6.55853841387458e-07;12824,11595,17180,17182!GO:0044420;extracellular matrix part;3.81878223203534e-06;12824,11595,12839,12815!GO:0043062;extracellular structure organization and biogenesis;4.39897247315514e-06;12824,11595,17180,17182!GO:0030020;extracellular matrix structural constituent conferring tensile strength;7.75836238883046e-06;12824,12839,12815!GO:0005581;collagen;1.23252054246797e-05;12824,12839,12815!GO:0005518;collagen binding;6.5611849078916e-05;17180,17182!GO:0044421;extracellular region part;6.68622318005401e-05;12824,12845,11595,17180,12950,12839,12815,17182!GO:0006817;phosphate transport;6.68622318005401e-05;12824,12839,12815!GO:0001502;cartilage condensation;0.000108032930554557;12824,11595!GO:0030199;collagen fibril organization;0.000233644177338014;12824,11595!GO:0005540;hyaluronic acid binding;0.000249129426871181;11595,12950!GO:0006029;proteoglycan metabolic process;0.000332456786598914;12824,11595!GO:0015698;inorganic anion transport;0.000429192999854446;12824,12839,12815!GO:0006820;anion transport;0.000671512432102679;12824,12839,12815!GO:0051216;cartilage development;0.00182731708572627;12824,11595!GO:0030246;carbohydrate binding;0.00238614933504166;11595,12950,403395!GO:0005615;extracellular space;0.00306266264442543;12824,12845,17180,12950,12839,12815!GO:0005539;glycosaminoglycan binding;0.00374314072995;11595,12950!GO:0030247;polysaccharide binding;0.0042839181942941;11595,12950!GO:0001871;pattern binding;0.00451696322521827;11595,12950!GO:0001501;skeletal development;0.0189008761426242;12824,11595!GO:0005529;sugar binding;0.0193667460790394;11595,403395!GO:0016337;cell-cell adhesion;0.0231487892777975;12824,11595!GO:0006811;ion transport;0.0260616293747252;12824,12839,12815!GO:0030166;proteoglycan biosynthetic process;0.0285255231838653;11595!GO:0044262;cellular carbohydrate metabolic process;0.0292110437925668;12824,11595!GO:0009888;tissue development;0.0345915528954376;12824,11595!GO:0005921;gap junction;0.039418383839295;208098!GO:0005975;carbohydrate metabolic 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|gostat_on_MCL_coexpression=GO:0005578;proteinaceous extracellular matrix;9.94805947125308e-09;12824,11595,17180,12950,12839,12815,17182!GO:0005201;extracellular matrix structural constituent;9.94805947125308e-09;12824,17180,12839,12815,17182!GO:0022610;biological adhesion;4.72297215510633e-07;213119,12824,12845,11595,12950,12839,12815!GO:0007155;cell adhesion;4.72297215510633e-07;213119,12824,12845,11595,12950,12839,12815!GO:0030198;extracellular matrix organization and biogenesis;6.55853841387458e-07;12824,11595,17180,17182!GO:0044420;extracellular matrix part;3.81878223203534e-06;12824,11595,12839,12815!GO:0043062;extracellular structure organization and biogenesis;4.39897247315514e-06;12824,11595,17180,17182!GO:0030020;extracellular matrix structural constituent conferring tensile strength;7.75836238883046e-06;12824,12839,12815!GO:0005581;collagen;1.23252054246797e-05;12824,12839,12815!GO:0005518;collagen binding;6.5611849078916e-05;17180,17182!GO:0044421;extracellular region part;6.68622318005401e-05;12824,12845,11595,17180,12950,12839,12815,17182!GO:0006817;phosphate transport;6.68622318005401e-05;12824,12839,12815!GO:0001502;cartilage condensation;0.000108032930554557;12824,11595!GO:0030199;collagen fibril organization;0.000233644177338014;12824,11595!GO:0005540;hyaluronic acid binding;0.000249129426871181;11595,12950!GO:0006029;proteoglycan metabolic process;0.000332456786598914;12824,11595!GO:0015698;inorganic anion transport;0.000429192999854446;12824,12839,12815!GO:0006820;anion transport;0.000671512432102679;12824,12839,12815!GO:0051216;cartilage development;0.00182731708572627;12824,11595!GO:0030246;carbohydrate binding;0.00238614933504166;11595,12950,403395!GO:0005615;extracellular space;0.00306266264442543;12824,12845,17180,12950,12839,12815!GO:0005539;glycosaminoglycan binding;0.00374314072995;11595,12950!GO:0030247;polysaccharide binding;0.0042839181942941;11595,12950!GO:0001871;pattern binding;0.00451696322521827;11595,12950!GO:0001501;skeletal development;0.0189008761426242;12824,11595!GO:0005529;sugar binding;0.0193667460790394;11595,403395!GO:0016337;cell-cell adhesion;0.0231487892777975;12824,11595!GO:0006811;ion transport;0.0260616293747252;12824,12839,12815!GO:0030166;proteoglycan biosynthetic process;0.0285255231838653;11595!GO:0044262;cellular carbohydrate metabolic process;0.0292110437925668;12824,11595!GO:0009888;tissue development;0.0345915528954376;12824,11595!GO:0005921;gap junction;0.039418383839295;208098!GO:0005975;carbohydrate metabolic process;0.0473343727651521;12824,11595!
}}

Latest revision as of 14:55, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:34822425..34822426,+p@chr10:34822425..34822426
+
Mm9::chr12:8954768..8954786,+p1@Matn3
Mm9::chr13:24247072..24247085,-p6@Lrrc16a
Mm9::chr13:89680450..89680470,+p1@Hapln1
Mm9::chr15:97806343..97806352,-p@chr15:97806343..97806352
-
Mm9::chr15:97806491..97806499,-p@chr15:97806491..97806499
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Mm9::chr15:97806555..97806573,-p@chr15:97806555..97806573
-
Mm9::chr15:97806587..97806603,-p@chr15:97806587..97806603
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Mm9::chr15:97807109..97807127,-p@chr15:97807109..97807127
-
Mm9::chr15:97807155..97807166,-p@chr15:97807155..97807166
-
Mm9::chr15:97807173..97807191,-p@chr15:97807173..97807191
-
Mm9::chr15:97807229..97807247,-p@chr15:97807229..97807247
-
Mm9::chr15:97807283..97807309,-p@chr15:97807283..97807309
-
Mm9::chr15:97807708..97807732,-p@chr15:97807708..97807732
-
Mm9::chr15:97808264..97808278,-p@chr15:97808264..97808278
-
Mm9::chr15:97808333..97808351,-p@chr15:97808333..97808351
-
Mm9::chr15:97835065..97835083,-p1@Col2a1
Mm9::chr17:34176407..34176426,+p1@Col11a2
Mm9::chr1:24184528..24184550,+p2@Col9a1
Mm9::chr1:89366833..89366856,+p1@3110079O15Rik
Mm9::chr1:89366868..89366879,+p3@3110079O15Rik
Mm9::chr1:89366883..89366905,+p2@3110079O15Rik
Mm9::chr2:29713767..29713788,+p@chr2:29713767..29713788
+
Mm9::chr2:77459335..77459343,-p@chr2:77459335..77459343
-
Mm9::chr3:113820930..113820931,+p@chr3:113820930..113820931
+
Mm9::chr3:144955680..144955740,+p1@Col24a1
Mm9::chr3:96449502..96449531,+p1@Itga10
Mm9::chr4:130500292..130500306,+p1@Matn1
Mm9::chr5:139882400..139882420,+p2@C130050O18Rik
Mm9::chr7:86198101..86198120,+p1@Acan
Mm9::chr7:86198122..86198151,+p2@Acan
Mm9::chr7:86198174..86198187,+p3@Acan
Mm9::chr7:86229411..86229424,+p@chr7:86229411..86229424
+
Mm9::chr8:116941895..116941911,+p1@Clec3a
Mm9::chr8:72897440..72897457,+p1@Comp
Mm9::chr9:37476743..37476752,-p2@Panx3
Mm9::chr9:37476755..37476811,-p1@Panx3
Mm9::chrX:147261468..147261472,+p1@ENSMUST00000145639


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:0005578proteinaceous extracellular matrix9.94805947125308e-09
GO:0005201extracellular matrix structural constituent9.94805947125308e-09
GO:0022610biological adhesion4.72297215510633e-07
GO:0007155cell adhesion4.72297215510633e-07
GO:0030198extracellular matrix organization and biogenesis6.55853841387458e-07
GO:0044420extracellular matrix part3.81878223203534e-06
GO:0043062extracellular structure organization and biogenesis4.39897247315514e-06
GO:0030020extracellular matrix structural constituent conferring tensile strength7.75836238883046e-06
GO:0005581collagen1.23252054246797e-05
GO:0005518collagen binding6.5611849078916e-05
GO:0044421extracellular region part6.68622318005401e-05
GO:0006817phosphate transport6.68622318005401e-05
GO:0001502cartilage condensation0.000108032930554557
GO:0030199collagen fibril organization0.000233644177338014
GO:0005540hyaluronic acid binding0.000249129426871181
GO:0006029proteoglycan metabolic process0.000332456786598914
GO:0015698inorganic anion transport0.000429192999854446
GO:0006820anion transport0.000671512432102679
GO:0051216cartilage development0.00182731708572627
GO:0030246carbohydrate binding0.00238614933504166
GO:0005615extracellular space0.00306266264442543
GO:0005539glycosaminoglycan binding0.00374314072995
GO:0030247polysaccharide binding0.0042839181942941
GO:0001871pattern binding0.00451696322521827
GO:0001501skeletal development0.0189008761426242
GO:0005529sugar binding0.0193667460790394
GO:0016337cell-cell adhesion0.0231487892777975
GO:0006811ion transport0.0260616293747252
GO:0030166proteoglycan biosynthetic process0.0285255231838653
GO:0044262cellular carbohydrate metabolic process0.0292110437925668
GO:0009888tissue development0.0345915528954376
GO:0005921gap junction0.039418383839295
GO:0005975carbohydrate metabolic process0.0473343727651521



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
appendage1.45e-1512
paired limb/fin1.45e-1512
limb1.45e-1512
paired limb/fin bud1.45e-1512
limb bud1.45e-1512
limb/fin field1.45e-1512
limb field1.45e-1512
appendage girdle complex4.52e-1413
surface structure4.80e-1222
forelimb1.43e-097
pectoral appendage1.43e-097
pectoral appendage bud1.43e-097
forelimb bud1.43e-097
forelimb/pectoral fin field1.43e-097
pectoral complex3.63e-088
subdivision of skeletal system5.86e-086
developing mesenchymal condensation5.86e-086
pre-cartilage condensation5.86e-086
cartilaginous condensation5.86e-086
hindlimb bud1.64e-075
stylopod1.64e-075
lower limb segment1.64e-075
multi-limb segment region1.64e-075
pelvic appendage1.64e-075
limb segment1.64e-075
paired limb/fin segment1.64e-075
pelvic appendage bud1.64e-075
subdivision of organism along appendicular axis1.64e-075
leg1.64e-075
hindlimb1.64e-075
hindlimb stylopod1.64e-075
posterior region of body1.64e-075
pelvic complex1.64e-075
hindlimb/pelvic fin field1.64e-075


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)
MA0003.10.208917
MA0004.10.0523019
MA0006.10.307617
MA0007.10.178699
MA0009.10.30322
MA0014.10.376865
MA0017.10.368292
MA0019.10.177916
MA0024.10.745934
MA0025.10.490939
MA0027.11.84332
MA0028.10.0625976
MA0029.10.255531
MA0030.10.260188
MA0031.10.235297
MA0038.10.114851
MA0040.10.312625
MA0041.10.122365
MA0042.10.111518
MA0043.10.37807
MA0046.10.330453
MA0048.11.13075
MA0050.10.0666657
MA0051.10.119487
MA0052.10.318728
MA0055.10.60771
MA0056.10
MA0057.10.285369
MA0058.10.0249251
MA0059.10.0277969
MA0060.10.0678139
MA0061.10.840046
MA0063.10
MA0066.10.71687
MA0067.10.587517
MA0068.10.0237618
MA0069.10.318986
MA0070.10.311646
MA0071.10.507269
MA0072.10.823673
MA0073.11.23114
MA0074.10.307062
MA0076.10.0191324
MA0077.10.289168
MA0078.10.13731
MA0081.10.135744
MA0083.10.377437
MA0084.10.888928
MA0087.10.343502
MA0088.10.329408
MA0089.10
MA0090.11.01672
MA0091.11.20933
MA0092.10.366076
MA0093.10.0143916
MA0095.10
MA0098.10
MA0100.10.292642
MA0101.10.859809
MA0103.10.394121
MA0105.10.966856
MA0106.12.00021
MA0107.11.29817
MA0108.20.56139
MA0109.10
MA0111.10.391982
MA0113.10.126154
MA0114.11.13193
MA0115.10.380305
MA0116.10.307163
MA0117.10.354763
MA0119.10.295109
MA0122.10.370415
MA0124.11.33622
MA0125.11.20061
MA0130.10
MA0131.10.519826
MA0132.10
MA0133.10
MA0135.11.04987
MA0136.10.10138
MA0139.10.20766
MA0140.10.0866252
MA0141.10.719674
MA0142.10.225403
MA0143.10.135052
MA0144.10.206664
MA0145.10.379282
MA0146.10.0245201
MA0147.10.230012
MA0148.11.22213
MA0149.10.0314134
MA0062.20.000890599
MA0035.20.0887515
MA0039.20.458645
MA0138.20.170255
MA0002.20.548365
MA0137.20.228652
MA0104.20.131384
MA0047.21.21458
MA0112.21.64242
MA0065.21.94543
MA0150.10.0472137
MA0151.10
MA0152.10.114512
MA0153.10.42102
MA0154.10.654845
MA0155.10.834128
MA0156.10.0189666
MA0157.10.204086
MA0158.10
MA0159.10.11994
MA0160.10.214615
MA0161.10
MA0162.10.0685264
MA0163.10.893125
MA0164.10.332928
MA0080.20.0166373
MA0018.20.10631
MA0099.20.166437
MA0079.20.0104093
MA0102.20.938682
MA0258.10.321845
MA0259.10.0976349
MA0442.10
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