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MCL coexpression mm9:333: Difference between revisions

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{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0.0798429213642297,0,0,0,-0.0285370623344958,-0.0152563996547418,-0.0186835468526769,-0.0614499919561927,-0.0573587214058547,-0.0573587214058547,-0.0614499919561927,-0.0573587214058547,-0.0614499919561927,-0.0614499919561927,0,0,-0.0614499919561927,-0.0573587214058547,-0.0573587214058547,-0.0614499919561927,0.0682179984609265,-0.0614499919561927,-0.0614499919561927,-0.000400756697994969,0,0,0,0,-0.0285370623344958,-0.0285370623344958,-0.0573587214058547,-0.0614499919561927,-0.0614499919561927,-0.0614499919561927,-0.0285370623344958,-0.0573587214058547,-0.0339434078067076,-0.0614499919561927,-0.0614499919561927,-0.0614499919561927,-0.0614499919561927,-0.0614499919561927,-0.0614499919561927,0.243251518964216,0.178080010683922,0.162667148310556,0.320412169639741,0.218555320865808,0.158173160405417,0.249863259792521,0.25794580045439,0,-0.0614499919561927,-0.0608236905358181,-0.0614499919561927,1.07855412470834,1.20165095215788,1.32637047231959,0,-0.0285370623344958,0,0.144212900699905,0.064807647117636,0,0,0,0.113809739605487,0.116276662684149,0,0,0,0.0138182428103459,0.0820341853970415,-0.00717593152252164,0,0,0,0,0,0,0,0,0.0127230388548122,0,0.0144939483469534,0,0.0653899056099829,0,0,0,0.108813204465849,0,-0.0285370623344958,-0.0285370623344958,0,-0.0285370623344958,0,0,0.0125380897752806,0,0,0,-0.0614499919561927,-0.0614499919561927,0,0,0,0.0469568706916304,0,0,0.0586745981681181,0.11523486805022,0.0735082565472611,0.0951741062977179,0.167012710201248,0.0896163527889306,0.0959343498639139,0.115902186124224,0,0.113764283648036,0.0510546073208872,0.110524574157343,-0.0573587214058547,0,0,0,-0.0614499919561927,-0.0614499919561927,-0.0614499919561927,0,0,0,0,0,0,0,0.120039909909813,0.0514436957843891,0,0,0,0,0,0.0591519123474142,0.0285860945550467,0.0104298716821509,0.0161820926542378,0.0974704356148325,0,0,0.0130305502092601,0.0502653334811999,0.109876475355953,0.15466836580152,0.0986015320380844,0,-0.0573587214058547,-0.0614499919561927,-0.0614499919561927,0.078529292234877,0.0457501310086346,0.0921287359176402,0.0927032537857093,0.0118612385359869,0.0795352258207201,0.128328319349571,0.186545793286102,0.148438635650065,0.0661618130246221,0.168038440707116,0.13157937095951,0.237241158130746,0.148575591340733,0.132880430559217,0,0,-0.0573587214058547,0,0,0,0,0,0.000714497237849865,0.000204348414572258,0,0.0572230325336606,0,0.0281950118751692,0,0,0.00488113844865883,0,0,0.046982063026719,0,0,0.0472974425465577,0.0432236120246624,0.0979324054608941,0.0534406776525719,0.0633328814307688,0.0764911299862343,0,0,0,0,-0.015483490993011,-0.0285370623344958,0,0,0,0,0.298338658052105,0,0,0,0.0466861735965537,0,0.104038656189849,0.00519792580516585,0.00396165884015649,0.0420995238857838,0.00291961399742432,0.0153821194840417,0.16894968105828,0.171618709493336,0.0912933562119048,0.159245076116426,0.144998238511638,0.239412599485906,0.180049562811606,0.214177149362663,-0.0288216590713588,-0.0614499919561927,0,0.020286239647971,0,0,0,0.0692305913255424,0,0,0,0,0.00078920651818161,0,0,0,0,0,0.0830839046778843,0.0571590845570374,0.0247231228611982,0.0912037957218741,0,0,0,0,0,0,0,0.0394160756134568,0,0,0,0,0.0209239912544316,0.0293695753751966,0.0070758392297261,0.0713015889234444,0.0406851584229821,0.130495525689528,0.0661577744756082,0.0542670189101823,0.0050324477648275,0.0876257955781274,0.00122016894929456,0.0662835200988411,0.0753891731456253,0.0256848978994156,0.0489745727197172,0.0139557880258478,0,0,0,0,0.0737896374598673,0,0,0.00184847114068823,-0.0446874359441825,-0.0285370623344958,-0.0573587214058547,0,0,0,0,0.0212926219951735,0.0139636295914856,0.0221249795076328,0.0252587578170624,0.0292654265114261,0.0238584120441542,0.0690224787466548,-0.0614499919561927,0,0,0.0514465464356286,0.0870631606472512,0.0197539253813575,0.0915665403705771,0.0792555651162322,0.0365440883446776,0.00409980173209458,0,-0.000240583120923677,0,0,-0.00610432678408875,0,0,0,0,0,-0.0166804656401898,-0.0079622833253209,-0.00862772833333165,-0.0176630553048964,-0.018885618295462,0,-0.0285370623344958,0,0,0.121111445942079,0.134336252040636,0.0730404042754446,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0604087735674538,0.0592498685919601,0,0,0.0871588832444397,0.10800616838155,0.0175498549470796,0.0353605628306278,0.105480910914462,0.091132325189722,0.108333835568361,0.0690084039747411,0.0440432083344519,0.0126878457709086,0.0264822828502986,0.0644633794913391,0.0612227127071683,0.126553092097482,0.142422577611925,0.0239689659037969,0.0853581705438539,0.0987730828969113,0.0782993698367999,0.0615375754883662,0.0729583017401753,0.0526664553367149,0.104353329269123,0.0186008617123536,0.0462377405478722,0.0408018333703219,0,0.0684197122192168,0.141704700595215,0.091804538796955,0.128002975951803,0.140953325604123,0.202710473642915,0.0845150599849736,0.0551115656993311
|gostat_on_MCL_coexpression=GO:0005229;intracellular calcium activated chloride channel activity;0.0387562788834409;12722!GO:0043185;vascular endothelial growth factor receptor 3 binding;0.0387562788834409;22341!GO:0015698;inorganic anion transport;0.0387562788834409;12722,12827!GO:0006820;anion transport;0.0387562788834409;12722,12827!GO:0005172;vascular endothelial growth factor receptor binding;0.0387562788834409;22341!GO:0005587;collagen type IV;0.0387562788834409;12827!GO:0030935;sheet-forming collagen;0.0387562788834409;12827!GO:0002052;positive regulation of neuroblast proliferation;0.0395571990453073;22341!
}}

Latest revision as of 15:07, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:43827555..43827566,+p@chr11:43827555..43827566
+
Mm9::chr11:61392802..61392849,-p@chr11:61392802..61392849
-
Mm9::chr14:124059337..124059431,+p1@Itgbl1
Mm9::chr14:124059443..124059455,+p4@Itgbl1
Mm9::chr14:124059487..124059506,+p3@Itgbl1
Mm9::chr14:124059513..124059533,+p2@Itgbl1
Mm9::chr1:74115215..74115251,-p@chr1:74115215..74115251
-
Mm9::chr2:26934891..26934905,+p1@Adamtsl2
Mm9::chr2:79879159..79879174,-p9@Pde1a
Mm9::chr3:144423693..144423710,-p1@Clca1
Mm9::chr3:53064740..53064776,+p@chr3:53064740..53064776
+
Mm9::chr3:53065121..53065127,+p@chr3:53065121..53065127
+
Mm9::chr6:35276123..35276155,-p1@Fam180a
Mm9::chr6:48791632..48791643,+p3@Tmem176a
Mm9::chr7:117773040..117773045,+p@chr7:117773040..117773045
+
Mm9::chr8:11218764..11218769,-p@chr8:11218764..11218769
-
Mm9::chr8:11239175..11239178,-p@chr8:11239175..11239178
-
Mm9::chr8:11354318..11354330,+p@chr8:11354318..11354330
+
Mm9::chr8:11398668..11398681,+p@chr8:11398668..11398681
+
Mm9::chr8:11398757..11398768,+p@chr8:11398757..11398768
+
Mm9::chr8:11448154..11448168,+p@chr8:11448154..11448168
+
Mm9::chr8:55162490..55162506,+p2@Vegfc
Mm9::chr8:55162518..55162537,+p1@Vegfc
Mm9::chr9:56096674..56096680,+p@chr9:56096674..56096680
+


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:0005229intracellular calcium activated chloride channel activity0.0387562788834409
GO:0043185vascular endothelial growth factor receptor 3 binding0.0387562788834409
GO:0015698inorganic anion transport0.0387562788834409
GO:0006820anion transport0.0387562788834409
GO:0005172vascular endothelial growth factor receptor binding0.0387562788834409
GO:0005587collagen type IV0.0387562788834409
GO:0030935sheet-forming collagen0.0387562788834409
GO:0002052positive regulation of neuroblast proliferation0.0395571990453073



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>


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)
MA0003.10.0806402
MA0004.10.398663
MA0006.10.0460466
MA0007.10.376537
MA0009.10.452863
MA0014.10.0802094
MA0017.10.452527
MA0019.10.818593
MA0024.10.415603
MA0025.10.660968
MA0027.12.04174
MA0028.10.0499059
MA0029.10.397373
MA0030.11.03991
MA0031.10.373333
MA0038.10.62805
MA0040.10.463641
MA0041.10.0860551
MA0042.10.0797095
MA0043.10.53743
MA0046.10.483941
MA0048.10.991119
MA0050.10.894815
MA0051.10.226644
MA0052.10.47061
MA0055.11.64597
MA0056.10
MA0057.10.644264
MA0058.10.264426
MA0059.10.0823381
MA0060.10.0217699
MA0061.10.537954
MA0063.10
MA0066.10.212546
MA0067.10.764133
MA0068.10.147887
MA0069.10.470904
MA0070.10.462521
MA0071.10.456242
MA0072.10.455219
MA0073.10.00262263
MA0074.10.187944
MA0076.10.064121
MA0077.10.436665
MA0078.10.250627
MA0081.10.312046
MA0083.10.536725
MA0084.11.07765
MA0087.10.4987
MA0088.10.262285
MA0089.10
MA0090.10.348685
MA0091.12.61269
MA0092.10.107655
MA0093.10.196448
MA0095.10
MA0098.10
MA0100.10.180237
MA0101.10.610312
MA0103.10.0606094
MA0105.10.669937
MA0106.10.256379
MA0107.10.462865
MA0108.20.85894
MA0109.10
MA0111.10.744051
MA0113.10.664215
MA0114.10.530742
MA0115.10.539917
MA0116.11.52467
MA0117.10.511373
MA0119.10.293473
MA0122.10.528896
MA0124.10.714453
MA0125.11.55773
MA0130.10
MA0131.10.299487
MA0132.10
MA0133.10
MA0135.10.569948
MA0136.10.201456
MA0139.10.0699025
MA0140.10.180161
MA0141.10.0690765
MA0142.10.361451
MA0143.10.247626
MA0144.11.67875
MA0145.10.29554
MA0146.10.067273
MA0147.10.135184
MA0148.10.136186
MA0149.10.0894222
MA0062.20.00879313
MA0035.20.18328
MA0039.20.145091
MA0138.20.293335
MA0002.20.187069
MA0137.21.32869
MA0104.20.0832154
MA0047.20.219739
MA0112.20.295523
MA0065.20.909541
MA0150.10.756591
MA0151.10
MA0152.10.62695
MA0153.10.584906
MA0154.10.973726
MA0155.10.354426
MA0156.10.227959
MA0157.10.8915
MA0158.10
MA0159.10.956625
MA0160.10.137981
MA0161.10
MA0162.10.00047031
MA0163.10.135343
MA0164.10.583987
MA0080.21.22611
MA0018.20.208409
MA0099.20.288477
MA0079.20.101621
MA0102.21.12863
MA0258.10.26175
MA0259.10.124592
MA0442.10
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