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MCL coexpression mm9:412: Difference between revisions

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{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0,1.16843678684713,1.16629681408021,1.17794784991095,1.08875823043872,1.2184351916281,1.20356358786045,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.17601646619461,1.19389152389717,1.12093970033437,1.12770288332837,1.13946524044868,1.45397510394301,1.31904853441945,1.24004278009778,0,0,0,1.35635183084229,1.25981970332324,1.29560523157895,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.28139687791545,0,0,0,0,0,0,0,0,0,0,0.621535950940314,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.31427984776847,0,0,1.2779576134024,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.896040781239864,1.20936365444213,0.119129528926274,0.41880363358974,0.921242305479476,1.13248829921051,1.09847195095419,1.12351238077462,1.17851949522646,1.11994007793494,1.09989429525217,1.15924282360905,1.10871645286605,1.30275680564114,1.1349101585403,1.1399184304729,0,0,0,0.040250349638994,0,0.0294389011296462,0.0855184943654863,0.0597943799295356,0.0909637028615074,0.0252666615705483,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0680912293502604,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0242354089326645,0,0,0.16004921783491,0,0,0,0.504338703551918,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.118424994141815,0,0,0,0,0,0,1.25678602414821,0,0,0,0,0,0,0,0,0,0,0,0,0.206814654737266,0.427086270225699,0.151730312771305,0.355742547956528,0.134210686612626,0.152078321852531,0.100975358632432,1.2762709487073,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.133294797899774,0.118803253255857,0.190760324464606,0.159715578577694,0.284295878965646,0.215330413983256,0.303366467725811,0.274831160334435,0.228647814177576,0.178449056319963,0.212033847661007,0.262638133757011,0.169172763866184,0.271431304043815,0.184235875491178,0.14986111676545,0.237214295925784,0.226790206858766,0.171495067223923,0.234342257396434,0.286655587363961,0.21908495302072,0.213268521121219,0.255853422905485,0.218127658883024,0.225056016595504,0.326803611095607,0.215606646836597,0.245635201366836,0.266099152720808,0.267296555876582,0.208101547368331,0,0.300603747997907,0.26939249630118,0,0,0
|gostat_on_MCL_coexpression=GO:0043565;sequence-specific DNA binding;0.00839438291231407;71597,30942,12590,12591!GO:0003700;transcription factor activity;0.0475543362686204;71597,30942,12590,12591!
|ontology_enrichment_celltype=CL:0002563!2.70e-11!9;CL:0002251!2.70e-11!9;CL:0000239!9.92e-08!6;CL:0000677!9.92e-08!6;CL:0000212!9.92e-08!6;CL:0000584!9.92e-08!6
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000160!2.88e-34!31;UBERON:0005409!1.06e-30!47;UBERON:0000344!6.00e-18!15;UBERON:0001242!8.92e-16!13;UBERON:0000060!8.92e-16!13;UBERON:0001262!8.92e-16!13;UBERON:0004786!8.92e-16!13;UBERON:0003350!2.70e-11!9;UBERON:0004808!2.70e-11!9;UBERON:0001277!2.70e-11!9;UBERON:0004923!2.64e-10!24;UBERON:0000485!9.80e-09!11;UBERON:0004119!5.90e-07!118;UBERON:0000925!5.90e-07!118;UBERON:0006595!5.90e-07!118;UBERON:0001007!8.22e-07!116;UBERON:0001555!8.22e-07!116;UBERON:0007026!8.22e-07!116
|tfbs_overrepresentation_for_novel_motifs=0.162057,0.559911,0.144778,0.191238,0.271545,1.73484,0.270195,0.0371334,0.15797,0.115943,0.236307,0.260789,0.0372188,0.766078,1.03205,0,1.1241,0.0750368,1.28115,0.278706,0.385752,2.15622,0.279154,0.26934,0.149704,0.301898,0.534309,0.216938,0.338701,0.393858,0.206597,1.31697,0.0739139,0.249044,0.0880674,0.314254,0.244093,0.257981,0.468707,0.177517,0.265799,0.210373,0.15533,0.620985,0.0747075,0.539875,0.974269,0.6478,0.222853,0.343195,0.426383,0.323798,0.61775,0.661847,0.67813,0.28555,0.110603,0.25091,0.27058,0.283926,0.513661,0.331566,0.69092,0.4166,0.294453,0.451957,0.806865,1.14503,0.509463,1.00145,0.132733,0.635773,0.0300638,0.709559,0.775285,0.445056,0.248898,0.363297,1.24575,0.392419,0.640048,2.99614,0.330377,0.139579,0.602212,0.695306,0.788585,0.394307,0.983412,1.30447,0.873554,0.606796,0.543309,0.280055,0.057338,1.12502,0.334928,1.34695,0.373124,1.17121,1.34549,0.531465,0.645628,0.4269,0.425983,0.21005,0.478524,0.225669,0.400135,1.26837,0.157325,0.647285,0.124928,0.67478,0.880323,0.263255,0.461856,0.565346,0.442771,0.880181,0.714636,0.398522,0.819386,0.362534,0.932468,0.501574,0.276618,0.53717,0.805419,0.59554,0.629874,0.546435,0.777296,0.296474,0.9011,2.56891,0.167758,0.607069,0.853868,1.66928,1.27308,0.811357,0.313144,1.33707,0.420352,0.210705,0.980089,1.62988,0.975672,0.0799646,0.0818785,0.28414,0.66331,0.194002,0.29573,1.75287,0.324625,0.0943424,0.938758,0.167568,0.862985,0.601424,0.501973,0.919703,0.417485,0.289792,0.52021,0.259556,0.405191
}}

Latest revision as of 15:15, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:128346052..128346083,+p2@Cd63
p2@LOC100505035
Mm9::chr11:100025961..100025968,+p@chr11:100025961..100025968
+
Mm9::chr11:116072277..116072320,+p2@2310004N24Rik
Mm9::chr17:28984921..28984925,+p@chr17:28984921..28984925
+
Mm9::chr18:61195843..61195864,-p2@Cdx1
Mm9::chr1:135060428..135060498,+p@chr1:135060428..135060498
+
Mm9::chr1:78306130..78306143,+p@chr1:78306130..78306143
+
Mm9::chr3:3508024..3508069,+p2@Hnf4g
Mm9::chr3:84074704..84074716,-p9@Trim2
Mm9::chr5:148118792..148118806,-p3@Cdx2
Mm9::chr5:148118809..148118832,-p5@Cdx2
Mm9::chr5:148118840..148118857,-p2@Cdx2
Mm9::chr6:18120560..18120620,+p1@Cftr
Mm9::chr6:40584806..40584863,+p@chr6:40584806..40584863
+
Mm9::chr7:148106756..148106780,+p2@Nlrp6
Mm9::chr7:36341097..36341108,-p7@Nudt19
Mm9::chr8:77396591..77396639,+p1@Isx
Mm9::chr9:76893457..76893477,-p3@Tinag


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:0043565sequence-specific DNA binding0.00839438291231407
GO:0003700transcription factor activity0.0475543362686204



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>cell_data<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)
MA0003.10.444916
MA0004.10.191582
MA0006.10.289293
MA0007.10.534201
MA0009.11.36778
MA0014.10.0191544
MA0017.12.24242
MA0019.11.02123
MA0024.10.516087
MA0025.10.773017
MA0027.12.16618
MA0028.10.304586
MA0029.10.496599
MA0030.10.502474
MA0031.11.18689
MA0038.10.815918
MA0040.10.567108
MA0041.10.140298
MA0042.10.131965
MA0043.10.644695
MA0046.12.4507
MA0048.10.332197
MA0050.10.626793
MA0051.10.309072
MA0052.10.574473
MA0055.10.230702
MA0056.10
MA0057.10.0539481
MA0058.10.127732
MA0059.10.13543
MA0060.10.404183
MA0061.11.2506
MA0063.10
MA0066.10.293002
MA0067.10.879099
MA0068.10.0116947
MA0069.10.574784
MA0070.10.565924
MA0071.10.219128
MA0072.10.558195
MA0073.11.05676
MA0074.10.264633
MA0076.10.110983
MA0077.10.538513
MA0078.10.89286
MA0081.10.150322
MA0083.10.643958
MA0084.11.1979
MA0087.10.604077
MA0088.10.0849312
MA0089.10
MA0090.10.167748
MA0091.10.582275
MA0092.10.167962
MA0093.10.0955883
MA0095.10
MA0098.10
MA0100.10.255651
MA0101.10.435524
MA0103.10.702489
MA0105.11.47812
MA0106.10.342589
MA0107.10.335745
MA0108.21.87232
MA0109.10
MA0111.10.525581
MA0113.10.319332
MA0114.12.8869
MA0115.11.56023
MA0116.10.288992
MA0117.10.617392
MA0119.10.141504
MA0122.10.635764
MA0124.10.828115
MA0125.10.757653
MA0130.10
MA0131.10.390422
MA0132.10
MA0133.10
MA0135.10.67864
MA0136.10.280269
MA0139.10.0357525
MA0140.10.710317
MA0141.11.23603
MA0142.13.00102
MA0143.10.332773
MA0144.10.478562
MA0145.10.370702
MA0146.10.221363
MA0147.10.0666796
MA0148.10.587598
MA0149.12.71653
MA0062.20.102085
MA0035.20.259203
MA0039.20.101993
MA0138.20.383644
MA0002.20.145768
MA0137.20.371067
MA0104.20.162663
MA0047.20.301217
MA0112.20.208001
MA0065.21.16061
MA0150.10.180943
MA0151.10
MA0152.10.301303
MA0153.14.04272
MA0154.10.325394
MA0155.10.66805
MA0156.10.110475
MA0157.11.09863
MA0158.10
MA0159.10.250417
MA0160.10.592791
MA0161.10
MA0162.10.166881
MA0163.10.0764052
MA0164.10.280556
MA0080.20.103116
MA0018.20.288261
MA0099.20.37828
MA0079.20.252153
MA0102.21.24942
MA0258.10.0535937
MA0259.10.0616796
MA0442.10
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