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MCL coexpression mm9:900: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0005801;cis-Golgi network;0.0218594203692544;16886!
|ontology_enrichment_celltype=CL:0000988!1.84e-12!32;CL:0002032!1.84e-12!32;CL:0000037!1.84e-12!32;CL:0000566!1.84e-12!32;CL:0000837!1.84e-12!32;CL:0002031!6.51e-10!25;CL:0000838!5.66e-09!12;CL:0000542!3.70e-08!13;CL:0000051!3.70e-08!13;CL:0000553!1.01e-07!6;CL:0000556!1.01e-07!6;CL:0000084!1.32e-07!11;CL:0000827!1.32e-07!11;CL:0002320!2.27e-07!46;CL:0000134!2.27e-07!46
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!7.74e-24!48;UBERON:0002405!7.74e-24!48;UBERON:0004177!9.06e-24!29;UBERON:0005057!9.06e-24!29;UBERON:0002390!9.24e-24!45;UBERON:0003061!9.24e-24!45;UBERON:0000077!1.13e-18!35;UBERON:0002370!2.88e-18!23;UBERON:0000974!2.88e-18!23;UBERON:0004807!2.88e-18!23;UBERON:0005058!2.88e-18!23;UBERON:0003351!2.88e-18!23;UBERON:0009113!2.88e-18!23;UBERON:0003295!2.88e-18!23;UBERON:0009722!2.88e-18!23;UBERON:0005562!2.88e-18!23;UBERON:0007690!2.88e-18!23;UBERON:0006562!2.56e-17!24;UBERON:0003408!2.56e-17!24;UBERON:0001557!2.56e-17!24;UBERON:0001042!2.56e-17!24;UBERON:0008814!2.56e-17!24;UBERON:0009145!2.56e-17!24;UBERON:0000072!6.78e-15!27;UBERON:0000065!2.54e-13!41;UBERON:0001004!7.09e-13!42;UBERON:0003081!2.08e-12!87;UBERON:0001041!1.67e-10!80;UBERON:0000063!1.70e-10!35;UBERON:0007811!4.37e-10!36;UBERON:0005911!3.77e-08!69;UBERON:0000153!9.00e-08!43;UBERON:0003929!1.32e-07!55;UBERON:0002384!2.27e-07!46;UBERON:0000926!7.11e-07!120;UBERON:0004120!7.11e-07!120;UBERON:0006603!7.11e-07!120
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.84953,0.367606,0.434198,1.32803,0.448401,0.538088,0.515265,0.181564,0.687027,0.494602,0.526159,0.173454,0.550255,0.756943,0,0.742571,0.252772,2.86938,0.620214,0.883862,0.223663,0.549359,0.258745,0.374936,0.577606,0.466037,0.469052,0.818708,0.376624,0.455168,0.843667,0.250677,0.136998,0.276324,0.363049,0.242032,0.522578,1.1836,1.08217,0.256422,0.460258,0.204736,0.761266,0.209497,0.423266,0.662995,0.484612,0.0447507,0.305876,0.725127,0.604356,0.362495,0.985264,1.00271,0.557354,0.314394,0.513517,0.145699,0.555328,1.92541,0.613749,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.922232,0.178433,0.0665967,1.03623,0.433216,0.409836,1.35784,0.651651,0.806481,1.60272,0.179489,0.759925,0.612313,0.501608,0.920903,0.025519,0.123242,0.118251,0.667883,1.65055,1.20871,0.925879,0.856465,0.733735,0.62322,0.202284,0.1711,0.859272,0.663249,0.101559,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.340849,0.333829,0.386136,0.96962,0.337254,0.499714,1.21576,0.708441,0.0359654,0.437894,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.740166,0.950857,0.427043,1.10792,0.570914,1.23736,0.829188,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,1.04134,0.261837,0.766041,0.203102,0.986833,0.207643,0.569994,1.06851,0.605358,0.287226,0.39061,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.240994,0.524587,0.0131724
}}

Latest revision as of 16:04, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:3309082..3309091,-p5@Limk2
Mm9::chr12:114663890..114663905,-p@chr12:114663890..114663905
-
Mm9::chr17:84174825..84174832,+p@chr17:84174825..84174832
+
Mm9::chr17:84174847..84174856,+p@chr17:84174847..84174856
+
Mm9::chr17:84174862..84174879,+p@chr17:84174862..84174879
+
Mm9::chr6:136780418..136780458,+p@chr6:136780418..136780458
+
Mm9::chr9:103391631..103391640,-p@chr9:103391631..103391640
-
Mm9::chr9:103391651..103391674,-p@chr9:103391651..103391674
-


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:0005801cis-Golgi network0.0218594203692544



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>

Uber Anatomy
Ontology termp-valuen
hemolymphoid system7.74e-2448
immune system7.74e-2448
hemopoietic organ9.06e-2429
immune organ9.06e-2429
hematopoietic system9.24e-2445
blood island9.24e-2445
mixed endoderm/mesoderm-derived structure1.13e-1835
thymus2.88e-1823
neck2.88e-1823
respiratory system epithelium2.88e-1823
hemolymphoid system gland2.88e-1823
pharyngeal epithelium2.88e-1823
thymic region2.88e-1823
pharyngeal gland2.88e-1823
entire pharyngeal arch endoderm2.88e-1823
thymus primordium2.88e-1823
early pharyngeal endoderm2.88e-1823
pharynx2.56e-1724
gland of gut2.56e-1724
upper respiratory tract2.56e-1724
chordate pharynx2.56e-1724
pharyngeal arch system2.56e-1724
pharyngeal region of foregut2.56e-1724
segment of respiratory tract6.78e-1527
respiratory tract2.54e-1341
respiratory system7.09e-1342
lateral plate mesoderm2.08e-1287
foregut1.67e-1080
organ segment1.70e-1035
craniocervical region4.37e-1036
endo-epithelium3.77e-0869
anterior region of body9.00e-0843
gut epithelium1.32e-0755
connective tissue2.27e-0746
mesoderm7.11e-07120
mesoderm-derived structure7.11e-07120
presumptive mesoderm7.11e-07120


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)
MA0003.10.0545917
MA0004.10.434673
MA0006.10.271714
MA0007.11.89281
MA0009.10.870101
MA0014.10.162935
MA0017.10.804572
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.281528
MA0029.10.804619
MA0030.10.811181
MA0031.10.775627
MA0038.10.577528
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.10.685543
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.11.2091
MA0056.10
MA0057.10.0935008
MA0058.10.341628
MA0059.10.353484
MA0060.10.197678
MA0061.10.224905
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.0965831
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.10.000129679
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.980744
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.064239
MA0089.10
MA0090.10.401197
MA0091.11.13691
MA0092.11.03695
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.362124
MA0103.10.827743
MA0105.10.133231
MA0106.10.626997
MA0107.10.301222
MA0108.20.710846
MA0109.10
MA0111.10.415012
MA0113.11.45892
MA0114.10.222763
MA0115.10.969632
MA0116.10.27152
MA0117.10.937363
MA0119.10.362692
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.10.683521
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.12.22005
MA0140.10.519484
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.10.527241
MA0146.10.0169049
MA0147.10.236889
MA0148.10.450593
MA0149.10.367458
MA0062.20.137653
MA0035.20.524137
MA0039.20.027551
MA0138.20.675599
MA0002.20.988033
MA0137.20.32312
MA0104.20.18504
MA0047.20.576767
MA0112.21.87605
MA0065.20.0704227
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.330759
MA0155.10.579465
MA0156.10.843735
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.10.453546
MA0161.10
MA0162.10.0925951
MA0163.10.0836563
MA0164.10.551114
MA0080.20.816435
MA0018.20.560731
MA0099.20.669311
MA0079.20.00265486
MA0102.21.59466
MA0258.12.51672
MA0259.10.227035
MA0442.10
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