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MCL coexpression mm9:868: Difference between revisions

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{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0,0.065002016191076,0,0.0573828993656285,0,0,0.0455894054315693,0.587559859632729,0.429665842895536,0.438397179103679,0.170020473907391,0.105030925370194,0.508611788039832,0.498531243513352,0.124865908594952,0.0950714588279644,0,0.306149543746875,0.335334952660016,0.277718933625524,0.0354470656487682,0.129239737494397,0.101207837822692,0,0.0896964873768703,0,0,0,0,0,0.0434877098916977,0.213525904512698,0.104094974270439,0,0.0551014608363205,0.0333929694362378,0,0.546587148837803,0.172954967691167,0.359360585787115,0.814836430503769,0.786276341439414,0.390322259497761,0.0514985917256918,0.0209679878844212,0,0,0,0,0.0385803330753519,0,0,0.856314656163621,0.800643271104138,0.502450721050023,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.303045967123761,0,0,0,0,0,0,0.0373973902764027,0,0,0,0,0,0,0,0,0,0,0.181236227563129,0.0175990736327917,0,0,0,0,0,0,0.047967174931957,0,0,0,0.0433296451889376,0,0,0,0,0,0.194684687714819,0.474627586445776,0.217136905765902,0,0,0,0,0,0,0,0.0210591418683525,0.096497738357694,0,0,0,0,0,0.0304819657131131,0,0,0.0388988969149198,0,0,0,0,0,0.0532734549622995,0,0,0,0.115506975370087,0.139890444252295,0.195436618912525,0,0,0,0,0,0,0,0,0,0,0,0.0169266687412288,0,0,0.0273460503695069,0,0.021268976479071,0,0,0,0,0,0,0,0,0.059460048139509,0,0,0,0,0,0,0.0528475443201592,0,0,0,0,0,0,0.0266298923127834,0,0,0.0482367431913278,0,0,0,0,0,0,0,0,0.0326283328848338,0.0595622930959812,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0659019793256198,0.00454228920164013,0.0293361777120366,0,0.214611175180145,0,0,0,0,0,0.04666668282863,0,0,0,0,0.0756156309604739,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.035450992781488,0,0,0.057716207064756,0,0,0,0,0.0164856588978665,0.0127170276859676,0,0,0,0,0.104046486402113,0,0,0,0.027821827298607,0,0.322868857438944,0.388679759833789,0.350158769047897,0,0,0,0,0,0,0.0153964725958214,0,0,0.0529304404135566,0,0,0,0,0,0,0,0,0,0.0433069931089932,0,0,0.206653659181725,0,0.0212308449966822,0,0.0715236385554987,0.112006449694472,0.161527300776181,0.135841920889656,0.205691101905468,0.174600143699057,0.162218816489202,0.127175124904042,0.197906332095909,0.311448843013874,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0134759471663239,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0278279104299399,0,0,0
|gostat_on_MCL_coexpression=
|ontology_enrichment_celltype=CL:0000988!5.55e-20!32;CL:0002032!5.55e-20!32;CL:0000037!5.55e-20!32;CL:0000566!5.55e-20!32;CL:0000837!5.55e-20!32;CL:0002031!2.26e-15!25;CL:0000838!9.12e-14!12;CL:0002320!2.49e-13!46;CL:0000134!2.49e-13!46;CL:0002242!6.59e-13!16;CL:0000084!1.52e-12!11;CL:0000827!1.52e-12!11;CL:0000542!2.19e-12!13;CL:0000051!2.19e-12!13;CL:0000791!4.68e-11!9;CL:0000789!4.68e-11!9;CL:0002420!4.68e-11!9;CL:0002419!4.68e-11!9;CL:0000790!4.68e-11!9;CL:0000219!8.26e-11!54;CL:0000738!3.29e-10!17;CL:0002087!3.29e-10!17;CL:0000624!6.41e-10!8;CL:0000049!3.39e-09!19;CL:0000034!1.28e-07!97;CL:0000893!1.46e-07!6;CL:0002489!1.46e-07!6;CL:0000898!1.46e-07!6;CL:0000809!1.46e-07!6;CL:0000810!1.46e-07!6;CL:0000895!1.46e-07!6;CL:0000808!1.46e-07!6;CL:0000894!1.46e-07!6;CL:0000806!1.46e-07!6;CL:0000807!1.46e-07!6;CL:0000805!1.46e-07!6;CL:0002425!1.46e-07!6;CL:0002436!1.46e-07!6;CL:0002427!1.46e-07!6;CL:0002428!1.46e-07!6;CL:0002429!1.46e-07!6;CL:0002433!1.46e-07!6;CL:0002431!1.46e-07!6;CL:0002432!1.46e-07!6
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!1.18e-14!48;UBERON:0002405!1.18e-14!48;UBERON:0002390!9.67e-14!45;UBERON:0003061!9.67e-14!45;UBERON:0002384!2.49e-13!46;UBERON:0002370!3.32e-12!23;UBERON:0000974!3.32e-12!23;UBERON:0004807!3.32e-12!23;UBERON:0005058!3.32e-12!23;UBERON:0003351!3.32e-12!23;UBERON:0009113!3.32e-12!23;UBERON:0003295!3.32e-12!23;UBERON:0009722!3.32e-12!23;UBERON:0005562!3.32e-12!23;UBERON:0007690!3.32e-12!23;UBERON:0006562!1.89e-11!24;UBERON:0003408!1.89e-11!24;UBERON:0001557!1.89e-11!24;UBERON:0001042!1.89e-11!24;UBERON:0008814!1.89e-11!24;UBERON:0009145!1.89e-11!24;UBERON:0004177!1.18e-10!29;UBERON:0005057!1.18e-10!29;UBERON:0000072!1.54e-09!27;UBERON:0000077!6.42e-09!35;UBERON:0003081!1.24e-08!87;UBERON:0000490!2.32e-07!66;UBERON:0007811!2.64e-07!36
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.534222,0.367606,0.434198,0.260188,0.448401,0.538088,0.173246,0.181564,0.386846,0.494602,1.30517,0.173454,0.550255,0.275867,0,0.742571,0.252772,0.483643,0.29826,0.332107,0.0622758,0.549359,0.258745,0.374936,0.577606,0.153291,0.469052,0.303071,0.757024,0.455168,0.843667,0.250677,0.136998,0.757987,0.185086,0.242032,0.522578,0.221921,0.570041,0.256422,0.460258,0.204736,0.27776,0.663502,0.423266,0.662995,1.21655,0.170971,0.305876,0.725127,0.604356,0.362495,0.985264,1.00271,0.557354,0.314394,0.513517,0.145699,0.555328,0.823643,0.613749,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,1.0125,0.236196,1.03623,0.433216,0.813951,0.42492,0.651651,0.806481,0.892913,0.530481,0.759925,0.612313,0.167672,0.920903,0.491838,0.0299392,0.376919,1.60318,1.65055,1.20871,0.925879,0.856465,0.733735,0.218233,0.585369,0.1711,0.859272,0.663249,0.332938,0.679141,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,1.20804,0.340849,0.333829,1.00333,0.96962,0.337254,0.499714,1.21576,1.30779,0.333069,0.437894,1.76093,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,1.34763,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.061199,1.03631,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.724779,0.766041,0.0553085,0.986833,0.598134,0.569994,1.06851,0.605358,0.782826,0.39061,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.240994,0.524587,0.166768
}}

Latest revision as of 16:01, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:61968605..61968608,+p@chr10:61968605..61968608
+
Mm9::chr17:34974117..34974137,+p4@Dom3z
Mm9::chr3:105694950..105694970,+p@chr3:105694950..105694970
+
Mm9::chr4:33334901..33334974,+p@chr4:33334901..33334974
+
Mm9::chr6:38483640..38483669,-p@chr6:38483640..38483669
-
Mm9::chr7:29166278..29166300,+p@chr7:29166278..29166300
+
Mm9::chr8:108582687..108582734,+p4@Nfatc3
Mm9::chr8:108583128..108583147,-p@chr8:108583128..108583147
-


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

no results for this coexpression

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>

Cell Type
Ontology termp-valuen
hematopoietic cell5.55e-2032
hematopoietic oligopotent progenitor cell5.55e-2032
hematopoietic stem cell5.55e-2032
angioblastic mesenchymal cell5.55e-2032
hematopoietic multipotent progenitor cell5.55e-2032
hematopoietic lineage restricted progenitor cell2.26e-1525
lymphoid lineage restricted progenitor cell9.12e-1412
connective tissue cell2.49e-1346
mesenchymal cell2.49e-1346
nucleate cell6.59e-1316
T cell1.52e-1211
pro-T cell1.52e-1211
lymphocyte2.19e-1213
common lymphoid progenitor2.19e-1213
mature alpha-beta T cell4.68e-119
alpha-beta T cell4.68e-119
immature T cell4.68e-119
mature T cell4.68e-119
immature alpha-beta T cell4.68e-119
motile cell8.26e-1154
leukocyte3.29e-1017
nongranular leukocyte3.29e-1017
CD4-positive, alpha-beta T cell6.41e-108
common myeloid progenitor3.39e-0919
stem cell1.28e-0797
thymocyte1.46e-076
double negative thymocyte1.46e-076
naive T cell1.46e-076
double-positive, alpha-beta thymocyte1.46e-076
CD4-positive, alpha-beta thymocyte1.46e-076
naive thymus-derived CD4-positive, alpha-beta T cell1.46e-076
DN4 thymocyte1.46e-076
DN1 thymic pro-T cell1.46e-076
DN2 thymocyte1.46e-076
DN3 thymocyte1.46e-076
immature single positive thymocyte1.46e-076
early T lineage precursor1.46e-076
mature CD4 single-positive thymocyte1.46e-076
resting double-positive thymocyte1.46e-076
double-positive blast1.46e-076
CD69-positive double-positive thymocyte1.46e-076
CD69-positive, CD4-positive single-positive thymocyte1.46e-076
CD4-positive, CD8-intermediate double-positive thymocyte1.46e-076
CD24-positive, CD4 single-positive thymocyte1.46e-076

Uber Anatomy
Ontology termp-valuen
hemolymphoid system1.18e-1448
immune system1.18e-1448
hematopoietic system9.67e-1445
blood island9.67e-1445
connective tissue2.49e-1346
thymus3.32e-1223
neck3.32e-1223
respiratory system epithelium3.32e-1223
hemolymphoid system gland3.32e-1223
pharyngeal epithelium3.32e-1223
thymic region3.32e-1223
pharyngeal gland3.32e-1223
entire pharyngeal arch endoderm3.32e-1223
thymus primordium3.32e-1223
early pharyngeal endoderm3.32e-1223
pharynx1.89e-1124
gland of gut1.89e-1124
upper respiratory tract1.89e-1124
chordate pharynx1.89e-1124
pharyngeal arch system1.89e-1124
pharyngeal region of foregut1.89e-1124
hemopoietic organ1.18e-1029
immune organ1.18e-1029
segment of respiratory tract1.54e-0927
mixed endoderm/mesoderm-derived structure6.42e-0935
lateral plate mesoderm1.24e-0887
unilaminar epithelium2.32e-0766
craniocervical region2.64e-0736


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)
MA0003.10.127295
MA0004.10.434673
MA0006.10.271714
MA0007.10.419994
MA0009.10.870101
MA0014.10.325341
MA0017.10.296816
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.769859
MA0029.10.804619
MA0030.10.811181
MA0031.11.82653
MA0038.10.577528
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.10.102483
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.10.0283571
MA0056.10
MA0057.10.643187
MA0058.10.341628
MA0059.10.353484
MA0060.12.42557
MA0061.10.638933
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.11.09399
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.10.433095
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.49616
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.10.401504
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.11.69377
MA0103.10.307078
MA0105.10.41549
MA0106.10.626997
MA0107.11.47808
MA0108.20.710846
MA0109.10
MA0111.11.06639
MA0113.10.598933
MA0114.10.222763
MA0115.10.969632
MA0116.11.36991
MA0117.10.937363
MA0119.10.951747
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.10.683521
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.10.169849
MA0140.10.519484
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.11.86541
MA0145.10.0701568
MA0146.10.0169049
MA0147.10.236889
MA0148.11.14345
MA0149.10.367458
MA0062.21.96779
MA0035.20.524137
MA0039.20.402847
MA0138.20.675599
MA0002.20.172399
MA0137.21.55649
MA0104.20.18504
MA0047.22.41253
MA0112.20.2464
MA0065.20.247168
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.330759
MA0155.10.275377
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.10.453546
MA0161.10
MA0162.10.230918
MA0163.10.669601
MA0164.10.551114
MA0080.21.48111
MA0018.21.37842
MA0099.20.669311
MA0079.20.685525
MA0102.21.59466
MA0258.10.210437
MA0259.10.227035
MA0442.10
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