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MCL coexpression mm9:420: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=
|ontology_enrichment_celltype=CL:0000838!1.75e-22!12;CL:0000988!9.02e-22!32;CL:0002032!9.02e-22!32;CL:0000037!9.02e-22!32;CL:0000566!9.02e-22!32;CL:0000837!9.02e-22!32;CL:0000791!6.93e-21!9;CL:0000789!6.93e-21!9;CL:0002420!6.93e-21!9;CL:0002419!6.93e-21!9;CL:0000790!6.93e-21!9;CL:0000542!1.49e-20!13;CL:0000051!1.49e-20!13;CL:0000084!2.65e-20!11;CL:0000827!2.65e-20!11;CL:0000624!1.25e-18!8;CL:0002031!9.11e-18!25;CL:0002242!3.29e-16!16;CL:0002320!3.25e-15!46;CL:0000134!3.25e-15!46;CL:0000738!4.20e-15!17;CL:0002087!4.20e-15!17;CL:0000893!5.52e-14!6;CL:0002489!5.52e-14!6;CL:0000898!5.52e-14!6;CL:0000809!5.52e-14!6;CL:0000810!5.52e-14!6;CL:0000895!5.52e-14!6;CL:0000808!5.52e-14!6;CL:0000894!5.52e-14!6;CL:0000806!5.52e-14!6;CL:0000807!5.52e-14!6;CL:0000805!5.52e-14!6;CL:0002425!5.52e-14!6;CL:0002436!5.52e-14!6;CL:0002427!5.52e-14!6;CL:0002428!5.52e-14!6;CL:0002429!5.52e-14!6;CL:0002433!5.52e-14!6;CL:0002431!5.52e-14!6;CL:0002432!5.52e-14!6;CL:0000219!3.17e-12!54;CL:0000034!6.15e-10!97;CL:0000723!6.87e-08!91;CL:0000048!6.87e-08!91
|ontology_enrichment_disease=DOID:0060100!1.22e-07!3;DOID:4045!1.22e-07!3
|ontology_enrichment_uberon=UBERON:0002370!9.06e-18!23;UBERON:0000974!9.06e-18!23;UBERON:0004807!9.06e-18!23;UBERON:0005058!9.06e-18!23;UBERON:0003351!9.06e-18!23;UBERON:0009113!9.06e-18!23;UBERON:0003295!9.06e-18!23;UBERON:0009722!9.06e-18!23;UBERON:0005562!9.06e-18!23;UBERON:0007690!9.06e-18!23;UBERON:0006562!7.01e-17!24;UBERON:0003408!7.01e-17!24;UBERON:0001557!7.01e-17!24;UBERON:0001042!7.01e-17!24;UBERON:0008814!7.01e-17!24;UBERON:0009145!7.01e-17!24;UBERON:0002390!5.75e-16!45;UBERON:0003061!5.75e-16!45;UBERON:0002384!3.25e-15!46;UBERON:0004177!3.34e-15!29;UBERON:0005057!3.34e-15!29;UBERON:0002193!1.18e-14!48;UBERON:0002405!1.18e-14!48;UBERON:0000072!1.30e-14!27;UBERON:0000077!1.44e-13!35;UBERON:0007811!1.55e-11!36;UBERON:0000063!1.77e-10!35;UBERON:0000490!2.41e-09!66;UBERON:0000153!4.56e-09!43;UBERON:0000065!1.87e-08!41;UBERON:0001004!3.57e-08!42;UBERON:0003929!3.04e-07!55
|tfbs_overrepresentation_for_novel_motifs=0.162057,0.380762,0.144778,0.191238,0.572598,0.583749,0.743966,0.146885,0.361988,0.222734,0.236307,0.260789,0.615635,0.766078,0.295744,0,0.44163,0.260255,0.130179,0.734378,0.772726,0.519892,0.279154,0.568642,0.89405,0.816061,0.121208,0.216938,1.14297,0.0175588,0.595646,0.531719,0.0739139,0.101305,0.0880674,0.200104,0.0693463,0.257981,0.812295,0.177517,0.265799,0.604618,0.961289,0.298695,0.240103,1.03234,0.974269,0.6478,0.565584,0.343195,1.09109,0.865292,0.61775,0.661847,0.67813,0.28555,0.110603,0.699566,0.111806,1.41536,0.513661,0.882655,1.06787,0.4166,0.294453,0.451957,0.806865,1.14503,0.509463,1.00145,0.414221,0.153772,0.194724,0.709559,0.481813,0.445056,0.101234,0.363297,1.24575,0.392419,0.3566,0.456892,0.330377,0.139579,0.602212,0.333038,0.138203,0.394307,0.377064,1.30447,0.873554,0.606796,0.543309,0.0821171,0.057338,0.416353,0.14406,0.545856,0.373124,0.0129514,0.523231,0.531465,0.645628,0.4269,0.425983,1.13772,0.478524,0.225669,0.127231,2.49231,0.476067,0.647285,0.124928,0.67478,0.880323,0.557702,0.461856,0.193921,0.442771,0.238974,0.714636,0.398522,0.819386,0.951399,0.932468,0.501574,0.276618,0.53717,0.805419,0.284377,0.629874,0.546435,0.777296,0.296474,0.9011,0.174785,0.501821,1.14299,0.853868,1.66928,1.27308,0.811357,0.313144,0.541193,0.420352,0.605406,0.375553,1.62988,0.505775,0.577124,0.660477,0.28414,0.66331,0.194002,0.29573,0.739975,0.867144,0.647202,0.160402,0.501353,0.862985,0.601424,0.501973,0.15582,0.417485,0.289792,1.33937,0.259556,0.979717
|tfbs_overrepresentation_jaspar=MA0003.1;1.60555,MA0004.1;0.191582,MA0006.1;1.50774,MA0007.1;0.181021,MA0009.1;0.5557,MA0014.1;0.393889,MA0017.1;0.0999826,MA0019.1;1.02123,MA0024.1;0.516087,MA0025.1;0.773017,MA0027.1;2.16618,MA0028.1;0.631409,MA0029.1;0.496599,MA0030.1;0.502474,MA0031.1;0.470779,MA0038.1;0.301835,MA0040.1;0.567108,MA0041.1;0.854076,MA0042.1;1.32684,MA0043.1;0.644695,MA0046.1;0.58854,MA0048.1;1.1804,MA0050.1;0.219748,MA0051.1;0.309072,MA0052.1;0.574473,MA0055.1;0.75569,MA0056.1;0,MA0057.1;0.772226,MA0058.1;0.127732,MA0059.1;0.421089,MA0060.1;0.0476793,MA0061.1;0.060618,MA0063.1;0,MA0066.1;0.795934,MA0067.1;0.879099,MA0068.1;0.153549,MA0069.1;0.574784,MA0070.1;0.565924,MA0071.1;0.219128,MA0072.1;0.558195,MA0073.1;6.80067e-06,MA0074.1;0.264633,MA0076.1;0.724696,MA0077.1;0.538513,MA0078.1;0.336143,MA0081.1;0.896655,MA0083.1;0.643958,MA0084.1;1.1979,MA0087.1;0.604077,MA0088.1;0.336188,MA0089.1;0,MA0090.1;0.969034,MA0091.1;0.200988,MA0092.1;0.167962,MA0093.1;0.0955883,MA0095.1;0,MA0098.1;0,MA0100.1;0.255651,MA0101.1;0.141127,MA0103.1;0.702489,MA0105.1;0.239813,MA0106.1;0.342589,MA0107.1;0.102611,MA0108.2;0.413973,MA0109.1;0,MA0111.1;0.177475,MA0113.1;0.319332,MA0114.1;0.215695,MA0115.1;0.647296,MA0116.1;0.288992,MA0117.1;0.617392,MA0119.1;0.436476,MA0122.1;0.635764,MA0124.1;0.828115,MA0125.1;0.757653,MA0130.1;0,MA0131.1;0.390422,MA0132.1;0,MA0133.1;0,MA0135.1;0.67864,MA0136.1;0.280269,MA0139.1;0.601065,MA0140.1;0.255562,MA0141.1;0.37559,MA0142.1;0.457961,MA0143.1;0.332773,MA0144.1;0.0609575,MA0145.1;0.584715,MA0146.1;1.15102,MA0147.1;0.509077,MA0148.1;1.74375,MA0149.1;0.144679,MA0062.2;1.11207,MA0035.2;0.259203,MA0039.2;0.062404,MA0138.2;0.997863,MA0002.2;0.611367,MA0137.2;0.116005,MA0104.2;0.371038,MA0047.2;0.814521,MA0112.2;0.208001,MA0065.2;0.372253,MA0150.1;0.53401,MA0151.1;0,MA0152.1;0.301303,MA0153.1;0.694211,MA0154.1;0.325394,MA0155.1;0.118163,MA0156.1;0.110475,MA0157.1;0.429861,MA0158.1;0,MA0159.1;0.250417,MA0160.1;0.205397,MA0161.1;0,MA0162.1;0.808204,MA0163.1;0.375837,MA0164.1;0.280556,MA0080.2;0.337091,MA0018.2;3.04165,MA0099.2;0.37828,MA0079.2;0.372091,MA0102.2;1.24942,MA0258.1;0.0535937,MA0259.1;0.221921,MA0442.1;0
}}

Latest revision as of 15:16, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:79604055..79604067,-p7@Dos
Mm9::chr11:82878889..82878900,+p@chr11:82878889..82878900
+
Mm9::chr12:77471362..77471381,-p@chr12:77471362..77471381
-
Mm9::chr13:54788670..54788684,+p@chr13:54788670..54788684
+
Mm9::chr18:10181301..10181312,+p@chr18:10181301..10181312
+
Mm9::chr18:21121370..21121377,+p@chr18:21121370..21121377
+
Mm9::chr19:53495804..53495818,+p@chr19:53495804..53495818
+
Mm9::chr19:53499218..53499234,-p@chr19:53499218..53499234
-
Mm9::chr1:53841323..53841334,+p@chr1:53841323..53841334
+
Mm9::chr1:95722040..95722067,-p@chr1:95722040..95722067
-
Mm9::chr2:58009575..58009583,+p@chr2:58009575..58009583
+
Mm9::chr2:58009949..58009967,+p@chr2:58009949..58009967
+
Mm9::chr3:21834958..21834966,-p@chr3:21834958..21834966
-
Mm9::chr3:87946096..87946116,-p@chr3:87946096..87946116
-
Mm9::chr5:22941197..22941214,+p@chr5:22941197..22941214
+
Mm9::chr8:129118593..129118612,+p@chr8:129118593..129118612
+
Mm9::chr8:87501401..87501449,-p@chr8:87501401..87501449
-
Mm9::chr8:87510243..87510252,+p@chr8:87510243..87510252
+


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>disease_data<br>

Cell Type
Ontology termp-valuen
lymphoid lineage restricted progenitor cell1.75e-2212
hematopoietic cell9.02e-2232
hematopoietic oligopotent progenitor cell9.02e-2232
hematopoietic stem cell9.02e-2232
angioblastic mesenchymal cell9.02e-2232
hematopoietic multipotent progenitor cell9.02e-2232
mature alpha-beta T cell6.93e-219
alpha-beta T cell6.93e-219
immature T cell6.93e-219
mature T cell6.93e-219
immature alpha-beta T cell6.93e-219
lymphocyte1.49e-2013
common lymphoid progenitor1.49e-2013
T cell2.65e-2011
pro-T cell2.65e-2011
CD4-positive, alpha-beta T cell1.25e-188
hematopoietic lineage restricted progenitor cell9.11e-1825
nucleate cell3.29e-1616
connective tissue cell3.25e-1546
mesenchymal cell3.25e-1546
leukocyte4.20e-1517
nongranular leukocyte4.20e-1517
thymocyte5.52e-146
double negative thymocyte5.52e-146
naive T cell5.52e-146
double-positive, alpha-beta thymocyte5.52e-146
CD4-positive, alpha-beta thymocyte5.52e-146
naive thymus-derived CD4-positive, alpha-beta T cell5.52e-146
DN4 thymocyte5.52e-146
DN1 thymic pro-T cell5.52e-146
DN2 thymocyte5.52e-146
DN3 thymocyte5.52e-146
immature single positive thymocyte5.52e-146
early T lineage precursor5.52e-146
mature CD4 single-positive thymocyte5.52e-146
resting double-positive thymocyte5.52e-146
double-positive blast5.52e-146
CD69-positive double-positive thymocyte5.52e-146
CD69-positive, CD4-positive single-positive thymocyte5.52e-146
CD4-positive, CD8-intermediate double-positive thymocyte5.52e-146
CD24-positive, CD4 single-positive thymocyte5.52e-146
motile cell3.17e-1254
stem cell6.15e-1097
somatic stem cell6.87e-0891
multi fate stem cell6.87e-0891

Uber Anatomy
Ontology termp-valuen
thymus9.06e-1823
neck9.06e-1823
respiratory system epithelium9.06e-1823
hemolymphoid system gland9.06e-1823
pharyngeal epithelium9.06e-1823
thymic region9.06e-1823
pharyngeal gland9.06e-1823
entire pharyngeal arch endoderm9.06e-1823
thymus primordium9.06e-1823
early pharyngeal endoderm9.06e-1823
pharynx7.01e-1724
gland of gut7.01e-1724
upper respiratory tract7.01e-1724
chordate pharynx7.01e-1724
pharyngeal arch system7.01e-1724
pharyngeal region of foregut7.01e-1724
hematopoietic system5.75e-1645
blood island5.75e-1645
connective tissue3.25e-1546
hemopoietic organ3.34e-1529
immune organ3.34e-1529
hemolymphoid system1.18e-1448
immune system1.18e-1448
segment of respiratory tract1.30e-1427
mixed endoderm/mesoderm-derived structure1.44e-1335
craniocervical region1.55e-1136
organ segment1.77e-1035
unilaminar epithelium2.41e-0966
anterior region of body4.56e-0943
respiratory tract1.87e-0841
respiratory system3.57e-0842
gut epithelium3.04e-0755

Disease
Ontology termp-valuen
musculoskeletal system cancer1.22e-073
muscle cancer1.22e-073


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)
MA0003.11.60555
MA0004.10.191582
MA0006.11.50774
MA0007.10.181021
MA0009.10.5557
MA0014.10.393889
MA0017.10.0999826
MA0019.11.02123
MA0024.10.516087
MA0025.10.773017
MA0027.12.16618
MA0028.10.631409
MA0029.10.496599
MA0030.10.502474
MA0031.10.470779
MA0038.10.301835
MA0040.10.567108
MA0041.10.854076
MA0042.11.32684
MA0043.10.644695
MA0046.10.58854
MA0048.11.1804
MA0050.10.219748
MA0051.10.309072
MA0052.10.574473
MA0055.10.75569
MA0056.10
MA0057.10.772226
MA0058.10.127732
MA0059.10.421089
MA0060.10.0476793
MA0061.10.060618
MA0063.10
MA0066.10.795934
MA0067.10.879099
MA0068.10.153549
MA0069.10.574784
MA0070.10.565924
MA0071.10.219128
MA0072.10.558195
MA0073.16.80067e-06
MA0074.10.264633
MA0076.10.724696
MA0077.10.538513
MA0078.10.336143
MA0081.10.896655
MA0083.10.643958
MA0084.11.1979
MA0087.10.604077
MA0088.10.336188
MA0089.10
MA0090.10.969034
MA0091.10.200988
MA0092.10.167962
MA0093.10.0955883
MA0095.10
MA0098.10
MA0100.10.255651
MA0101.10.141127
MA0103.10.702489
MA0105.10.239813
MA0106.10.342589
MA0107.10.102611
MA0108.20.413973
MA0109.10
MA0111.10.177475
MA0113.10.319332
MA0114.10.215695
MA0115.10.647296
MA0116.10.288992
MA0117.10.617392
MA0119.10.436476
MA0122.10.635764
MA0124.10.828115
MA0125.10.757653
MA0130.10
MA0131.10.390422
MA0132.10
MA0133.10
MA0135.10.67864
MA0136.10.280269
MA0139.10.601065
MA0140.10.255562
MA0141.10.37559
MA0142.10.457961
MA0143.10.332773
MA0144.10.0609575
MA0145.10.584715
MA0146.11.15102
MA0147.10.509077
MA0148.11.74375
MA0149.10.144679
MA0062.21.11207
MA0035.20.259203
MA0039.20.062404
MA0138.20.997863
MA0002.20.611367
MA0137.20.116005
MA0104.20.371038
MA0047.20.814521
MA0112.20.208001
MA0065.20.372253
MA0150.10.53401
MA0151.10
MA0152.10.301303
MA0153.10.694211
MA0154.10.325394
MA0155.10.118163
MA0156.10.110475
MA0157.10.429861
MA0158.10
MA0159.10.250417
MA0160.10.205397
MA0161.10
MA0162.10.808204
MA0163.10.375837
MA0164.10.280556
MA0080.20.337091
MA0018.23.04165
MA0099.20.37828
MA0079.20.372091
MA0102.21.24942
MA0258.10.0535937
MA0259.10.221921
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:420&oldid=3072419"