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MCL coexpression mm9:269: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=
|ontology_enrichment_celltype=CL:0000988!1.89e-25!32;CL:0002032!1.89e-25!32;CL:0000037!1.89e-25!32;CL:0000566!1.89e-25!32;CL:0000837!1.89e-25!32;CL:0000791!2.09e-25!9;CL:0000789!2.09e-25!9;CL:0002420!2.09e-25!9;CL:0002419!2.09e-25!9;CL:0000790!2.09e-25!9;CL:0000838!5.75e-23!12;CL:0000624!8.88e-23!8;CL:0000542!4.80e-21!13;CL:0000051!4.80e-21!13;CL:0000084!1.77e-20!11;CL:0000827!1.77e-20!11;CL:0002320!1.60e-18!46;CL:0000134!1.60e-18!46;CL:0000893!1.23e-17!6;CL:0002489!1.23e-17!6;CL:0000898!1.23e-17!6;CL:0000809!1.23e-17!6;CL:0000810!1.23e-17!6;CL:0000895!1.23e-17!6;CL:0000808!1.23e-17!6;CL:0000894!1.23e-17!6;CL:0000806!1.23e-17!6;CL:0000807!1.23e-17!6;CL:0000805!1.23e-17!6;CL:0002425!1.23e-17!6;CL:0002436!1.23e-17!6;CL:0002427!1.23e-17!6;CL:0002428!1.23e-17!6;CL:0002429!1.23e-17!6;CL:0002433!1.23e-17!6;CL:0002431!1.23e-17!6;CL:0002432!1.23e-17!6;CL:0000219!6.97e-17!54;CL:0002242!1.01e-16!16;CL:0000738!1.28e-15!17;CL:0002087!1.28e-15!17;CL:0002031!2.84e-14!25;CL:0000034!8.50e-10!97;CL:0000049!3.05e-08!19;CL:0000723!2.83e-07!91;CL:0000048!2.83e-07!91
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002384!1.60e-18!46;UBERON:0002193!2.94e-16!48;UBERON:0002405!2.94e-16!48;UBERON:0002370!1.12e-14!23;UBERON:0000974!1.12e-14!23;UBERON:0004807!1.12e-14!23;UBERON:0005058!1.12e-14!23;UBERON:0003351!1.12e-14!23;UBERON:0009113!1.12e-14!23;UBERON:0003295!1.12e-14!23;UBERON:0009722!1.12e-14!23;UBERON:0005562!1.12e-14!23;UBERON:0007690!1.12e-14!23;UBERON:0006562!5.80e-14!24;UBERON:0003408!5.80e-14!24;UBERON:0001557!5.80e-14!24;UBERON:0001042!5.80e-14!24;UBERON:0008814!5.80e-14!24;UBERON:0009145!5.80e-14!24;UBERON:0002390!9.24e-14!45;UBERON:0003061!9.24e-14!45;UBERON:0000072!3.85e-12!27;UBERON:0004177!3.89e-11!29;UBERON:0005057!3.89e-11!29;UBERON:0000077!1.74e-10!35;UBERON:0000063!8.11e-09!35;UBERON:0007811!1.66e-08!36;UBERON:0000065!3.48e-07!41;UBERON:0003081!4.02e-07!87;UBERON:0001004!5.85e-07!42;UBERON:0000153!9.61e-07!43
|tfbs_overrepresentation_for_novel_motifs=1.27185,0.431763,0.432388,0.275278,0.0895641,0.293623,0.417775,0.204568,0.395089,0.904261,0.110217,0.400509,0.578224,0.435601,0.252098,0,0.740836,0.407946,0.513917,0.195714,0.040141,0.783037,0.855514,0.0883885,0.203316,0.476423,0.0718027,0.320983,0.554665,0.0942073,0.302501,0.345924,0.979842,0.852788,0.47524,0.267427,0.626079,0.395367,0.546738,0.124404,0.0865113,0.0927543,0.362012,0.0244445,0.740218,0.941084,0.212558,0.34211,0.263671,0.890239,0.711629,0.174075,1.18111,0.462148,0.477006,0.446098,0.138573,0.382447,1.2249,0.14413,1.58167,1.01904,1.29777,0.248044,0.903332,0.277492,0.596353,0.920398,0.871514,0.781435,0.698446,0.383821,0.844989,0.505848,0.25361,0.224639,0.852313,0.204903,0.316915,0.16073,0.608364,0.28165,0.179134,0.192046,0.408287,1.7184,0.442631,0.0944002,0.617678,1.07627,0.659258,0.412394,0.356069,0.0941476,0.532436,0.724405,0.824044,0.358304,0.610209,0.391759,0.194195,0.345703,0.44741,0.25656,0.255799,0.30866,0.299999,0.336675,0.671486,0.158288,0.216311,0.448913,0.660158,0.112926,0.665677,0.67732,0.189976,0.280013,0.269784,0.61238,0.510527,0.233232,0.479162,0.59017,1.70178,0.319766,0.847582,0.925191,0.594996,0.733714,0.433157,0.56298,0.568676,0.153414,0.685415,0.0991348,3.01489,0.642872,0.640623,1.43657,1.04548,0.600569,0.16595,0.354213,0.25114,0.0929729,0.214675,1.39749,1.31906,0.433531,0.719264,0.357058,0.46348,0.752137,0.15286,0.533955,0.174709,0.272723,0.832173,1.81755,0.649247,0.407582,0.857031,0.213736,0.694619,0.45395,0.0161929,0.794153,1.90568
}}

Latest revision as of 15:00, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:80217659..80217683,-p@chr10:80217659..80217683
-
Mm9::chr11:32432845..32432870,+p3@Stk10
Mm9::chr11:60745182..60745203,-p4@Gm16516
Mm9::chr13:30909362..30909373,-p@chr13:30909362..30909373
-
Mm9::chr15:96472050..96472062,-p16@Slc38a1
Mm9::chr16:55838757..55838774,-p2@Nfkbiz
Mm9::chr16:55838779..55838788,-p9@Nfkbiz
Mm9::chr18:7868875..7868886,+p14@Wac
Mm9::chr1:158545949..158545993,+p@chr1:158545949..158545993
+
Mm9::chr1:158546008..158546017,+p@chr1:158546008..158546017
+
Mm9::chr2:151799924..151799935,-p16@Fam110a
Mm9::chr2:156665889..156665900,+p8@Tgif2
Mm9::chr2:34813622..34813633,-p10@Traf1
Mm9::chr2:34817203..34817218,+p@chr2:34817203..34817218
+
Mm9::chr2:34817222..34817237,+p@chr2:34817222..34817237
+
Mm9::chr2:34817239..34817272,+p@chr2:34817239..34817272
+
Mm9::chr3:30993974..30994045,+p1@Skil
Mm9::chr3:30994819..30994854,+p@chr3:30994819..30994854
+
Mm9::chr3:31020619..31020623,+p@chr3:31020619..31020623
+
Mm9::chr3:88893621..88893638,-p5@Rusc1
Mm9::chr4:133228897..133228917,-p3@Pigv
Mm9::chr4:43466657..43466670,+p@chr4:43466657..43466670
+
Mm9::chr4:43466697..43466710,+p@chr4:43466697..43466710
+
Mm9::chr7:138553839..138553860,-p2@Ikzf5
Mm9::chr7:26472144..26472155,+p4@Tgfb1
Mm9::chr7:90804001..90804008,-p4@Il16
Mm9::chr9:75257159..75257190,-p4@Mapk6
Mm9::chr9:75257758..75257846,-p1@Mapk6
Mm9::chr9:7872917..7872935,-p6@Birc3
Mm9::chr9:7872951..7872958,-p11@Birc3
Mm9::chr9:7872971..7872978,-p13@Birc3


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 cell1.89e-2532
hematopoietic oligopotent progenitor cell1.89e-2532
hematopoietic stem cell1.89e-2532
angioblastic mesenchymal cell1.89e-2532
hematopoietic multipotent progenitor cell1.89e-2532
mature alpha-beta T cell2.09e-259
alpha-beta T cell2.09e-259
immature T cell2.09e-259
mature T cell2.09e-259
immature alpha-beta T cell2.09e-259
lymphoid lineage restricted progenitor cell5.75e-2312
CD4-positive, alpha-beta T cell8.88e-238
lymphocyte4.80e-2113
common lymphoid progenitor4.80e-2113
T cell1.77e-2011
pro-T cell1.77e-2011
connective tissue cell1.60e-1846
mesenchymal cell1.60e-1846
thymocyte1.23e-176
double negative thymocyte1.23e-176
naive T cell1.23e-176
double-positive, alpha-beta thymocyte1.23e-176
CD4-positive, alpha-beta thymocyte1.23e-176
naive thymus-derived CD4-positive, alpha-beta T cell1.23e-176
DN4 thymocyte1.23e-176
DN1 thymic pro-T cell1.23e-176
DN2 thymocyte1.23e-176
DN3 thymocyte1.23e-176
immature single positive thymocyte1.23e-176
early T lineage precursor1.23e-176
mature CD4 single-positive thymocyte1.23e-176
resting double-positive thymocyte1.23e-176
double-positive blast1.23e-176
CD69-positive double-positive thymocyte1.23e-176
CD69-positive, CD4-positive single-positive thymocyte1.23e-176
CD4-positive, CD8-intermediate double-positive thymocyte1.23e-176
CD24-positive, CD4 single-positive thymocyte1.23e-176
motile cell6.97e-1754
nucleate cell1.01e-1616
leukocyte1.28e-1517
nongranular leukocyte1.28e-1517
hematopoietic lineage restricted progenitor cell2.84e-1425
stem cell8.50e-1097
common myeloid progenitor3.05e-0819
somatic stem cell2.83e-0791
multi fate stem cell2.83e-0791

Uber Anatomy
Ontology termp-valuen
connective tissue1.60e-1846
hemolymphoid system2.94e-1648
immune system2.94e-1648
thymus1.12e-1423
neck1.12e-1423
respiratory system epithelium1.12e-1423
hemolymphoid system gland1.12e-1423
pharyngeal epithelium1.12e-1423
thymic region1.12e-1423
pharyngeal gland1.12e-1423
entire pharyngeal arch endoderm1.12e-1423
thymus primordium1.12e-1423
early pharyngeal endoderm1.12e-1423
pharynx5.80e-1424
gland of gut5.80e-1424
upper respiratory tract5.80e-1424
chordate pharynx5.80e-1424
pharyngeal arch system5.80e-1424
pharyngeal region of foregut5.80e-1424
hematopoietic system9.24e-1445
blood island9.24e-1445
segment of respiratory tract3.85e-1227
hemopoietic organ3.89e-1129
immune organ3.89e-1129
mixed endoderm/mesoderm-derived structure1.74e-1035
organ segment8.11e-0935
craniocervical region1.66e-0836
respiratory tract3.48e-0741
lateral plate mesoderm4.02e-0787
respiratory system5.85e-0742
anterior region of body9.61e-0743


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)
MA0003.14.10295
MA0004.10.275884
MA0006.11.49695
MA0007.10.257336
MA0009.10.366963
MA0014.10.295074
MA0017.10.535828
MA0019.10.650431
MA0024.10.884334
MA0025.10.564682
MA0027.11.93116
MA0028.10.262309
MA0029.10.315482
MA0030.10.320542
MA0031.11.44983
MA0038.10.157421
MA0040.10.377038
MA0041.10.0501054
MA0042.10.173505
MA0043.10.446565
MA0046.10.396073
MA0048.10.0692225
MA0050.10.669135
MA0051.10.48978
MA0052.10.383564
MA0055.10.0776044
MA0056.10
MA0057.10.512875
MA0058.10.043314
MA0059.10.40278
MA0060.10.00889506
MA0061.19.70627
MA0063.10
MA0066.10.150832
MA0067.11.59617
MA0068.10.226704
MA0069.10.383839
MA0070.10.37599
MA0071.10.324912
MA0072.10.369163
MA0073.10.0205889
MA0074.11.90599
MA0076.10.139184
MA0077.10.351866
MA0078.10.183594
MA0081.10.204366
MA0083.10.445897
MA0084.10.971934
MA0087.10.409958
MA0088.12.98356
MA0089.10
MA0090.10.234247
MA0091.10.0866349
MA0092.10.234618
MA0093.10.276659
MA0095.10
MA0098.10
MA0100.10.123725
MA0101.111.4571
MA0103.10.131431
MA0105.18.1616
MA0106.10.552556
MA0107.113.6641
MA0108.20.245881
MA0109.10
MA0111.10.251142
MA0113.10.170658
MA0114.10.326395
MA0115.10.448923
MA0116.13.57235
MA0117.10.42191
MA0119.10.741159
MA0122.11.11729
MA0124.10.616327
MA0125.10.55037
MA0130.10
MA0131.10.64304
MA0132.10
MA0133.10
MA0135.10.477472
MA0136.10.436338
MA0139.10.560351
MA0140.10.123662
MA0141.10.0381379
MA0142.10.282551
MA0143.10.180984
MA0144.10.333849
MA0145.11.41804
MA0146.11.24417
MA0147.10.906014
MA0148.10.088079
MA0149.10.0525422
MA0062.20.610483
MA0035.20.126246
MA0039.22.27701
MA0138.20.221177
MA0002.20.57298
MA0137.20.0372603
MA0104.20.915095
MA0047.20.475155
MA0112.20.895869
MA0065.21.14703
MA0150.10.546781
MA0151.10
MA0152.10.475315
MA0153.10.491737
MA0154.13.21612
MA0155.11.9472
MA0156.10.588508
MA0157.12.04145
MA0158.10
MA0159.10.389805
MA0160.10.089496
MA0161.10
MA0162.13.61279
MA0163.11.58136
MA0164.10.141659
MA0080.21.70465
MA0018.20.883988
MA0099.21.16412
MA0079.21.91325
MA0102.21.0223
MA0258.10.145079
MA0259.11.19432
MA0442.10
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