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MCL coexpression mm9:241: Difference between revisions

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{{MCL_coexpression_mm9
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growth factor receptor binding;0.00313765220463548;14170,14174!GO:0006334;nucleosome assembly;0.0213505593954297;319158,621893!GO:0000786;nucleosome;0.0213505593954297;319158,621893!GO:0031497;chromatin assembly;0.0213505593954297;319158,621893!GO:0003913;DNA photolyase activity;0.0213505593954297;12953!GO:0065004;protein-DNA complex assembly;0.0213505593954297;319158,621893!GO:0006333;chromatin assembly or disassembly;0.0213505593954297;319158,621893!GO:0006259;DNA metabolic process;0.0213505593954297;319158,621893,12953!GO:0008083;growth factor activity;0.0219511109229636;14170,14174!GO:0000785;chromatin;0.032931276727162;319158,621893!GO:0005125;cytokine activity;0.0366841803551525;14170,14174!GO:0048538;thymus development;0.0372475257366139;14174!GO:0009881;photoreceptor activity;0.0372475257366139;12953!GO:0018298;protein-chromophore linkage;0.0372475257366139;12953!GO:0006325;establishment and/or maintenance of chromatin architecture;0.0372475257366139;319158,621893!GO:0006323;DNA packaging;0.0372475257366139;319158,621893!GO:0010092;specification of organ identity;0.0372475257366139;14174!GO:0001759;induction of an organ;0.0372475257366139;14174!GO:0044427;chromosomal part;0.0372475257366139;319158,621893!GO:0031128;induction;0.0372475257366139;14174!GO:0045168;cell-cell signaling during cell fate commitment;0.0372475257366139;14174!GO:0065003;macromolecular complex assembly;0.0390702222401256;319158,621893!GO:0005634;nucleus;0.0416675625033155;13984,319158,621893,12953,14174!GO:0005694;chromosome;0.0451706917797152;319158,621893!GO:0022607;cellular component assembly;0.0470825267985147;319158,621893!GO:0051276;chromosome organization and biogenesis;0.0470825267985147;319158,621893!GO:0001755;neural crest cell 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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0.0527413783866199,0.107744855247029,0.0980717522394092,0.0686377264886741,0.0333321253665857,0,0.00778924557152608,0.124865908594952,0.0800761525331175,0,0,0,0,0,0.113232148794519,0.100783889465809,0,0,0,0,0,0,0,0,1.19328340666379,1.00970459132992,0,0,0.0365114486438769,0.0806875710728457,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.125665098325543,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0442292988327851,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.215406472988399,0.294102271313619,0.178482233814886,0,0,0,0,0,0,0,0,0,0,0,0.0180820377824806,0,0,0.0227964488975564,0,0,0,0,0,0,0,0,0,0,0,0,0,0.180325425270187,0.195436618912525,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.123200893884637,0.0779341159210384,0.0880872011895838,0.0567421053125483,0.093833775061694,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0271101471817823,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0528318955547673,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0685090053637401,0,0,0.0749511157581746,0.0386461207130453,0.0139246950889782,0.127090816446242,0.193070533481811,0.19594636787938,0,0.042760311293496,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0174479355311515,0,0,0,0,0,0,0.0424616899933645,0,0,0,0.0492938041367021,0,0.0417740847988257,0.031895734489288,0.041718751492076,0,0.0281485884445105,0,0,0.0764286795155946,0.0373124733443448,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0411161634894185,0,0.0684580848992459,0,0,0,0,0,0,0,0,0,0,0.0216169666084292,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=GO:0005104;fibroblast growth factor receptor binding;0.00313765220463548;14170,14174!GO:0006334;nucleosome assembly;0.0213505593954297;319158,621893!GO:0000786;nucleosome;0.0213505593954297;319158,621893!GO:0031497;chromatin assembly;0.0213505593954297;319158,621893!GO:0003913;DNA photolyase activity;0.0213505593954297;12953!GO:0065004;protein-DNA complex assembly;0.0213505593954297;319158,621893!GO:0006333;chromatin assembly or disassembly;0.0213505593954297;319158,621893!GO:0006259;DNA metabolic process;0.0213505593954297;319158,621893,12953!GO:0008083;growth factor activity;0.0219511109229636;14170,14174!GO:0000785;chromatin;0.032931276727162;319158,621893!GO:0005125;cytokine activity;0.0366841803551525;14170,14174!GO:0048538;thymus development;0.0372475257366139;14174!GO:0009881;photoreceptor activity;0.0372475257366139;12953!GO:0018298;protein-chromophore linkage;0.0372475257366139;12953!GO:0006325;establishment and/or maintenance of chromatin architecture;0.0372475257366139;319158,621893!GO:0006323;DNA packaging;0.0372475257366139;319158,621893!GO:0010092;specification of organ identity;0.0372475257366139;14174!GO:0001759;induction of an organ;0.0372475257366139;14174!GO:0044427;chromosomal part;0.0372475257366139;319158,621893!GO:0031128;induction;0.0372475257366139;14174!GO:0045168;cell-cell signaling during cell fate commitment;0.0372475257366139;14174!GO:0065003;macromolecular complex assembly;0.0390702222401256;319158,621893!GO:0005634;nucleus;0.0416675625033155;13984,319158,621893,12953,14174!GO:0005694;chromosome;0.0451706917797152;319158,621893!GO:0022607;cellular component assembly;0.0470825267985147;319158,621893!GO:0051276;chromosome organization and biogenesis;0.0470825267985147;319158,621893!GO:0001755;neural crest cell migration;0.0475237234237468;14170!
|ontology_enrichment_celltype=CL:0000988!2.48e-16!32;CL:0002032!2.48e-16!32;CL:0000037!2.48e-16!32;CL:0000566!2.48e-16!32;CL:0000837!2.48e-16!32;CL:0002242!1.12e-12!16;CL:0000838!2.88e-11!12;CL:0002320!3.66e-11!46;CL:0000134!3.66e-11!46;CL:0002031!1.93e-10!25;CL:0000542!2.94e-10!13;CL:0000051!2.94e-10!13;CL:0000084!1.18e-09!11;CL:0000827!1.18e-09!11;CL:0000219!8.76e-09!54;CL:0000034!3.45e-08!97;CL:0000049!1.14e-07!19;CL:0000624!1.34e-07!8;CL:0000738!2.03e-07!17;CL:0002087!2.03e-07!17;CL:0000893!2.29e-07!6;CL:0002489!2.29e-07!6;CL:0000898!2.29e-07!6;CL:0000809!2.29e-07!6;CL:0000810!2.29e-07!6;CL:0000895!2.29e-07!6;CL:0000808!2.29e-07!6;CL:0000894!2.29e-07!6;CL:0000806!2.29e-07!6;CL:0000807!2.29e-07!6;CL:0000805!2.29e-07!6;CL:0002425!2.29e-07!6;CL:0002436!2.29e-07!6;CL:0002427!2.29e-07!6;CL:0002428!2.29e-07!6;CL:0002429!2.29e-07!6;CL:0002433!2.29e-07!6;CL:0002431!2.29e-07!6;CL:0002432!2.29e-07!6
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002384!3.66e-11!46;UBERON:0004177!5.09e-10!29;UBERON:0005057!5.09e-10!29;UBERON:0002390!6.61e-10!45;UBERON:0003061!6.61e-10!45;UBERON:0002193!5.29e-09!48;UBERON:0002405!5.29e-09!48;UBERON:0000077!5.70e-09!35;UBERON:0003929!2.97e-07!55;UBERON:0002370!6.14e-07!23;UBERON:0000974!6.14e-07!23;UBERON:0004807!6.14e-07!23;UBERON:0005058!6.14e-07!23;UBERON:0003351!6.14e-07!23;UBERON:0009113!6.14e-07!23;UBERON:0003295!6.14e-07!23;UBERON:0009722!6.14e-07!23;UBERON:0005562!6.14e-07!23;UBERON:0007690!6.14e-07!23
|tfbs_overrepresentation_for_novel_motifs=0.179293,0.0752559,0.353019,0.224784,0.169613,0.88676,0.355593,0.0637648,0.296659,0.648525,0.298295,0.339541,0.271958,1.22758,0.930644,0,0.234849,0.059344,0.233646,0.675985,0.120003,0.412111,0.37098,0.333169,0.36717,0.131253,0.359043,0.266282,0.7287,0.223466,0.24944,0.830362,0.80476,0.457471,0.625698,0.0994184,0.762338,0.33477,0.428683,0.0868443,0.16413,0.543836,1.05941,0.0762499,0.196692,0.0584129,1.02705,0.597765,0.491779,0.456879,0.63414,0.880283,0.112722,1.07812,0.434849,0.382021,0.480429,0.663481,0.193018,0.761483,0.796396,0.462675,0.329551,0.215255,0.126192,1.26392,0.551407,0.871196,0.289732,0.733632,0.318591,0.0219808,0.317273,0.462927,0.474893,0.618838,0.170117,0.174925,0.280507,0.294464,0.290274,1.97878,0.151098,0.419379,0.963995,0.877886,0.838608,0.223872,0.544194,1.02598,1.48882,0.372211,0.317967,0.0678504,0.112877,0.093986,0.434111,0.320112,1.0277,0.0895173,0.499565,0.308028,1.047,0.635092,0.222555,0.255044,0.264397,0.082328,0.879616,0.535364,0.389135,0.407566,0.86501,0.304852,0.619492,0.545356,0.494916,0.0641298,0.235751,0.0101565,0.467488,0.583146,0.81937,0.174363,0.668374,0.773729,0.114301,0.312808,0.550077,0.893686,0.392297,0.472633,0.524295,0.40098,0.638919,0.0571551,0.737039,0.0739723,0.59486,1.3849,0.995371,0.555542,0.430144,0.316186,0.218168,0.073569,0.184016,1.34592,0.0511204,0.172038,0.230707,1.28657,0.421705,0.865536,0.399685,0.490348,0.14703,0.406532,0.176772,0.418776,0.603336,0.367562,0.283555,0.683845,0.215941,0.778934,1.07117,0.337444,0.0767843
}}

Latest revision as of 14:57, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:104171122..104171127,+p@chr11:104171122..104171127
+
Mm9::chr11:52174441..52174457,-p@chr11:52174441..52174457
-
Mm9::chr11:68886926..68886931,+p1@ENSMUST00000082965
Mm9::chr11:95720195..95720215,+p1@ENSMUST00000146868
p1@uc007law.1
Mm9::chr13:22133226..22133232,-p5@Hist1h4c
p5@Hist1h4d
p5@Hist1h4f
p5@Hist1h4h
p5@Hist1h4i
p5@Hist1h4j
p5@Hist1h4k
p5@Hist1h4m
p5@Hist1h4n
p6@Hist1h4a
p6@Hist1h4b
p6@Hist2h4
p6@Hist4h4
Mm9::chr16:17148308..17148320,-p@chr16:17148308..17148320
-
Mm9::chr16:17554899..17554907,-p2@4930451C15Rik
Mm9::chr17:39982953..39982969,-p@chr17:39982953..39982969
-
Mm9::chr17:69766631..69766643,-p@chr17:69766631..69766643
-
Mm9::chr18:85018335..85018342,+p@chr18:85018335..85018342
+
Mm9::chr19:7093818..7093829,-p3@Fermt3
Mm9::chr2:12901236..12901237,-p1@ENSMUST00000158941
Mm9::chr2:156853529..156853540,-p7@9830001H06Rik
Mm9::chr2:31095001..31095006,-p@chr2:31095001..31095006
-
Mm9::chr2:92274608..92274611,-p2@Cry2
Mm9::chr3:106525050..106525057,+p@chr3:106525050..106525057
+
Mm9::chr3:88100320..88100332,-p@chr3:88100320..88100332
-
Mm9::chr3:96023781..96023796,+p2@Hist2h2ab
Mm9::chr4:107475970..107475974,-p@chr4:107475970..107475974
-
Mm9::chr4:107476279..107476302,-p@chr4:107476279..107476302
-
Mm9::chr4:134409768..134409794,-p@chr4:134409768..134409794
-
Mm9::chr4:135734188..135734201,+p@chr4:135734188..135734201
+
Mm9::chr4:154975381..154975386,+p7@Slc35e2
Mm9::chr6:47738177..47738187,-p2@ENSMUST00000083767
Mm9::chr7:134339697..134339710,+p@chr7:134339697..134339710
+
Mm9::chr7:148744394..148744397,+p@chr7:148744394..148744397
+
Mm9::chr7:152024495..152024519,+p1@Fgf3
Mm9::chr7:152082369..152082376,+p2@Fgf15
Mm9::chr7:29595220..29595257,-p@chr7:29595220..29595257
-
Mm9::chr7:4740532..4740555,+p@chr7:4740532..4740555
+
Mm9::chr8:129468876..129468878,-p1@ENSMUST00000083703
Mm9::chr8:26610056..26610057,-p@chr8:26610056..26610057
-
Mm9::chr9:20837766..20837781,-p@chr9:20837766..20837781
-
Mm9::chrX:11582947..11582949,+p@chrX:11582947..11582949
+
Mm9::chrX:133654667..133654672,-p1@Esx1


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:0005104fibroblast growth factor receptor binding0.00313765220463548
GO:0006334nucleosome assembly0.0213505593954297
GO:0000786nucleosome0.0213505593954297
GO:0031497chromatin assembly0.0213505593954297
GO:0003913DNA photolyase activity0.0213505593954297
GO:0065004protein-DNA complex assembly0.0213505593954297
GO:0006333chromatin assembly or disassembly0.0213505593954297
GO:0006259DNA metabolic process0.0213505593954297
GO:0008083growth factor activity0.0219511109229636
GO:0000785chromatin0.032931276727162
GO:0005125cytokine activity0.0366841803551525
GO:0048538thymus development0.0372475257366139
GO:0009881photoreceptor activity0.0372475257366139
GO:0018298protein-chromophore linkage0.0372475257366139
GO:0006325establishment and/or maintenance of chromatin architecture0.0372475257366139
GO:0006323DNA packaging0.0372475257366139
GO:0010092specification of organ identity0.0372475257366139
GO:0001759induction of an organ0.0372475257366139
GO:0044427chromosomal part0.0372475257366139
GO:0031128induction0.0372475257366139
GO:0045168cell-cell signaling during cell fate commitment0.0372475257366139
GO:0065003macromolecular complex assembly0.0390702222401256
GO:0005634nucleus0.0416675625033155
GO:0005694chromosome0.0451706917797152
GO:0022607cellular component assembly0.0470825267985147
GO:0051276chromosome organization and biogenesis0.0470825267985147
GO:0001755neural crest cell migration0.0475237234237468



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 cell2.48e-1632
hematopoietic oligopotent progenitor cell2.48e-1632
hematopoietic stem cell2.48e-1632
angioblastic mesenchymal cell2.48e-1632
hematopoietic multipotent progenitor cell2.48e-1632
nucleate cell1.12e-1216
lymphoid lineage restricted progenitor cell2.88e-1112
connective tissue cell3.66e-1146
mesenchymal cell3.66e-1146
hematopoietic lineage restricted progenitor cell1.93e-1025
lymphocyte2.94e-1013
common lymphoid progenitor2.94e-1013
T cell1.18e-0911
pro-T cell1.18e-0911
motile cell8.76e-0954
stem cell3.45e-0897
common myeloid progenitor1.14e-0719
CD4-positive, alpha-beta T cell1.34e-078
leukocyte2.03e-0717
nongranular leukocyte2.03e-0717
thymocyte2.29e-076
double negative thymocyte2.29e-076
naive T cell2.29e-076
double-positive, alpha-beta thymocyte2.29e-076
CD4-positive, alpha-beta thymocyte2.29e-076
naive thymus-derived CD4-positive, alpha-beta T cell2.29e-076
DN4 thymocyte2.29e-076
DN1 thymic pro-T cell2.29e-076
DN2 thymocyte2.29e-076
DN3 thymocyte2.29e-076
immature single positive thymocyte2.29e-076
early T lineage precursor2.29e-076
mature CD4 single-positive thymocyte2.29e-076
resting double-positive thymocyte2.29e-076
double-positive blast2.29e-076
CD69-positive double-positive thymocyte2.29e-076
CD69-positive, CD4-positive single-positive thymocyte2.29e-076
CD4-positive, CD8-intermediate double-positive thymocyte2.29e-076
CD24-positive, CD4 single-positive thymocyte2.29e-076


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)
MA0003.10.148698
MA0004.10.842581
MA0006.11.6705
MA0007.10.457898
MA0009.10.328429
MA0014.10.661859
MA0017.10.0905336
MA0019.10.198145
MA0024.11.45639
MA0025.10.520387
MA0027.11.87879
MA0028.10.645459
MA0029.10.764415
MA0030.10.283968
MA0031.10.258132
MA0038.10.410329
MA0040.10.338117
MA0041.10.146748
MA0042.10.316403
MA0043.10.405289
MA0046.10.356455
MA0048.10.169921
MA0050.10.270889
MA0051.10.422996
MA0052.10.344399
MA0055.10.179681
MA0056.10
MA0057.10.238856
MA0058.10.557854
MA0059.10.931317
MA0060.11.10406
MA0061.10.252382
MA0063.10
MA0066.10.788488
MA0067.10.61835
MA0068.10.0799178
MA0069.10.344664
MA0070.10.337108
MA0071.10.269872
MA0072.10.330543
MA0073.10.0441315
MA0074.10.704165
MA0076.10.482152
MA0077.10.313935
MA0078.10.470801
MA0081.10.161577
MA0083.10.404641
MA0084.10.922325
MA0087.10.369857
MA0088.10.195583
MA0089.10
MA0090.10.188011
MA0091.10.240385
MA0092.10.0504056
MA0093.10.999318
MA0095.10
MA0098.10
MA0100.10.100766
MA0101.10.618087
MA0103.10.0987072
MA0105.11.14077
MA0106.10.482278
MA0107.10.0940025
MA0108.22.53638
MA0109.10
MA0111.10.447568
MA0113.10.143312
MA0114.10.0418883
MA0115.10.407576
MA0116.10.607582
MA0117.10.992963
MA0119.11.38438
MA0122.10.397452
MA0124.10.571
MA0125.10.506387
MA0130.10
MA0131.10.568408
MA0132.10
MA0133.10
MA0135.10.435302
MA0136.10.372901
MA0139.10.139227
MA0140.10.677264
MA0141.10.276137
MA0142.10.692442
MA0143.10.152801
MA0144.10.122105
MA0145.11.93554
MA0146.10.444594
MA0147.11.80227
MA0148.10.522825
MA0149.10.0391014
MA0062.20.908139
MA0035.20.336844
MA0039.20.936988
MA0138.20.556107
MA0002.20.439726
MA0137.20.112139
MA0104.22.08864
MA0047.20.40925
MA0112.20.0774274
MA0065.20.140929
MA0150.10.795545
MA0151.10
MA0152.10.409401
MA0153.10.449181
MA0154.10.799863
MA0155.10.287842
MA0156.11.12761
MA0157.10.225588
MA0158.10
MA0159.10.149694
MA0160.10.0705387
MA0161.10
MA0162.10.444043
MA0163.10.498195
MA0164.10.373396
MA0080.20.44645
MA0018.20.122026
MA0099.20.186055
MA0079.20.0541572
MA0102.22.2297
MA0258.10.0356434
MA0259.11.3264
MA0442.10
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