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MCL coexpression mm9:570: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=
|ontology_enrichment_celltype=CL:0000791!8.21e-33!9;CL:0000789!8.21e-33!9;CL:0002420!8.21e-33!9;CL:0002419!8.21e-33!9;CL:0000790!8.21e-33!9;CL:0000624!3.64e-29!8;CL:0000084!1.37e-26!11;CL:0000827!1.37e-26!11;CL:0000838!2.97e-24!12;CL:0000893!1.30e-22!6;CL:0002489!1.30e-22!6;CL:0000898!1.30e-22!6;CL:0000809!1.30e-22!6;CL:0000810!1.30e-22!6;CL:0000895!1.30e-22!6;CL:0000808!1.30e-22!6;CL:0000894!1.30e-22!6;CL:0000806!1.30e-22!6;CL:0000807!1.30e-22!6;CL:0000805!1.30e-22!6;CL:0002425!1.30e-22!6;CL:0002436!1.30e-22!6;CL:0002427!1.30e-22!6;CL:0002428!1.30e-22!6;CL:0002429!1.30e-22!6;CL:0002433!1.30e-22!6;CL:0002431!1.30e-22!6;CL:0002432!1.30e-22!6;CL:0000542!2.82e-22!13;CL:0000051!2.82e-22!13;CL:0002242!7.96e-18!16;CL:0000738!1.09e-16!17;CL:0002087!1.09e-16!17;CL:0002031!3.51e-16!25;CL:0000988!3.33e-12!32;CL:0002032!3.33e-12!32;CL:0000037!3.33e-12!32;CL:0000566!3.33e-12!32;CL:0000837!3.33e-12!32;CL:0002320!6.96e-08!46;CL:0000134!6.96e-08!46
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004177!5.89e-33!29;UBERON:0005057!5.89e-33!29;UBERON:0002370!5.99e-33!23;UBERON:0000974!5.99e-33!23;UBERON:0004807!5.99e-33!23;UBERON:0005058!5.99e-33!23;UBERON:0003351!5.99e-33!23;UBERON:0009113!5.99e-33!23;UBERON:0003295!5.99e-33!23;UBERON:0009722!5.99e-33!23;UBERON:0005562!5.99e-33!23;UBERON:0007690!5.99e-33!23;UBERON:0006562!1.85e-31!24;UBERON:0003408!1.85e-31!24;UBERON:0001557!1.85e-31!24;UBERON:0001042!1.85e-31!24;UBERON:0008814!1.85e-31!24;UBERON:0009145!1.85e-31!24;UBERON:0000072!1.19e-27!27;UBERON:0000077!9.12e-27!35;UBERON:0002193!1.20e-26!48;UBERON:0002405!1.20e-26!48;UBERON:0002390!1.53e-25!45;UBERON:0003061!1.53e-25!45;UBERON:0000063!1.10e-20!35;UBERON:0007811!4.97e-20!36;UBERON:0000065!3.07e-17!41;UBERON:0001004!9.25e-17!42;UBERON:0000153!2.65e-16!43;UBERON:0003929!4.04e-12!55;UBERON:0003081!1.67e-11!87;UBERON:0002368!7.19e-11!60;UBERON:0001041!6.79e-10!80;UBERON:0002530!8.20e-10!65;UBERON:0000490!1.28e-09!66;UBERON:0005911!4.46e-09!69;UBERON:0000949!1.40e-08!72;UBERON:0000064!1.57e-08!99;UBERON:0002384!6.96e-08!46;UBERON:0000926!2.39e-07!120;UBERON:0004120!2.39e-07!120;UBERON:0006603!2.39e-07!120
|tfbs_overrepresentation_for_novel_motifs=0.244604,0.189434,0.223558,1.39884,0.848472,0.792702,0.370193,0.566731,0.283485,0.138274,0.331725,0.35958,0.567414,0.381063,0.15081,0,0.557619,0.824658,0.244912,0.119642,2.40441,0.0768335,0.38026,0.137915,0.229596,0.405649,0.501183,0.309422,0.171781,0.169823,0.297405,0.653099,0.412165,0.202991,0.151158,0.332588,0.125578,0.356403,0.111088,0.640643,0.42301,0.301802,0.347242,2.08439,0.0153958,0.270091,0.48361,0.322976,0.742531,0.173974,0.541299,0.429887,0.160439,0.788877,0.805733,0.387424,0.533349,0.348382,0.218496,0.385607,0.634076,0.438439,0.628157,0.5308,0.397364,0.568642,0.938213,1.28193,0.629645,1.13654,0.208654,0.277751,0.0836286,0.838198,0.0571922,0.427563,0.202885,0.473159,0.617814,0.198007,0.279684,0.573903,0.437131,0.258127,0.72691,0.00415894,0.0888017,0.170021,0.488122,1.44275,1.0064,0.731688,0.665283,0.143149,0.713238,0.0973538,0.264364,0.667958,0.483845,0.329451,0.125632,1.5718,0.772062,0.541854,0.54087,0.301427,0.596902,0.319507,0.201775,0.196131,0.238877,0.773781,0.577235,0.336214,1.01331,0.134943,0.037872,0.772215,0.558838,1.27048,0.843435,0.511336,1.04956,1.19021,1.06644,0.621313,0.984184,0.658832,0.936732,0.145259,0.755703,0.751079,0.907893,0.399614,1.03449,0.193774,0.251471,0.303003,0.986296,1.80931,1.41113,0.942814,1.07314,0.66306,0.53483,0.302189,0.486482,1.76978,0.253405,0.433248,0.0455135,0.0139939,0.790393,0.101059,0.398786,0.869538,0.430798,0.481451,0.242603,0.251242,0.995609,0.726089,0.621734,0.237049,0.531751,1.79771,0.786757,0.941787,0.00980506
}}

Latest revision as of 15:31, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:29320098..29320105,-p@chr12:29320098..29320105
-
Mm9::chr14:53989688..53989700,+p1@uc007trz.1
p1@uc007tsa.1
Mm9::chr14:54382812..54382860,+p1@ENSMUST00000103669
Mm9::chr14:54827851..54827895,+p@chr14:54827851..54827895
+
Mm9::chr14:54843708..54843722,+p@chr14:54843708..54843722
+
Mm9::chr15:66277121..66277159,+p@chr15:66277121..66277159
+
Mm9::chr17:19096061..19096064,-p@chr17:19096061..19096064
-
Mm9::chr17:19105945..19105962,-p1@uc008apx.1
Mm9::chr17:19105991..19106024,-p2@uc008apx.1
Mm9::chr17:29567158..29567162,-p@chr17:29567158..29567162
-
Mm9::chr4:32252125..32252136,+p@chr4:32252125..32252136
+
Mm9::chr4:32378680..32378685,+p@chr4:32378680..32378685
+
Mm9::chr7:89077761..89077781,+p@chr7:89077761..89077781
+


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
mature alpha-beta T cell8.21e-339
alpha-beta T cell8.21e-339
immature T cell8.21e-339
mature T cell8.21e-339
immature alpha-beta T cell8.21e-339
CD4-positive, alpha-beta T cell3.64e-298
T cell1.37e-2611
pro-T cell1.37e-2611
lymphoid lineage restricted progenitor cell2.97e-2412
thymocyte1.30e-226
double negative thymocyte1.30e-226
naive T cell1.30e-226
double-positive, alpha-beta thymocyte1.30e-226
CD4-positive, alpha-beta thymocyte1.30e-226
naive thymus-derived CD4-positive, alpha-beta T cell1.30e-226
DN4 thymocyte1.30e-226
DN1 thymic pro-T cell1.30e-226
DN2 thymocyte1.30e-226
DN3 thymocyte1.30e-226
immature single positive thymocyte1.30e-226
early T lineage precursor1.30e-226
mature CD4 single-positive thymocyte1.30e-226
resting double-positive thymocyte1.30e-226
double-positive blast1.30e-226
CD69-positive double-positive thymocyte1.30e-226
CD69-positive, CD4-positive single-positive thymocyte1.30e-226
CD4-positive, CD8-intermediate double-positive thymocyte1.30e-226
CD24-positive, CD4 single-positive thymocyte1.30e-226
lymphocyte2.82e-2213
common lymphoid progenitor2.82e-2213
nucleate cell7.96e-1816
leukocyte1.09e-1617
nongranular leukocyte1.09e-1617
hematopoietic lineage restricted progenitor cell3.51e-1625
hematopoietic cell3.33e-1232
hematopoietic oligopotent progenitor cell3.33e-1232
hematopoietic stem cell3.33e-1232
angioblastic mesenchymal cell3.33e-1232
hematopoietic multipotent progenitor cell3.33e-1232
connective tissue cell6.96e-0846
mesenchymal cell6.96e-0846

Uber Anatomy
Ontology termp-valuen
hemopoietic organ5.89e-3329
immune organ5.89e-3329
thymus5.99e-3323
neck5.99e-3323
respiratory system epithelium5.99e-3323
hemolymphoid system gland5.99e-3323
pharyngeal epithelium5.99e-3323
thymic region5.99e-3323
pharyngeal gland5.99e-3323
entire pharyngeal arch endoderm5.99e-3323
thymus primordium5.99e-3323
early pharyngeal endoderm5.99e-3323
pharynx1.85e-3124
gland of gut1.85e-3124
upper respiratory tract1.85e-3124
chordate pharynx1.85e-3124
pharyngeal arch system1.85e-3124
pharyngeal region of foregut1.85e-3124
segment of respiratory tract1.19e-2727
mixed endoderm/mesoderm-derived structure9.12e-2735
hemolymphoid system1.20e-2648
immune system1.20e-2648
hematopoietic system1.53e-2545
blood island1.53e-2545
organ segment1.10e-2035
craniocervical region4.97e-2036
respiratory tract3.07e-1741
respiratory system9.25e-1742
anterior region of body2.65e-1643
gut epithelium4.04e-1255
lateral plate mesoderm1.67e-1187
endocrine gland7.19e-1160
foregut6.79e-1080
gland8.20e-1065
unilaminar epithelium1.28e-0966
endo-epithelium4.46e-0969
endocrine system1.40e-0872
organ part1.57e-0899
connective tissue6.96e-0846
mesoderm2.39e-07120
mesoderm-derived structure2.39e-07120
presumptive mesoderm2.39e-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)
MA0003.10.00492315
MA0004.10.279808
MA0006.10.14766
MA0007.10.737361
MA0009.10.678286
MA0014.10.0332236
MA0017.10.166909
MA0019.10.506787
MA0024.10.636635
MA0025.10.9035
MA0027.12.3071
MA0028.10.155127
MA0029.10.616052
MA0030.10.622264
MA0031.12.45115
MA0038.10.405578
MA0040.10.690239
MA0041.10.622762
MA0042.10.207696
MA0043.10.771094
MA0046.10.712646
MA0048.10.332541
MA0050.10.312673
MA0051.10.413609
MA0052.10.697946
MA0055.10.0835619
MA0056.10
MA0057.10.0312525
MA0058.10.202403
MA0059.10.212009
MA0060.10.646504
MA0061.10.363764
MA0063.10
MA0066.10.395746
MA0067.11.01206
MA0068.10.132828
MA0069.10.698271
MA0070.10.688999
MA0071.10.311956
MA0072.10.680902
MA0073.11.52093e-08
MA0074.10.363923
MA0076.10.181159
MA0077.10.660245
MA0078.11.12807
MA0081.10.651709
MA0083.14.36691
MA0084.11.33532
MA0087.10.728855
MA0088.10.0799097
MA0089.10
MA0090.10.251458
MA0091.10.290854
MA0092.10.251716
MA0093.10.161141
MA0095.10
MA0098.10
MA0100.10.353762
MA0101.10.219061
MA0103.10.519343
MA0105.10.196316
MA0106.10.450539
MA0107.10.170338
MA0108.22.25321
MA0109.10
MA0111.10.263095
MA0113.10.424958
MA0114.10.111687
MA0115.10.773793
MA0116.10.147513
MA0117.10.742722
MA0119.10.219527
MA0122.10.761823
MA0124.10.959967
MA0125.10.887718
MA0130.10
MA0131.10.502588
MA0132.10
MA0133.10
MA0135.10.806261
MA0136.10.38151
MA0139.10.0756871
MA0140.10.931776
MA0141.11.05803
MA0142.10.575041
MA0143.10.439766
MA0144.10.737036
MA0145.10.0201868
MA0146.10.00215921
MA0147.10.121834
MA0148.10.796977
MA0149.10.223436
MA0062.20.0556611
MA0035.20.940904
MA0039.20.00534808
MA0138.20.495254
MA0002.21.96954
MA0137.20.55008
MA0104.20.0856657
MA0047.21.04434
MA0112.20.0892873
MA0065.20.0897174
MA0150.10.267221
MA0151.10
MA0152.11.04455
MA0153.10.822355
MA0154.10.139881
MA0155.10.258579
MA0156.11.02086
MA0157.12.3091
MA0158.10
MA0159.10.128669
MA0160.10.296006
MA0161.10
MA0162.10.0186388
MA0163.10.0025245
MA0164.10.993886
MA0080.20.509758
MA0018.21.01279
MA0099.20.489441
MA0079.21.03424e-05
MA0102.21.38728
MA0258.10.336791
MA0259.10.114734
MA0442.10
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