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MCL coexpression mm9:3098: Difference between revisions

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{{MCL_coexpression_mm9
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tethering or rolling;0.00230099161781625;20345!GO:0045123;cellular extravasation;0.00345148742672437;20345!GO:0007159;leukocyte adhesion;0.00383498602969375;20345!GO:0050900;leukocyte migration;0.00891634251903797;20345!GO:0005529;sugar binding;0.0372760642086232;20345!GO:0016337;cell-cell adhesion;0.0372760642086232;20345!GO:0030246;carbohydrate binding;0.0372760642086232;20345!GO:0016477;cell migration;0.0372760642086232;20345!GO:0051674;localization of cell;0.0372760642086232;20345!GO:0006928;cell 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|gostat_on_MCL_coexpression=GO:0050901;leukocyte tethering or rolling;0.00230099161781625;20345!GO:0045123;cellular extravasation;0.00345148742672437;20345!GO:0007159;leukocyte adhesion;0.00383498602969375;20345!GO:0050900;leukocyte migration;0.00891634251903797;20345!GO:0005529;sugar binding;0.0372760642086232;20345!GO:0016337;cell-cell adhesion;0.0372760642086232;20345!GO:0030246;carbohydrate binding;0.0372760642086232;20345!GO:0016477;cell migration;0.0372760642086232;20345!GO:0051674;localization of cell;0.0372760642086232;20345!GO:0006928;cell motility;0.0372760642086232;20345!
|ontology_enrichment_celltype=CL:0000988!7.63e-16!32;CL:0002032!7.63e-16!32;CL:0000037!7.63e-16!32;CL:0000566!7.63e-16!32;CL:0000837!7.63e-16!32;CL:0000738!1.88e-15!17;CL:0002087!1.88e-15!17;CL:0002031!3.07e-13!25;CL:0000838!1.22e-12!12;CL:0002320!3.07e-12!46;CL:0000134!3.07e-12!46;CL:0000084!3.68e-12!11;CL:0000827!3.68e-12!11;CL:0000542!2.28e-11!13;CL:0000051!2.28e-11!13;CL:0000791!3.51e-10!9;CL:0000789!3.51e-10!9;CL:0002420!3.51e-10!9;CL:0002419!3.51e-10!9;CL:0000790!3.51e-10!9;CL:0000219!7.82e-10!54;CL:0000624!5.60e-09!8;CL:0002242!1.55e-08!16;CL:0000557!9.50e-08!7;CL:0000034!1.43e-07!97;CL:0000723!7.90e-07!91;CL:0000048!7.90e-07!91
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!1.05e-28!48;UBERON:0002405!1.05e-28!48;UBERON:0002390!3.04e-26!45;UBERON:0003061!3.04e-26!45;UBERON:0004177!2.99e-16!29;UBERON:0005057!2.99e-16!29;UBERON:0000077!2.63e-13!35;UBERON:0003081!8.68e-13!87;UBERON:0002370!1.68e-12!23;UBERON:0000974!1.68e-12!23;UBERON:0004807!1.68e-12!23;UBERON:0005058!1.68e-12!23;UBERON:0003351!1.68e-12!23;UBERON:0009113!1.68e-12!23;UBERON:0003295!1.68e-12!23;UBERON:0009722!1.68e-12!23;UBERON:0005562!1.68e-12!23;UBERON:0007690!1.68e-12!23;UBERON:0002384!3.07e-12!46;UBERON:0006562!9.87e-12!24;UBERON:0003408!9.87e-12!24;UBERON:0001557!9.87e-12!24;UBERON:0001042!9.87e-12!24;UBERON:0008814!9.87e-12!24;UBERON:0009145!9.87e-12!24;UBERON:0002371!1.89e-10!16;UBERON:0000072!8.75e-10!27;UBERON:0000926!2.13e-09!120;UBERON:0004120!2.13e-09!120;UBERON:0006603!2.13e-09!120;UBERON:0001474!1.08e-08!22;UBERON:0004765!1.08e-08!22;UBERON:0001434!1.08e-08!22;UBERON:0000065!3.46e-08!41;UBERON:0001004!7.76e-08!42;UBERON:0002204!1.10e-07!32
}}

Latest revision as of 19:34, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr17:36005663..36005675,+p@chr17:36005663..36005675
+
Mm9::chr5:114270108..114270129,-p@chr5:114270108..114270129
-
Mm9::chr5:114270168..114270180,-p@chr5:114270168..114270180
-


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:0050901leukocyte tethering or rolling0.00230099161781625
GO:0045123cellular extravasation0.00345148742672437
GO:0007159leukocyte adhesion0.00383498602969375
GO:0050900leukocyte migration0.00891634251903797
GO:0005529sugar binding0.0372760642086232
GO:0016337cell-cell adhesion0.0372760642086232
GO:0030246carbohydrate binding0.0372760642086232
GO:0016477cell migration0.0372760642086232
GO:0051674localization of cell0.0372760642086232
GO:0006928cell motility0.0372760642086232



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 cell7.63e-1632
hematopoietic oligopotent progenitor cell7.63e-1632
hematopoietic stem cell7.63e-1632
angioblastic mesenchymal cell7.63e-1632
hematopoietic multipotent progenitor cell7.63e-1632
leukocyte1.88e-1517
nongranular leukocyte1.88e-1517
hematopoietic lineage restricted progenitor cell3.07e-1325
lymphoid lineage restricted progenitor cell1.22e-1212
connective tissue cell3.07e-1246
mesenchymal cell3.07e-1246
T cell3.68e-1211
pro-T cell3.68e-1211
lymphocyte2.28e-1113
common lymphoid progenitor2.28e-1113
mature alpha-beta T cell3.51e-109
alpha-beta T cell3.51e-109
immature T cell3.51e-109
mature T cell3.51e-109
immature alpha-beta T cell3.51e-109
motile cell7.82e-1054
CD4-positive, alpha-beta T cell5.60e-098
nucleate cell1.55e-0816
granulocyte monocyte progenitor cell9.50e-087
stem cell1.43e-0797
somatic stem cell7.90e-0791
multi fate stem cell7.90e-0791

Uber Anatomy
Ontology termp-valuen
hemolymphoid system1.05e-2848
immune system1.05e-2848
hematopoietic system3.04e-2645
blood island3.04e-2645
hemopoietic organ2.99e-1629
immune organ2.99e-1629
mixed endoderm/mesoderm-derived structure2.63e-1335
lateral plate mesoderm8.68e-1387
thymus1.68e-1223
neck1.68e-1223
respiratory system epithelium1.68e-1223
hemolymphoid system gland1.68e-1223
pharyngeal epithelium1.68e-1223
thymic region1.68e-1223
pharyngeal gland1.68e-1223
entire pharyngeal arch endoderm1.68e-1223
thymus primordium1.68e-1223
early pharyngeal endoderm1.68e-1223
connective tissue3.07e-1246
pharynx9.87e-1224
gland of gut9.87e-1224
upper respiratory tract9.87e-1224
chordate pharynx9.87e-1224
pharyngeal arch system9.87e-1224
pharyngeal region of foregut9.87e-1224
bone marrow1.89e-1016
segment of respiratory tract8.75e-1027
mesoderm2.13e-09120
mesoderm-derived structure2.13e-09120
presumptive mesoderm2.13e-09120
bone element1.08e-0822
skeletal element1.08e-0822
skeletal system1.08e-0822
respiratory tract3.46e-0841
respiratory system7.76e-0842
musculoskeletal system1.10e-0732


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)
MA0003.10.245953
MA0004.10.801718
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.10.133574
MA0017.10.635031
MA0019.11.08369
MA0024.11.23079
MA0025.11.51835
MA0027.12.9431
MA0028.10.61552
MA0029.11.20789
MA0030.11.21482
MA0031.11.17722
MA0038.10.963265
MA0040.11.28983
MA0041.10.714279
MA0042.10.69885
MA0043.11.3775
MA0046.11.31428
MA0048.10.353763
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.11.6728
MA0056.10
MA0057.10.337566
MA0058.10.690848
MA0059.10.705317
MA0060.10.502699
MA0061.11.33581
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.10.343188
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.10.971751
MA0074.10.911576
MA0076.10.657929
MA0077.11.2569
MA0078.11.0091
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.10.27999
MA0089.10
MA0090.10.762482
MA0091.10.816659
MA0092.10.762845
MA0093.10.62555
MA0095.10
MA0098.10
MA0100.10.89873
MA0101.10.71579
MA0103.10.647985
MA0105.12.75918
MA0106.11.01755
MA0107.10.640607
MA0108.21.10817
MA0109.10
MA0111.10.778753
MA0113.10.986839
MA0114.10.537669
MA0115.11.38041
MA0116.12.49617
MA0117.11.34691
MA0119.10.716476
MA0122.11.36752
MA0124.11.57762
MA0125.11.5017
MA0130.10
MA0131.11.07881
MA0132.10
MA0133.10
MA0135.11.4152
MA0136.10.933582
MA0139.10.462282
MA0140.10.898603
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.10.541532
MA0145.10.794492
MA0146.10.151124
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.20.412742
MA0035.20.903829
MA0039.20.181475
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.20.48458
MA0047.20.962424
MA0112.20.29236
MA0065.20.292912
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.12.49819
MA0155.11.52001
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.10.166722
MA0163.10.477233
MA0164.12.15144
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.20.288542
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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