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{{MCL_coexpression_mm9
{
|coexpression_dpi_cluster_scores_mean=0.0396986551919192

Latest revision as of 15:25, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:117878100..117878106,+p1@Ifng
Mm9::chr12:114099183..114099192,-p2@Gpr132
Mm9::chr15:57526415..57526425,+p7@Zhx2
Mm9::chr19:53608314..53608329,+p@chr19:53608314..53608329
+
Mm9::chr19:53608416..53608432,+p@chr19:53608416..53608432
+
Mm9::chr5:104182581..104182598,+p@chr5:104182581..104182598
+
Mm9::chr5:104182694..104182724,+p8@Aff1
Mm9::chr5:104182725..104182737,+p17@Aff1
Mm9::chr5:115938931..115938941,-p@chr5:115938931..115938941
-
Mm9::chr6:39327613..39327630,-p3@Slc37a3
Mm9::chr6:48687331..48687339,+p@chr6:48687331..48687339
+
Mm9::chr7:16531372..16531383,-p4@Gltscr2
Mm9::chr9:120019615..120019626,+p5@Slc25a38
Mm9::chrX:75691974..75691976,+p@chrX:75691974..75691976
+


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:0050716positive regulation of interleukin-1 secretion0.0132424415555956
GO:0050706regulation of interleukin-1 beta secretion0.0132424415555956
GO:0005133interferon-gamma receptor binding0.0132424415555956
GO:0050702interleukin-1 beta secretion0.0132424415555956
GO:0050718positive regulation of interleukin-1 beta secretion0.0132424415555956
GO:0050704regulation of interleukin-1 secretion0.0132424415555956
GO:0050701interleukin-1 secretion0.0132424415555956
GO:0050715positive regulation of cytokine secretion0.0154473990081625
GO:0031641regulation of myelination0.0154473990081625
GO:0001781neutrophil apoptosis0.0154473990081625
GO:0031642negative regulation of myelination0.0154473990081625
GO:0006925inflammatory cell apoptosis0.0154473990081625
GO:0045348positive regulation of MHC class II biosynthetic process0.0213857767070597
GO:0045342MHC class II biosynthetic process0.021790176931256
GO:0045346regulation of MHC class II biosynthetic process0.021790176931256
GO:0001780neutrophil homeostasis0.021790176931256
GO:0050714positive regulation of protein secretion0.021790176931256
GO:0045084positive regulation of interleukin-12 biosynthetic process0.021790176931256
GO:0031645negative regulation of neurological process0.021790176931256
GO:0050707regulation of cytokine secretion0.021790176931256
GO:0045080positive regulation of chemokine biosynthetic process0.021790176931256
GO:0045410positive regulation of interleukin-6 biosynthetic process0.021790176931256
GO:0050663cytokine secretion0.021790176931256
GO:0048304positive regulation of isotype switching to IgG isotypes0.021790176931256
GO:0045075regulation of interleukin-12 biosynthetic process0.021790176931256
GO:0042090interleukin-12 biosynthetic process0.021790176931256
GO:0045073regulation of chemokine biosynthetic process0.021790176931256
GO:0050755chemokine metabolic process0.021790176931256
GO:0042033chemokine biosynthetic process0.021790176931256
GO:0045893positive regulation of transcription, DNA-dependent0.021790176931256
GO:0032602chemokine production0.021790176931256
GO:0002262myeloid cell homeostasis0.021790176931256
GO:0048302regulation of isotype switching to IgG isotypes0.021790176931256
GO:0048291isotype switching to IgG isotypes0.021790176931256
GO:0045830positive regulation of isotype switching0.0231488920247131
GO:0045408regulation of interleukin-6 biosynthetic process0.0231488920247131
GO:0051047positive regulation of secretion0.0243639173930027
GO:0042226interleukin-6 biosynthetic process0.0243639173930027
GO:0045941positive regulation of transcription0.024588616002105
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0249884364350635
GO:0030593neutrophil chemotaxis0.0252429620842483
GO:0032615interleukin-12 production0.0252429620842483
GO:0045191regulation of isotype switching0.0252429620842483
GO:0030968unfolded protein response0.0252429620842483
GO:0050708regulation of protein secretion0.0287877882763368
GO:0031325positive regulation of cellular metabolic process0.031491687820385
GO:0032635interleukin-6 production0.031491687820385
GO:0009893positive regulation of metabolic process0.0338567739381659
GO:0006984ER-nuclear signaling pathway0.0339727947245004
GO:0030595leukocyte chemotaxis0.0351381559381551
GO:0002208somatic diversification of immunoglobulins during immune response0.0366285591008257
GO:0002204somatic recombination of immunoglobulin genes during immune response0.0366285591008257
GO:0045190isotype switching0.0366285591008257
GO:0002381immunoglobulin production during immune response0.037657011545733
GO:0000082G1/S transition of mitotic cell cycle0.0399153947925838
GO:0050871positive regulation of B cell activation0.0399153947925838
GO:0031644regulation of neurological process0.0399153947925838
GO:0001776leukocyte homeostasis0.0399153947925838
GO:0016447somatic recombination of immunoglobulin gene segments0.0399153947925838
GO:0042552myelination0.0399153947925838
GO:0006402mRNA catabolic process0.0399153947925838
GO:0048872homeostasis of number of cells0.0399153947925838
GO:0007272ensheathment of neurons0.0399153947925838
GO:0016444somatic cell DNA recombination0.0399153947925838
GO:0008366axon ensheathment0.0399153947925838
GO:0002562somatic diversification of immune receptors via germline recombination within a single locus0.0399153947925838
GO:0009306protein secretion0.0399153947925838
GO:0016445somatic diversification of immunoglobulins0.0399153947925838
GO:0006986response to unfolded protein0.0399153947925838
GO:0050900leukocyte migration0.0399153947925838
GO:0051789response to protein stimulus0.0399153947925838
GO:0002200somatic diversification of immune receptors0.0399153947925838
GO:0006401RNA catabolic process0.0399153947925838
GO:0042108positive regulation of cytokine biosynthetic process0.0399153947925838
GO:0001608nucleotide receptor activity, G-protein coupled0.0421348562320759
GO:0045028purinergic nucleotide receptor activity, G-protein coupled0.0421348562320759
GO:0016502nucleotide receptor activity0.0421348562320759
GO:0001614purinergic nucleotide receptor activity0.0421348562320759
GO:0001508regulation of action potential0.0421348562320759
GO:0005351sugar:hydrogen ion symporter activity0.0421348562320759
GO:0050864regulation of B cell activation0.0421348562320759
GO:0051119sugar transmembrane transporter activity0.0423108307625072
GO:0005126hematopoietin/interferon-class (D200-domain) cytokine receptor binding0.0423108307625072
GO:0002377immunoglobulin production0.0423108307625072
GO:0015144carbohydrate transmembrane transporter activity0.0423108307625072
GO:0002440production of molecular mediator of immune response0.042392315721844
GO:0045727positive regulation of translation0.042392315721844
GO:0051325interphase0.0424698555447445
GO:0051329interphase of mitotic cell cycle0.0424698555447445
GO:0031328positive regulation of cellular biosynthetic process0.0440345887227541
GO:0006355regulation of transcription, DNA-dependent0.0469885842929266
GO:0006351transcription, DNA-dependent0.0478399343710492
GO:0032774RNA biosynthetic process0.0478399343710492
GO:0009615response to virus0.0480042215885874
GO:0042035regulation of cytokine biosynthetic process0.0484616437683431
GO:0051046regulation of secretion0.0494937473468433
GO:0045449regulation of transcription0.0494937473468433
GO:0009891positive regulation of biosynthetic process0.0497763615691983



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 cell2.01e-229
alpha-beta T cell2.01e-229
immature T cell2.01e-229
mature T cell2.01e-229
immature alpha-beta T cell2.01e-229
lymphoid lineage restricted progenitor cell2.97e-2012
CD4-positive, alpha-beta T cell4.83e-208
lymphocyte1.61e-1813
common lymphoid progenitor1.61e-1813
T cell5.44e-1811
pro-T cell5.44e-1811
thymocyte2.64e-156
double negative thymocyte2.64e-156
naive T cell2.64e-156
double-positive, alpha-beta thymocyte2.64e-156
CD4-positive, alpha-beta thymocyte2.64e-156
naive thymus-derived CD4-positive, alpha-beta T cell2.64e-156
DN4 thymocyte2.64e-156
DN1 thymic pro-T cell2.64e-156
DN2 thymocyte2.64e-156
DN3 thymocyte2.64e-156
immature single positive thymocyte2.64e-156
early T lineage precursor2.64e-156
mature CD4 single-positive thymocyte2.64e-156
resting double-positive thymocyte2.64e-156
double-positive blast2.64e-156
CD69-positive double-positive thymocyte2.64e-156
CD69-positive, CD4-positive single-positive thymocyte2.64e-156
CD4-positive, CD8-intermediate double-positive thymocyte2.64e-156
CD24-positive, CD4 single-positive thymocyte2.64e-156
nucleate cell1.29e-1416
leukocyte1.27e-1317
nongranular leukocyte1.27e-1317
hematopoietic cell2.58e-1232
hematopoietic oligopotent progenitor cell2.58e-1232
hematopoietic stem cell2.58e-1232
angioblastic mesenchymal cell2.58e-1232
hematopoietic multipotent progenitor cell2.58e-1232
hematopoietic lineage restricted progenitor cell3.05e-1225
connective tissue cell7.68e-0946
mesenchymal cell7.68e-0946
motile cell4.39e-0854

Uber Anatomy
Ontology termp-valuen
thymus1.45e-2223
neck1.45e-2223
respiratory system epithelium1.45e-2223
hemolymphoid system gland1.45e-2223
pharyngeal epithelium1.45e-2223
thymic region1.45e-2223
pharyngeal gland1.45e-2223
entire pharyngeal arch endoderm1.45e-2223
thymus primordium1.45e-2223
early pharyngeal endoderm1.45e-2223
pharynx1.84e-2124
gland of gut1.84e-2124
upper respiratory tract1.84e-2124
chordate pharynx1.84e-2124
pharyngeal arch system1.84e-2124
pharyngeal region of foregut1.84e-2124
hemopoietic organ2.89e-1929
immune organ2.89e-1929
segment of respiratory tract1.20e-1827
mixed endoderm/mesoderm-derived structure2.19e-1735
hemolymphoid system1.20e-1448
immune system1.20e-1448
hematopoietic system3.88e-1445
blood island3.88e-1445
organ segment1.65e-1335
craniocervical region5.00e-1336
respiratory tract5.56e-1141
respiratory system1.24e-1042
anterior region of body2.68e-1043
gut epithelium1.30e-0955
connective tissue7.68e-0946
endocrine gland2.14e-0760
unilaminar epithelium2.49e-0766
endo-epithelium7.74e-0769
lateral plate mesoderm8.14e-0787


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)
MA0003.10.0100854
MA0004.10.258473
MA0006.10.1319
MA0007.10.246385
MA0009.10.649874
MA0014.10.0625332
MA0017.10.458117
MA0019.10.480432
MA0024.10.608636
MA0025.10.873493
MA0027.12.275
MA0028.10.430035
MA0029.10.588275
MA0030.11.44943
MA0031.10.561217
MA0038.10.381016
MA0040.10.661716
MA0041.10.198922
MA0042.10.553522
MA0043.10.74191
MA0046.10.683926
MA0048.10.534002
MA0050.11.43876
MA0051.11.78642
MA0052.10.669354
MA0055.10.45021
MA0056.10
MA0057.10.489127
MA0058.10.541281
MA0059.10.19314
MA0060.10.0819399
MA0061.12.89705
MA0063.10
MA0066.10.371389
MA0067.10.981551
MA0068.16.50096
MA0069.10.669676
MA0070.10.660488
MA0071.10.289658
MA0072.10.652465
MA0073.118.7148
MA0074.10.340281
MA0076.10.952244
MA0077.10.632005
MA0078.10.418168
MA0081.10.210747
MA0083.10.741151
MA0084.11.30392
MA0087.10.699999
MA0088.10.171343
MA0089.10
MA0090.10.231074
MA0091.10.741628
MA0092.10.231323
MA0093.10.444403
MA0095.10
MA0098.10
MA0100.10.330364
MA0101.11.72541
MA0103.10.927638
MA0105.11.05934
MA0106.10.425111
MA0107.12.80186
MA0108.20.50131
MA0109.10
MA0111.10.242308
MA0113.10.400008
MA0114.11.10492
MA0115.10.744589
MA0116.10.131762
MA0117.10.713754
MA0119.10.200349
MA0122.10.732707
MA0124.10.929684
MA0125.10.857794
MA0130.10
MA0131.11.19873
MA0132.10
MA0133.10
MA0135.10.77683
MA0136.10.940193
MA0139.10.231431
MA0140.10.330266
MA0141.10.511953
MA0142.10.547747
MA0143.10.414534
MA0144.10.100037
MA0145.10.189432
MA0146.10.170737
MA0147.10.107632
MA0148.10.271704
MA0149.10.204102
MA0062.20.39919
MA0035.20.33429
MA0039.20.753752
MA0138.20.469076
MA0002.20.5079
MA0137.20.169785
MA0104.20.0740839
MA0047.20.380343
MA0112.20.189423
MA0065.20.371748
MA0150.10.246295
MA0151.10
MA0152.10.380437
MA0153.10.792819
MA0154.10.0285118
MA0155.10.0879017
MA0156.10.949678
MA0157.10.518122
MA0158.10
MA0159.10.365914
MA0160.10.753068
MA0161.10
MA0162.10.108524
MA0163.10.0388292
MA0164.10.357779
MA0080.20.912084
MA0018.20.366212
MA0099.20.463355
MA0079.21.43677
MA0102.21.35579
MA0258.10.0900907
MA0259.10.101001
MA0442.10
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