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{{MCL_coexpression_mm9
{
|coexpression_dpi_cluster_scores_mean=-0

Latest revision as of 15:33, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:12684247..12684278,-p3@Stx11
Mm9::chr11:70265457..70265476,+p2@Med11
Mm9::chr13:42147384..42147441,+p1@Hivep1
Mm9::chr19:46379199..46379301,+p1@Nfkb2
Mm9::chr19:46380172..46380231,+p2@Nfkb2
Mm9::chr19:46380235..46380277,+p3@Nfkb2
Mm9::chr1:179726582..179726645,-p1@Adss
Mm9::chr3:135354452..135354475,-p5@Nfkb1
Mm9::chr6:140573180..140573187,-p@chr6:140573180..140573187
-
Mm9::chr7:20214704..20214800,-p1@Relb
Mm9::chr7:29551464..29551487,-p2@Nfkbib
Mm9::chr9:7872886..7872909,-p3@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

GO IDGO nameFDR corrected p-value
GO:0048535lymph node development0.00570946332167024
GO:0048534hemopoietic or lymphoid organ development0.0128876724140671
GO:0002520immune system development0.0128876724140671
GO:0045083negative regulation of interleukin-12 biosynthetic process0.0130337800136663
GO:0006355regulation of transcription, DNA-dependent0.0130337800136663
GO:0002250adaptive immune response0.0130337800136663
GO:0002460adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.0130337800136663
GO:0006351transcription, DNA-dependent0.0130337800136663
GO:0032774RNA biosynthetic process0.0130337800136663
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0130337800136663
GO:0044424intracellular part0.0130337800136663
GO:0004019adenylosuccinate synthase activity0.0130337800136663
GO:0002266follicular dendritic cell activation0.0130337800136663
GO:0002268follicular dendritic cell differentiation0.0130337800136663
GO:0045449regulation of transcription0.0130337800136663
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0132348084367286
GO:0006350transcription0.0132348084367286
GO:0005622intracellular0.0132348084367286
GO:0050794regulation of cellular process0.0132348084367286
GO:0010468regulation of gene expression0.0132348084367286
GO:0045063T-helper 1 cell differentiation0.0137294915714405
GO:0031323regulation of cellular metabolic process0.0144716931784834
GO:0019222regulation of metabolic process0.0160142300704282
GO:0005484SNAP receptor activity0.0160142300704282
GO:0016070RNA metabolic process0.0169374732737577
GO:0016564transcription repressor activity0.0175102895173719
GO:0050789regulation of biological process0.0175102895173719
GO:0043011myeloid dendritic cell differentiation0.0187319398928385
GO:0042090interleukin-12 biosynthetic process0.0187319398928385
GO:0002467germinal center formation0.0187319398928385
GO:0045075regulation of interleukin-12 biosynthetic process0.0187319398928385
GO:0001773myeloid dendritic cell activation0.0187319398928385
GO:0045892negative regulation of transcription, DNA-dependent0.0187319398928385
GO:0048536spleen development0.0187319398928385
GO:0002294CD4-positive, alpha-beta T cell differentiation during immune response0.0187319398928385
GO:0002292T cell differentiation during immune response0.0187319398928385
GO:0042093T-helper cell differentiation0.0187319398928385
GO:0002285lymphocyte activation during immune response0.0187319398928385
GO:0042088T-helper 1 type immune response0.0187319398928385
GO:0002293alpha-beta T cell differentiation during immune response0.0187319398928385
GO:0002286T cell activation during immune response0.0187319398928385
GO:0065007biological regulation0.0189737725871486
GO:0002376immune system process0.019196031657158
GO:0002366leukocyte activation during immune response0.019196031657158
GO:0002263cell activation during immune response0.019196031657158
GO:0005634nucleus0.0193334072601023
GO:0010467gene expression0.0197681334926949
GO:0042036negative regulation of cytokine biosynthetic process0.0197681334926949
GO:0001775cell activation0.0197681334926949
GO:0043367CD4-positive, alpha beta T cell differentiation0.0211063835598012
GO:0016481negative regulation of transcription0.0213149087903502
GO:0003700transcription factor activity0.0213149087903502
GO:0032615interleukin-12 production0.0213149087903502
GO:0016566specific transcriptional repressor activity0.0213149087903502
GO:0048523negative regulation of cellular process0.0217987727723372
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0228427797082627
GO:0048519negative regulation of biological process0.0257071905748928
GO:0031324negative regulation of cellular metabolic process0.0286053142831292
GO:0003677DNA binding0.0286053142831292
GO:0043231intracellular membrane-bound organelle0.0300439899962125
GO:0043227membrane-bound organelle0.0300439899962125
GO:0000119mediator complex0.0319093911503508
GO:0046632alpha-beta T cell differentiation0.0319093911503508
GO:0009892negative regulation of metabolic process0.0323932094042333
GO:0006944membrane fusion0.0323932094042333
GO:0017148negative regulation of translation0.0357783254503515
GO:0005515protein binding0.0357783254503515
GO:0031327negative regulation of cellular biosynthetic process0.0365618912224776
GO:0002274myeloid leukocyte activation0.0374096624706259
GO:0046631alpha-beta T cell activation0.0423011722615465
GO:0009890negative regulation of biosynthetic process0.0430412916192999



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>

Uber Anatomy
Ontology termp-valuen
hemolymphoid system1.89e-1748
immune system1.89e-1748
hematopoietic system1.36e-1545
blood island1.36e-1545
lateral plate mesoderm1.61e-1487
mixed endoderm/mesoderm-derived structure4.55e-1135
endoderm-derived structure1.38e-10118
endoderm1.38e-10118
presumptive endoderm1.38e-10118
mesoderm1.60e-10120
mesoderm-derived structure1.60e-10120
presumptive mesoderm1.60e-10120
hemopoietic organ2.31e-1029
immune organ2.31e-1029
digestive system2.85e-10116
digestive tract2.85e-10116
primitive gut2.85e-10116
segment of respiratory tract6.29e-1027
respiratory system1.36e-0942
subdivision of digestive tract2.10e-09114
respiratory tract2.55e-0941
gland of gut4.29e-0924
pharynx6.31e-0924
upper respiratory tract6.31e-0924
chordate pharynx6.31e-0924
pharyngeal arch system6.31e-0924
pharyngeal region of foregut6.31e-0924
thymus7.81e-0923
neck7.81e-0923
respiratory system epithelium7.81e-0923
hemolymphoid system gland7.81e-0923
pharyngeal epithelium7.81e-0923
thymic region7.81e-0923
pharyngeal gland7.81e-0923
entire pharyngeal arch endoderm7.81e-0923
thymus primordium7.81e-0923
early pharyngeal endoderm7.81e-0923
connective tissue1.62e-0846
organ component layer1.34e-0724
organ segment4.56e-0735
musculoskeletal system5.62e-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)
MA0003.15.27524
MA0004.10.303605
MA0006.10.960584
MA0007.10.290695
MA0009.10.709264
MA0014.15.47643
MA0017.10.546298
MA0019.10.535691
MA0024.10.667197
MA0025.10.936082
MA0027.12.34178
MA0028.10.173587
MA0029.10.64639
MA0030.10.65267
MA0031.10.618697
MA0038.10.432665
MA0040.10.721328
MA0041.10.239557
MA0042.10.228771
MA0043.10.802848
MA0046.10.743934
MA0048.10.382561
MA0050.10.337476
MA0051.10.440863
MA0052.10.729105
MA0055.10.10681
MA0056.10
MA0057.10.983678
MA0058.10.635024
MA0059.10.233271
MA0060.10.713464
MA0061.115.1152
MA0063.10
MA0066.10.422624
MA0067.11.04514
MA0068.11.43405
MA0069.10.729433
MA0070.10.720077
MA0071.10.336739
MA0072.10.711905
MA0073.10.486225
MA0074.11.01196
MA0076.10.200996
MA0077.10.691048
MA0078.10.471303
MA0081.10.252371
MA0083.10.802078
MA0084.11.3693
MA0087.10.760279
MA0088.11.49046
MA0089.10
MA0090.10.753315
MA0091.10.315003
MA0092.10.753925
MA0093.10.531567
MA0095.10
MA0098.10
MA0100.10.989129
MA0101.113.4863
MA0103.10.19444
MA0105.19.32904
MA0106.14.19338
MA0107.119.7892
MA0108.20.557195
MA0109.10
MA0111.10.286331
MA0113.10.452439
MA0114.11.29784
MA0115.10.805567
MA0116.12.91832
MA0117.10.774259
MA0119.10.241106
MA0122.10.793507
MA0124.10.992825
MA0125.10.920215
MA0130.10
MA0131.10.531427
MA0132.10
MA0133.10
MA0135.10.838263
MA0136.10.408073
MA0139.11.53598
MA0140.10.379562
MA0141.10.603844
MA0142.10.604892
MA0143.10.467531
MA0144.10.406018
MA0145.10.109043
MA0146.14.26321
MA0147.10.845188
MA0148.10.317692
MA0149.10.245177
MA0062.20.507063
MA0035.20.383789
MA0039.210.9843
MA0138.20.523978
MA0002.20.302282
MA0137.20.207733
MA0104.20.670538
MA0047.20.431964
MA0112.20.494696
MA0065.21.15835
MA0150.10.290598
MA0151.10
MA0152.10.432062
MA0153.10.854464
MA0154.11.97011
MA0155.11.26717
MA0156.10.580656
MA0157.10.574484
MA0158.10
MA0159.10.145521
MA0160.10.320315
MA0161.10
MA0162.14.05719
MA0163.13.36551
MA0164.10.408402
MA0080.21.06013
MA0018.21.88337
MA0099.20.518072
MA0079.29.9816
MA0102.21.42135
MA0258.10.118033
MA0259.10.408856
MA0442.10
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