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{{Coexpression_clusters
{
|full_id=C4271_cord_migratory_CD14_immature_b_xeroderma_Dendritic
|

Latest revision as of 12:42, 17 September 2013


Full id: C4271_cord_migratory_CD14_immature_b_xeroderma_Dendritic



Phase1 CAGE Peaks

Hg19::chr3:119278376..119278390,-p2@CD80
Hg19::chr9:114246503..114246515,-p12@KIAA0368
Hg19::chr9:114246521..114246540,-p5@KIAA0368


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

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0045627positive regulation of T-helper 1 cell differentiation0.00585830455523893
GO:0045425positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process0.00585830455523893
GO:0045625regulation of T-helper 1 cell differentiation0.00585830455523893
GO:0045624positive regulation of T-helper cell differentiation0.00585830455523893
GO:0045423regulation of granulocyte macrophage colony-stimulating factor biosynthetic process0.00585830455523893
GO:0045063T-helper 1 cell differentiation0.00585830455523893
GO:0032604granulocyte macrophage colony-stimulating factor production0.00585830455523893
GO:0042253granulocyte macrophage colony-stimulating factor biosynthetic process0.00585830455523893
GO:0045622regulation of T-helper cell differentiation0.00585830455523893
GO:0002294CD4-positive, alpha-beta T cell differentiation during immune response0.00585830455523893
GO:0002292T cell differentiation during immune response0.00585830455523893
GO:0042093T-helper cell differentiation0.00585830455523893
GO:0002366leukocyte activation during immune response0.00585830455523893
GO:0002285lymphocyte activation during immune response0.00585830455523893
GO:0002293alpha-beta T cell differentiation during immune response0.00585830455523893
GO:0002286T cell activation during immune response0.00585830455523893
GO:0002263cell activation during immune response0.00585830455523893
GO:0043367CD4-positive, alpha beta T cell differentiation0.00585830455523893
GO:0045086positive regulation of interleukin-2 biosynthetic process0.00585830455523893
GO:0030433ER-associated protein catabolic process0.00585830455523893
GO:0006515misfolded or incompletely synthesized protein catabolic process0.00585830455523893
GO:0042088T-helper 1 type immune response0.00610029345454885
GO:0030134ER to Golgi transport vesicle0.00662708906093496
GO:0045076regulation of interleukin-2 biosynthetic process0.00662708906093496
GO:0015026coreceptor activity0.00662708906093496
GO:0042094interleukin-2 biosynthetic process0.00662708906093496
GO:0046632alpha-beta T cell differentiation0.00662708906093496
GO:0050731positive regulation of peptidyl-tyrosine phosphorylation0.00678970780813472
GO:0046631alpha-beta T cell activation0.00732660892338999
GO:0032623interleukin-2 production0.00782767272809414
GO:0043161proteasomal ubiquitin-dependent protein catabolic process0.00803710586941609
GO:0042327positive regulation of phosphorylation0.00803710586941609
GO:0045937positive regulation of phosphate metabolic process0.00838605134778403
GO:0001934positive regulation of protein amino acid phosphorylation0.00838605134778403
GO:0033240positive regulation of amine metabolic process0.00838605134778403
GO:0045764positive regulation of amino acid metabolic process0.00838605134778403
GO:0050730regulation of peptidyl-tyrosine phosphorylation0.00846147677070778
GO:0042108positive regulation of cytokine biosynthetic process0.0114266798003558
GO:0030217T cell differentiation0.0114266798003558
GO:0018108peptidyl-tyrosine phosphorylation0.0114266798003558
GO:0005793ER-Golgi intermediate compartment0.0114266798003558
GO:0018212peptidyl-tyrosine modification0.0114266798003558
GO:0001932regulation of protein amino acid phosphorylation0.0114266798003558
GO:0033238regulation of amine metabolic process0.0114266798003558
GO:0006521regulation of amino acid metabolic process0.0114266798003558
GO:0005769early endosome0.0119067654502945
GO:0005770late endosome0.0121287229252704
GO:0045727positive regulation of translation0.0123414047328301
GO:0042035regulation of cytokine biosynthetic process0.0132576707148612
GO:0031328positive regulation of cellular biosynthetic process0.0132576707148612
GO:0030133transport vesicle0.0132576707148612
GO:0042325regulation of phosphorylation0.0132576707148612
GO:0030098lymphocyte differentiation0.0132576707148612
GO:0042089cytokine biosynthetic process0.0132576707148612
GO:0042107cytokine metabolic process0.0132576707148612
GO:0051174regulation of phosphorus metabolic process0.0132576707148612
GO:0019220regulation of phosphate metabolic process0.0132576707148612
GO:0005798Golgi-associated vesicle0.0132576707148612
GO:0009891positive regulation of biosynthetic process0.0132576707148612
GO:0000502proteasome complex (sensu Eukaryota)0.0136963456940561
GO:0002250adaptive immune response0.0136963456940561
GO:0002460adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.0136963456940561
GO:0051247positive regulation of protein metabolic process0.0150731348966164
GO:0002521leukocyte differentiation0.0157092605783575
GO:0042110T cell activation0.0168404898544839
GO:0001816cytokine production0.019119673830591
GO:0018193peptidyl-amino acid modification0.0201653291102759
GO:0005813centrosome0.0211799199203176
GO:0045595regulation of cell differentiation0.0231093223870945
GO:0030135coated vesicle0.0231093223870945
GO:0005815microtubule organizing center0.0231093223870945
GO:0009967positive regulation of signal transduction0.023696587742515
GO:0046649lymphocyte activation0.023696587742515
GO:0030097hemopoiesis0.0242791059133819
GO:0048534hemopoietic or lymphoid organ development0.025736321880546
GO:0045321leukocyte activation0.0263156658080161
GO:0002520immune system development0.0263156658080161
GO:0006417regulation of translation0.0263156658080161
GO:0005768endosome0.0272498221085682
GO:0031326regulation of cellular biosynthetic process0.0277432975632526
GO:0001775cell activation0.0287734637137277
GO:0009889regulation of biosynthetic process0.0295070275349378
GO:0050793regulation of developmental process0.0316950642195714
GO:0045941positive regulation of transcription0.0361358867797147
GO:0006511ubiquitin-dependent protein catabolic process0.0361358867797147
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0361358867797147
GO:0019941modification-dependent protein catabolic process0.0361358867797147
GO:0043632modification-dependent macromolecule catabolic process0.0361358867797147
GO:0051603proteolysis involved in cellular protein catabolic process0.0361358867797147
GO:0044257cellular protein catabolic process0.0361358867797147
GO:0016563transcription activator activity0.0378099684071082
GO:0016023cytoplasmic membrane-bound vesicle0.0419746224953009
GO:0031988membrane-bound vesicle0.0421184849722903
GO:0030163protein catabolic process0.0421414493810656
GO:0031325positive regulation of cellular metabolic process0.0427463215061124
GO:0009893positive regulation of metabolic process0.045296838372318
GO:0044431Golgi apparatus part0.0477196729912479
GO:0051246regulation of protein metabolic process0.0477196729912479
GO:0031410cytoplasmic vesicle0.0477196729912479
GO:0031982vesicle0.0480156090498826
GO:0043285biopolymer catabolic process0.0499449550303376



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
immune system3.73e-1593
bone marrow1.23e-1476
bone element2.31e-1482
hemolymphoid system1.27e-13108
skeletal element3.61e-1390
hematopoietic system5.31e-1398
blood island5.31e-1398
skeletal system1.26e-10100


Overrepresented TFBS (DNA) motifs on this co-expression cluster<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)
MA0003.11.0927
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.24048
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.11.15625
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.12.15449
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.11.55947
MA0103.10.628063
MA0105.11.5295
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.11.16674
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.11.84145
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.311277
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
BATF#10538216.23853452820240.004917462407809970.0230024121650587
CTCF#1066435.360256373075030.0064925092527670.0280356889874197
FOSL1#8061226.47571981091530.001869833702590980.0110273624747247
FOSL2#2355211.28680040304110.0100534586973120.0376861265887285
SMARCB1#6598212.16847718743830.008675002221921740.0330021694188353
YY1#752834.911170749853860.008441455341808260.0330329781723973



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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