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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 10:52, 17 September 2013


Full id: C189_b_splenic_tonsil_CD19_lymph_appendix_spleen



Phase1 CAGE Peaks

Hg19::chr10:267221..267230,+p@chr10:267221..267230
+
Hg19::chr10:37455757..37455787,+p@chr10:37455757..37455787
+
Hg19::chr10:79970622..79970624,+p@chr10:79970622..79970624
+
Hg19::chr12:123416933..123416944,-p@chr12:123416933..123416944
-
Hg19::chr12:68835921..68835926,-p2@ENST00000546086
Hg19::chr13:100375524..100375531,+p@chr13:100375524..100375531
+
Hg19::chr13:100377188..100377194,+p@chr13:100377188..100377194
+
Hg19::chr13:100377368..100377389,+p@chr13:100377368..100377389
+
Hg19::chr14:101036119..101036130,-p20@BEGAIN
Hg19::chr14:106161355..106161362,-p@chr14:106161355..106161362
-
Hg19::chr14:106327961..106327980,-p2@DQ431661
Hg19::chr14:106351913..106351948,-p1@IGHD3-22
Hg19::chr14:106877761..106877767,-p1@AF460681
p1@AF460715
p1@AF460721
p1@AF460739
p1@AF460749
p1@AF460752
p1@AF460755
p1@AF460757
p1@AF460765
p1@AF460795
p1@AF460799
p1@AF460809
p1@AF460810
p1@AF460812
p1@AF460813
p1@AF460814
p1@AF460816
p1@AF460819
p1@AF460820
p1@AF460831
p1@AF460842
Hg19::chr14:106878083..106878099,-p1@IGHV4-39
Hg19::chr14:75981521..75981530,+p@chr14:75981521..75981530
+
Hg19::chr15:45028719..45028738,+p6@TRIM69
Hg19::chr15:45671019..45671033,-p7@GATM
Hg19::chr15:52404161..52404166,+p@chr15:52404161..52404166
+
Hg19::chr15:52404181..52404187,+p@chr15:52404181..52404187
+
Hg19::chr15:57506462..57506496,+p36@TCF12
Hg19::chr15:78177670..78177678,+p@chr15:78177670..78177678
+
Hg19::chr16:4975293..4975294,+p@chr16:4975293..4975294
+
Hg19::chr16:53412335..53412342,+p@chr16:53412335..53412342
+
Hg19::chr16:53412381..53412387,+p@chr16:53412381..53412387
+
Hg19::chr16:76613424..76613434,+p@chr16:76613424..76613434
+
Hg19::chr16:76613646..76613671,+p@chr16:76613646..76613671
+
Hg19::chr17:48994960..48994968,+p@chr17:48994960..48994968
+
Hg19::chr17:55334804..55334824,+p@chr17:55334804..55334824
+
Hg19::chr17:70420105..70420110,+p@chr17:70420105..70420110
+
Hg19::chr17:70420494..70420517,+p@chr17:70420494..70420517
+
Hg19::chr17:78371475..78371480,+p@chr17:78371475..78371480
+
Hg19::chr17:80328570..80328583,+p@chr17:80328570..80328583
+
Hg19::chr17:80328744..80328754,+p@chr17:80328744..80328754
+
Hg19::chr18:74240756..74240772,+p2@LOC284276
Hg19::chr1:173379658..173379666,-p@chr1:173379658..173379666
-
Hg19::chr1:207105167..207105184,-p5@PIGR
Hg19::chr1:207105188..207105210,-p3@PIGR
Hg19::chr1:207105216..207105252,-p4@PIGR
Hg19::chr1:22502943..22502969,+p@chr1:22502943..22502969
+
Hg19::chr1:25799245..25799271,+p@chr1:25799245..25799271
+
Hg19::chr1:31896395..31896404,+p@chr1:31896395..31896404
+
Hg19::chr1:31896446..31896458,+p@chr1:31896446..31896458
+
Hg19::chr21:43704482..43704491,+p9@ABCG1
Hg19::chr21:43706764..43706775,+p@chr21:43706764..43706775
+
Hg19::chr22:22930643..22930649,+p1@IGLV2-33
Hg19::chr22:23040132..23040138,+p1@IGLV2-23
Hg19::chr22:23040389..23040405,+p1@ENST00000385095
Hg19::chr22:23040696..23040701,+p1@AJ408281
Hg19::chr22:34616800..34616810,+p@chr22:34616800..34616810
+
Hg19::chr22:34653635..34653640,+p@chr22:34653635..34653640
+
Hg19::chr22:37484895..37484906,-p@chr22:37484895..37484906
-
Hg19::chr22:37484928..37484953,-p@chr22:37484928..37484953
-
Hg19::chr2:111538269..111538279,+p@chr2:111538269..111538279
+
Hg19::chr2:160779191..160779202,-p@chr2:160779191..160779202
-
Hg19::chr2:170998413..170998419,-p@chr2:170998413..170998419
-
Hg19::chr2:170998667..170998714,+p@chr2:170998667..170998714
+
Hg19::chr2:54810455..54810472,-p@chr2:54810455..54810472
-
Hg19::chr3:108014582..108014611,+p@chr3:108014582..108014611
+
Hg19::chr3:118484990..118484992,-p@chr3:118484990..118484992
-
Hg19::chr3:119299336..119299359,+p12@ADPRH
Hg19::chr3:166801172..166801180,-p@chr3:166801172..166801180
-
Hg19::chr3:171076173..171076182,-p@chr3:171076173..171076182
-
Hg19::chr3:31431437..31431441,+p@chr3:31431437..31431441
+
Hg19::chr3:61896640..61896646,+p@chr3:61896640..61896646
+
Hg19::chr3:96533659..96533667,+p11@EPHA6
Hg19::chr3:96533671..96533680,+p10@EPHA6
Hg19::chr3:96533682..96533687,+p13@EPHA6
Hg19::chr5:169494477..169494513,+p@chr5:169494477..169494513
+
Hg19::chr5:26877471..26877484,+p@chr5:26877471..26877484
+
Hg19::chr5:26877490..26877500,+p@chr5:26877490..26877500
+
Hg19::chr5:26877504..26877517,+p@chr5:26877504..26877517
+
Hg19::chr5:26877541..26877549,+p@chr5:26877541..26877549
+
Hg19::chr5:63461151..63461183,+p4@RNF180
Hg19::chr5:63461191..63461205,+p5@RNF180
Hg19::chr5:80255013..80255020,+p@chr5:80255013..80255020
+
Hg19::chr6:113971101..113971111,-p@chr6:113971101..113971111
-
Hg19::chr6:113971125..113971136,-p@chr6:113971125..113971136
-
Hg19::chr6:149353791..149353807,-p3@ENST00000433442
Hg19::chr6:149353870..149353873,-p8@ENST00000433442
Hg19::chr7:30803690..30803693,-p@chr7:30803690..30803693
-
Hg19::chr8:72753886..72753911,+p@chr8:72753886..72753911
+
Hg19::chr8:87719795..87719814,+p1@ENST00000519041
Hg19::chr8:87719833..87719844,+p2@ENST00000519041
Hg19::chr9:128397835..128397850,-p@chr9:128397835..128397850
-
Hg19::chr9:5580708..5580720,-p@chr9:5580708..5580720
-
Hg19::chrX:114701086..114701089,+p@chrX:114701086..114701089
+
Hg19::chrX:11682523..11682558,-p26@ARHGAP6
Hg19::chrX:48792308..48792316,-p20@OTUD5
Hg19::chrX:48792324..48792350,-p14@OTUD5


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:0009720detection of hormone stimulus0.0238912751849613
GO:0019534toxin transporter activity0.0238912751849613
GO:0015068glycine amidinotransferase activity0.0238912751849613
GO:0015067amidinotransferase activity0.0238912751849613
GO:0006600creatine metabolic process0.0238912751849613
GO:0033700phospholipid efflux0.0238912751849613
GO:0006601creatine biosynthetic process0.0238912751849613
GO:0009726detection of endogenous stimulus0.0238912751849613
GO:0055091phospholipid homeostasis0.0238912751849613
GO:0006599phosphagen metabolic process0.0243383958235739
GO:0042396phosphagen biosynthetic process0.0243383958235739
GO:0051725protein amino acid de-ADP-ribosylation0.0243383958235739
GO:0003875ADP-ribosylarginine hydrolase activity0.0243383958235739
GO:0032365intracellular lipid transport0.0243383958235739
GO:0032366intracellular sterol transport0.0243383958235739
GO:0032367intracellular cholesterol transport0.0243383958235739
GO:0008565protein transporter activity0.0243383958235739
GO:0005515protein binding0.0243383958235739
GO:0033344cholesterol efflux0.0339267824801768
GO:0044446intracellular organelle part0.0341777671594579
GO:0044422organelle part0.0341777671594579
GO:0005885Arp2/3 protein complex0.0341777671594579
GO:0042987amyloid precursor protein catabolic process0.0373554338073769
GO:0043531ADP binding0.0402667158160958
GO:0017127cholesterol transporter activity0.0472295975431517



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
spleen2.59e-123
gastrointestinal system mesentery2.59e-123
stomach region2.59e-123
mesentery2.59e-123
gastrointestinal system serosa2.59e-123
mesentery of stomach2.59e-123
gut mesentery2.59e-123
dorsal mesentery2.59e-123
dorsal mesogastrium2.59e-123
peritoneal cavity2.59e-123
spleen primordium2.59e-123


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)
MA0003.14.23682e-10
MA0004.10.281587
MA0006.10.0225914
MA0007.10.244446
MA0009.10.760252
MA0014.11.03779e-09
MA0017.11.63758
MA0019.11.35198
MA0024.10.54623
MA0025.10.191338
MA0027.11.49225
MA0028.10.00233493
MA0029.10.0812927
MA0030.10.265296
MA0031.10.200013
MA0038.10.80359
MA0040.11.48987
MA0041.10.514613
MA0042.10.254695
MA0043.10.11901
MA0046.10.113665
MA0048.10.271509
MA0050.11.51253
MA0051.10.518071
MA0052.10.602957
MA0055.10.618411
MA0056.10
MA0057.10.0103758
MA0058.10.518049
MA0059.10.512978
MA0060.10.0266038
MA0061.16.66592
MA0063.10
MA0066.10.0580767
MA0067.10.314198
MA0068.10.497094
MA0069.10.111854
MA0070.10.704972
MA0071.10.664077
MA0072.10.695529
MA0073.16.5402e-06
MA0074.10.0555466
MA0076.10.0269542
MA0077.11.12563
MA0078.10.274624
MA0081.10.345964
MA0083.11.84214
MA0084.10.459529
MA0087.10.338192
MA0088.10.0631036
MA0089.10
MA0090.10.284355
MA0091.10.155122
MA0092.10.213933
MA0093.10.44375
MA0095.10
MA0098.10
MA0100.10.0136353
MA0101.11.63285
MA0103.11.47931
MA0105.19.45743
MA0106.10.393271
MA0107.13.74129
MA0108.20.197132
MA0109.10
MA0111.10.185749
MA0113.11.4156
MA0114.10.403637
MA0115.10.260375
MA0116.10.44433
MA0117.10.137664
MA0119.10.0166961
MA0122.10.461265
MA0124.10.23275
MA0125.11.02173
MA0130.10
MA0131.10.126975
MA0132.10
MA0133.10
MA0135.10.417297
MA0136.10.0612768
MA0139.10.0666166
MA0140.10.114695
MA0141.10.506172
MA0142.10.387248
MA0143.10.428026
MA0144.10.010424
MA0145.10.000174044
MA0146.16.66582e-07
MA0147.10.222561
MA0148.10.185303
MA0149.10.0367459
MA0062.20.000448957
MA0035.20.0400218
MA0039.28.32646e-09
MA0138.20.0274059
MA0002.20.636094
MA0137.20.0323353
MA0104.20.14453
MA0047.20.612178
MA0112.20.012126
MA0065.20.106116
MA0150.10.0764368
MA0151.10
MA0152.10.437585
MA0153.10.17096
MA0154.11.31589
MA0155.10.00474304
MA0156.10.372604
MA0157.10.618344
MA0158.10
MA0159.10.0821153
MA0160.10.583777
MA0161.10
MA0162.12.24348e-08
MA0163.10.00165253
MA0164.10.0223446
MA0080.20.0238
MA0018.20.0177289
MA0099.20.678947
MA0079.21.18685e-12
MA0102.20.490261
MA0258.10.131979
MA0259.10.247519
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#10538102.736831662056590.003574132678959090.0181062690559667
EBF1#1879202.001453223948090.001804936358579670.010918375230449



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

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C189&oldid=3067307"