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{{Coexpression_clusters
{{Coexpression_clusters|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.792499364813583,0.656058064194994,0.749958686168173,0,0,0,0,0,0,0.476104631631565,0.440007690464119,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.440903172569491,0.421343244616932,0.420420416580576,0.382016982250322,0.378947486591567,0.476815863426597,0.420275926297205,0.290936506658587,0.330094213592205,0.59507560647308,0.464096826824654,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0527252499877161,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0408118974110906,0.0424157448713552,0.0440407241264263,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0390744040629657,0,0,0,0,0.178242227335072,0,0,0.13101233739175,0.205179773171894,0.108540960151002,0.0937647931713765,0.126805304144253,0,0,0,0.502587185436355,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.262178501405346,0,0,0.512671986293146,0,0,0,0,0.0408567533019575,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0377285380125452,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.399630802862919,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0201011396294926,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.125810625376375,0,0,0,0,0,0,0,0,0,0.0886074497308223,0.0111016828724432,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0220321056448849,0,0,0.087489893808421,0,0.652399296743096,0,0,0,0,0,0,0,0,0,0,0,0.025420400879005,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0133515564209632,0,0.18984326733154,0,0,0,0,0,0,0,0,0.662696015070327,0,0,0,0,0,0.0316640867750834,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0161429629723438,0,0,0,0,0,0,0,0,0.309072365801438,0.1192526399866,0.0602540516591541,0,0,0,0,0.163974701329705,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0261550693490902,0,0.0394174507877591,0,0,0,0.199594177092918,0.0300822291072195,0,0,0,0,0,0,0,0,0,0.253783400445552,0.434722935368077|full_id=C995_B_plasma_lymphoma_xeroderma_acute_Burkitt_b|gostat_on_coexpression_clusters=GO:0003835!beta-galactoside alpha-2,6-sialyltransferase activity!0.0268432668755767!6480$GO:0009311!oligosaccharide metabolic process!0.0408673311549087!6480$GO:0008373!sialyltransferase activity!0.0408673311549087!6480$GO:0006955!immune response!0.0408673311549087!6480;931$GO:0005887!integral to plasma membrane!0.0408673311549087!931;5284$GO:0031226!intrinsic to plasma membrane!0.0408673311549087!931;5284$GO:0002376!immune system process!0.0408673311549087!6480;931$GO:0009306!protein secretion!0.0408673311549087!5284$GO:0030173!integral to Golgi membrane!0.0408673311549087!6480$GO:0042113!B cell activation!0.0408673311549087!931$GO:0031228!intrinsic to Golgi membrane!0.0418550013339888!6480$GO:0006959!humoral immune response!0.0418550013339888!6480$GO:0016021!integral to membrane!0.0422278845053486!6480;931;5284$GO:0031224!intrinsic to membrane!0.0422278845053486!6480;931;5284$GO:0044425!membrane part!0.048599195518169!6480;931;5284$GO:0031301!integral to organelle membrane!0.048599195518169!6480$GO:0044459!plasma membrane part!0.048599195518169!931;5284$GO:0031300!intrinsic to organelle membrane!0.048599195518169!6480$GO:0008565!protein transporter activity!0.048599195518169!5284$GO:0046649!lymphocyte activation!0.048599195518169!931$GO:0006486!protein amino acid glycosylation!0.048599195518169!6480$GO:0005057!receptor signaling protein activity!0.048599195518169!931$GO:0043413!biopolymer glycosylation!0.048599195518169!6480$GO:0045321!leukocyte activation!0.048599195518169!931$GO:0009101!glycoprotein biosynthetic 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156.1;0.865715,MA0157.1;0.697424,MA0158.1;0,MA0159.1;0.243637,MA0160.1;1.23953,MA0161.1;0,MA0162.1;0.0163939,MA0163.1;0.0517199,MA0164.1;0.627336,MA0080.2;0.818924,MA0018.2;2.48749,MA0099.2;0.523145,MA0079.2;0.00346431,MA0102.2;1.46209,MA0258.1;0.209744,MA0259.1;0.25092,MA0442.1;0}}
|full_id=C995_B_plasma_lymphoma_xeroderma_acute_Burkitt_b
|gostat_on_coexpression_clusters=GO:0003835!beta-galactoside alpha-2,6-sialyltransferase activity!0.0268432668755767!6480$GO:0009311!oligosaccharide metabolic process!0.0408673311549087!6480$GO:0008373!sialyltransferase activity!0.0408673311549087!6480$GO:0006955!immune response!0.0408673311549087!6480;931$GO:0005887!integral to plasma membrane!0.0408673311549087!931;5284$GO:0031226!intrinsic to plasma membrane!0.0408673311549087!931;5284$GO:0002376!immune system process!0.0408673311549087!6480;931$GO:0009306!protein secretion!0.0408673311549087!5284$GO:0030173!integral to Golgi membrane!0.0408673311549087!6480$GO:0042113!B cell activation!0.0408673311549087!931$GO:0031228!intrinsic to Golgi membrane!0.0418550013339888!6480$GO:0006959!humoral immune response!0.0418550013339888!6480$GO:0016021!integral to membrane!0.0422278845053486!6480;931;5284$GO:0031224!intrinsic to membrane!0.0422278845053486!6480;931;5284$GO:0044425!membrane part!0.048599195518169!6480;931;5284$GO:0031301!integral to organelle membrane!0.048599195518169!6480$GO:0044459!plasma membrane part!0.048599195518169!931;5284$GO:0031300!intrinsic to organelle membrane!0.048599195518169!6480$GO:0008565!protein transporter activity!0.048599195518169!5284$GO:0046649!lymphocyte activation!0.048599195518169!931$GO:0006486!protein amino acid glycosylation!0.048599195518169!6480$GO:0005057!receptor signaling protein activity!0.048599195518169!931$GO:0043413!biopolymer glycosylation!0.048599195518169!6480$GO:0045321!leukocyte activation!0.048599195518169!931$GO:0009101!glycoprotein biosynthetic process!0.048599195518169!6480
|id=C995
|ontology_enrichment_celltype=CL:0000945!1.21e-27!24;CL:0000826!1.21e-27!24;CL:0000236!2.36e-16!14;CL:0002087!3.63e-12!119;CL:0000542!9.90e-12!53;CL:0000051!9.90e-12!53;CL:0000838!5.76e-11!52;CL:0000738!9.08e-11!140;CL:0002031!1.38e-09!124;CL:0000037!2.15e-09!172;CL:0000566!2.15e-09!172;CL:0002032!2.19e-08!165;CL:0000837!2.19e-08!165;CL:0000988!6.29e-08!182
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.19e-49!115;UBERON:0001049!3.05e-12!57;UBERON:0005068!3.05e-12!57;UBERON:0006241!3.05e-12!57;UBERON:0007135!3.05e-12!57;UBERON:0002780!3.25e-11!41;UBERON:0001890!3.25e-11!41;UBERON:0006240!3.25e-11!41;UBERON:0003080!9.36e-11!42;UBERON:0000178!9.89e-10!15;UBERON:0000179!9.89e-10!15;UBERON:0000463!9.89e-10!15;UBERON:0002616!1.09e-09!59;UBERON:0001893!2.49e-09!34;UBERON:0002020!5.43e-09!34;UBERON:0003528!5.43e-09!34;UBERON:0002791!8.88e-09!33;UBERON:0001869!3.54e-08!32;UBERON:0000955!4.41e-08!69;UBERON:0006238!4.41e-08!69;UBERON:0001017!4.47e-08!82;UBERON:0005743!9.74e-08!86;UBERON:0002308!1.90e-07!9;UBERON:0000125!1.90e-07!9;UBERON:0003075!3.18e-07!86;UBERON:0007284!3.18e-07!86
}}

Latest revision as of 11:35, 17 September 2013


Full id: C995_B_plasma_lymphoma_xeroderma_acute_Burkitt_b



Phase1 CAGE Peaks

Hg19::chr11:60233507..60233518,+p3@MS4A1
Hg19::chr1:207103754..207103765,-p12@PIGR
Hg19::chr3:105975093..105975118,+p@chr3:105975093..105975118
+
Hg19::chr3:186739681..186739693,+p7@ST6GAL1
Hg19::chr3:186739710..186739719,+p14@ST6GAL1
Hg19::chr3:186739722..186739731,+p13@ST6GAL1
Hg19::chr8:110535027..110535055,+p2@PKHD1L1
Hg19::chr8:110535062..110535067,+p4@PKHD1L1


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:0003835beta-galactoside alpha-2,6-sialyltransferase activity0.0268432668755767
GO:0009311oligosaccharide metabolic process0.0408673311549087
GO:0008373sialyltransferase activity0.0408673311549087
GO:0006955immune response0.0408673311549087
GO:0005887integral to plasma membrane0.0408673311549087
GO:0031226intrinsic to plasma membrane0.0408673311549087
GO:0002376immune system process0.0408673311549087
GO:0009306protein secretion0.0408673311549087
GO:0030173integral to Golgi membrane0.0408673311549087
GO:0042113B cell activation0.0408673311549087
GO:0031228intrinsic to Golgi membrane0.0418550013339888
GO:0006959humoral immune response0.0418550013339888
GO:0016021integral to membrane0.0422278845053486
GO:0031224intrinsic to membrane0.0422278845053486
GO:0044425membrane part0.048599195518169
GO:0031301integral to organelle membrane0.048599195518169
GO:0044459plasma membrane part0.048599195518169
GO:0031300intrinsic to organelle membrane0.048599195518169
GO:0008565protein transporter activity0.048599195518169
GO:0046649lymphocyte activation0.048599195518169
GO:0006486protein amino acid glycosylation0.048599195518169
GO:0005057receptor signaling protein activity0.048599195518169
GO:0043413biopolymer glycosylation0.048599195518169
GO:0045321leukocyte activation0.048599195518169
GO:0009101glycoprotein biosynthetic process0.048599195518169



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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
blood1.14e-1715
haemolymphatic fluid1.14e-1715
organism substance1.14e-1715
spleen1.68e-113
gastrointestinal system mesentery1.68e-113
stomach region1.68e-113
mesentery1.68e-113
gastrointestinal system serosa1.68e-113
mesentery of stomach1.68e-113
gut mesentery1.68e-113
dorsal mesentery1.68e-113
dorsal mesogastrium1.68e-113
peritoneal cavity1.68e-113
spleen primordium1.68e-113
adult organism1.28e-10114
major salivary gland2.61e-082
hemopoietic organ2.64e-087
immune organ2.64e-087
Disease
Ontology termp-valuen
lymphoma3.62e-1310


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)
MA0003.10.140538
MA0004.11.15451
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.00962431
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.0955945
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.028436
MA0056.10
MA0057.10.0912556
MA0058.11.69448
MA0059.11.69011
MA0060.10.190336
MA0061.10.165998
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.823119
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.0041831
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.054222
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.10.421159
MA0093.11.48478
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.792149
MA0105.10.0818021
MA0106.10.59853
MA0107.10.666147
MA0108.22.97762
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.155155
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.10.0613434
MA0146.10.113833
MA0147.10.681318
MA0148.10.480298
MA0149.10.506665
MA0062.20.161302
MA0035.20.515566
MA0039.20.0817047
MA0138.20.653421
MA0002.20.179788
MA0137.20.321796
MA0104.20.55506
MA0047.20.586412
MA0112.20.0572179
MA0065.20.844872
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.274121
MA0155.10.197713
MA0156.10.865715
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.11.23953
MA0161.10
MA0162.10.0163939
MA0163.10.0517199
MA0164.10.627336
MA0080.20.818924
MA0018.22.48749
MA0099.20.523145
MA0079.20.00346431
MA0102.21.46209
MA0258.10.209744
MA0259.10.25092
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
EBF1#187955.566541779105630.0007445813282558610.00586406223827116
NFE2#4778219.30106516290730.004458388692795240.0210988108517306
NFKB1#479074.802055496169614.48248622098168e-050.000794006747681658
PAX5#507975.83586983978061.18321811145587e-050.000299283401168177
POU2F2#545277.967858550524711.39153702916505e-065.41470699660838e-05
SPI1#668844.102161754261360.01027800662400760.0381933724890493
SRF#672246.89858913108390.001522071904568780.0097017801428904
TAF1#687262.507284714308970.01111734475613860.0408846920309293
TBP#690873.243424351209340.0006354223620492050.005213928038188
ZEB1#693536.333162006578950.009275222683824870.0350417805627255



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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