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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0,

Latest revision as of 11:20, 17 September 2013


Full id: C350_b_lymph_acute_CD19_lymphoma_spleen_B



Phase1 CAGE Peaks

Hg19::chr14:106320405..106320425,-p8@IGHM
Hg19::chr14:106321136..106321178,+p@chr14:106321136..106321178
+
Hg19::chr14:106321203..106321218,+p@chr14:106321203..106321218
+
Hg19::chr14:106321227..106321242,+p@chr14:106321227..106321242
+
Hg19::chr14:106321246..106321254,-p3@J00257
Hg19::chr14:106321254..106321276,+p@chr14:106321254..106321276
+
Hg19::chr14:106321619..106321630,-p8@FJ197674
Hg19::chr14:106321667..106321674,-p9@FJ197674
Hg19::chr14:106321677..106321684,-p10@FJ197674
Hg19::chr14:106321687..106321692,-p12@FJ197674
Hg19::chr14:106321710..106321722,-p3@FJ197674
Hg19::chr14:106321725..106321735,-p7@FJ197674
Hg19::chr14:106321756..106321783,-p1@FJ197674
Hg19::chr14:106321811..106321832,-p5@FJ197674
Hg19::chr14:106321813..106321821,+p5@AY671148
p5@AY671772
p5@AY671782
p5@AY671783
Hg19::chr14:106321849..106321852,-p11@FJ197674
Hg19::chr14:106321854..106321877,-p2@FJ197674
Hg19::chr14:106321879..106321890,+p2@AY671148
p2@AY671772
p2@AY671782
p2@AY671783
Hg19::chr14:106321882..106321895,-p6@FJ197674
Hg19::chr14:106322016..106322079,+p1@AY671148
p1@AY671760
p1@AY671772
p1@AY671782
p1@AY671783
Hg19::chr14:106322056..106322063,-p4@AJ294734
Hg19::chr14:106322107..106322112,-p6@AJ294734
Hg19::chr14:106322129..106322143,-p1@AJ294734
Hg19::chr14:106322148..106322185,+p1@HM995588
Hg19::chr14:106322154..106322163,-p3@AJ294734
Hg19::chr14:106322242..106322254,-p2@AJ294734
Hg19::chr14:106322276..106322283,-p5@AJ294734
Hg19::chr14:106322288..106322325,-p2@IGHM
Hg19::chr14:106328131..106328143,-p4@IGHM
Hg19::chr14:106725347..106725368,-p1@AF460666
p1@AF460671
p1@AF460672
p1@AF460678
p1@AF460691
p1@AF460699
p1@AF460700
p1@AF460800
p1@DQ454508
p1@U64467
Hg19::chr17:3599428..3599456,-p1@ENST00000550383
Hg19::chr21:43955104..43955124,-p@chr21:43955104..43955124
-


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:0006955immune response0.00395619922288943
GO:0002376immune system process0.00395619922288943
GO:0003823antigen binding0.00395619922288943
GO:0045321leukocyte activation0.00395619922288943
GO:0042571immunoglobulin complex, circulating0.00395619922288943
GO:0001775cell activation0.00420175109836318
GO:0005153interleukin-8 receptor binding0.00565154680679548
GO:0045022early endosome to late endosome transport0.00593394946336459
GO:0019814immunoglobulin complex0.00593394946336459
GO:0019815B cell receptor complex0.00593394946336459
GO:0045091regulation of retroviral genome replication0.00719245428245118
GO:0045090retroviral genome replication0.00904548478924136
GO:0042119neutrophil activation0.00904548478924136
GO:0042127regulation of cell proliferation0.00904548478924136
GO:0050930induction of positive chemotaxis0.00941702662374834
GO:0005615extracellular space0.00941702662374834
GO:0030890positive regulation of B cell proliferation0.00941702662374834
GO:0050926regulation of positive chemotaxis0.00941702662374834
GO:0030888regulation of B cell proliferation0.00941702662374834
GO:0050927positive regulation of positive chemotaxis0.00941702662374834
GO:0050918positive chemotaxis0.00941702662374834
GO:0050853B cell receptor signaling pathway0.0094576917801139
GO:0050921positive regulation of chemotaxis0.0094576917801139
GO:0050920regulation of chemotaxis0.009491803941921
GO:0030593neutrophil chemotaxis0.009491803941921
GO:0045069regulation of viral genome replication0.00988700469035434
GO:0005624membrane fraction0.00991146325799091
GO:0008283cell proliferation0.0104670522674057
GO:0050792regulation of viral reproduction0.0104670522674057
GO:0001772immunological synapse0.0104670522674057
GO:0050731positive regulation of peptidyl-tyrosine phosphorylation0.0104670522674057
GO:0045807positive regulation of endocytosis0.0104670522674057
GO:0050871positive regulation of B cell activation0.0104670522674057
GO:0042100B cell proliferation0.0104670522674057
GO:0042327positive regulation of phosphorylation0.0115598019496547
GO:0030595leukocyte chemotaxis0.0115598019496547
GO:0000267cell fraction0.0115598019496547
GO:0044421extracellular region part0.0115598019496547
GO:0045937positive regulation of phosphate metabolic process0.0115598019496547
GO:0050864regulation of B cell activation0.0115598019496547
GO:0001934positive regulation of protein amino acid phosphorylation0.0115598019496547
GO:0002274myeloid leukocyte activation0.0115598019496547
GO:0033240positive regulation of amine metabolic process0.0115598019496547
GO:0045764positive regulation of amino acid metabolic process0.0115598019496547
GO:0050851antigen receptor-mediated signaling pathway0.0115598019496547
GO:0050730regulation of peptidyl-tyrosine phosphorylation0.0115598019496547
GO:0019079viral genome replication0.0115598019496547
GO:0032946positive regulation of mononuclear cell proliferation0.0115598019496547
GO:0002455humoral immune response mediated by circulating immunoglobulin0.0115598019496547
GO:0002429immune response-activating cell surface receptor signaling pathway0.0115598019496547
GO:0050671positive regulation of lymphocyte proliferation0.0115598019496547
GO:0050900leukocyte migration0.0115598019496547
GO:0002768immune response-regulating cell surface receptor signaling pathway0.0115598019496547
GO:0002757immune response-activating signal transduction0.011711378025305
GO:0002764immune response-regulating signal transduction0.0118574210887758
GO:0030100regulation of endocytosis0.0119982275520463
GO:0019722calcium-mediated signaling0.0128266931832893
GO:0051050positive regulation of transport0.0129458524290536
GO:0016197endosome transport0.013383863320157
GO:0018108peptidyl-tyrosine phosphorylation0.013383863320157
GO:0050670regulation of lymphocyte proliferation0.013383863320157
GO:0032944regulation of mononuclear cell proliferation0.013383863320157
GO:0018212peptidyl-tyrosine modification0.0137685000000387
GO:0001932regulation of protein amino acid phosphorylation0.0137685000000387
GO:0033238regulation of amine metabolic process0.0137685000000387
GO:0006521regulation of amino acid metabolic process0.0137685000000387
GO:0019058viral infectious cycle0.014339572658952
GO:0009897external side of plasma membrane0.014339572658952
GO:0051251positive regulation of lymphocyte activation0.014339572658952
GO:0016064immunoglobulin mediated immune response0.014339572658952
GO:0019724B cell mediated immunity0.014339572658952
GO:0032943mononuclear cell proliferation0.014339572658952
GO:0046651lymphocyte proliferation0.014339572658952
GO:0000187activation of MAPK activity0.0150087881311616
GO:0022415viral reproductive process0.0150087881311616
GO:0042113B cell activation0.0158488264866682
GO:0042325regulation of phosphorylation0.0162004792785023
GO:0048471perinuclear region of cytoplasm0.0162004792785023
GO:0043406positive regulation of MAP kinase activity0.0162881160672838
GO:0030155regulation of cell adhesion0.0162881160672838
GO:0051174regulation of phosphorus metabolic process0.0166116880525676
GO:0019220regulation of phosphate metabolic process0.0166116880525676
GO:0002253activation of immune response0.0168543714380707
GO:0002449lymphocyte mediated immunity0.0168543714380707
GO:0006959humoral immune response0.0168543714380707
GO:0002250adaptive immune response0.0168543714380707
GO:0008009chemokine activity0.0168543714380707
GO:0002460adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.0168543714380707
GO:0051249regulation of lymphocyte activation0.0168543714380707
GO:0042379chemokine receptor binding0.0168859071514165
GO:0002443leukocyte mediated immunity0.016916737003196
GO:0050865regulation of cell activation0.0171608959655122
GO:0050778positive regulation of immune response0.0178428776647907
GO:0051247positive regulation of protein metabolic process0.0178428776647907
GO:0002684positive regulation of immune system process0.0178622382061167
GO:0043405regulation of MAP kinase activity0.0191109896713727
GO:0050776regulation of immune response0.0199279131796443
GO:0002682regulation of immune system process0.0201212644956015
GO:0007050cell cycle arrest0.0201212644956015
GO:0001664G-protein-coupled receptor binding0.0205015089564397
GO:0051240positive regulation of multicellular organismal process0.0205015089564397
GO:0007242intracellular signaling cascade0.0206565267277989
GO:0043235receptor complex0.0206565267277989
GO:0002252immune effector process0.0206565267277989
GO:0051049regulation of transport0.0206565267277989
GO:0018193peptidyl-amino acid modification0.0225005239824122
GO:0001525angiogenesis0.0237583710023897
GO:0045860positive regulation of protein kinase activity0.0255539605278058
GO:0033674positive regulation of kinase activity0.0255539605278058
GO:0042330taxis0.0255539605278058
GO:0006935chemotaxis0.0255539605278058
GO:0051347positive regulation of transferase activity0.0255696250733866
GO:0048514blood vessel morphogenesis0.0255696250733866
GO:0009986cell surface0.0255696250733866
GO:0000165MAPKKK cascade0.0256882967032008
GO:0048646anatomical structure formation0.0259738855056701
GO:0046649lymphocyte activation0.0260869742473664
GO:0001568blood vessel development0.0273422372844919
GO:0001944vasculature development0.0273422372844919
GO:0007166cell surface receptor linked signal transduction0.0273422372844919
GO:0007626locomotory behavior0.029433244533981
GO:0010324membrane invagination0.0314993158407173
GO:0006897endocytosis0.0314993158407173
GO:0005515protein binding0.0336362671547079
GO:0045786negative regulation of progression through cell cycle0.0350908007506085
GO:0008285negative regulation of cell proliferation0.0350908007506085
GO:0016477cell migration0.0357622432664774
GO:0008284positive regulation of cell proliferation0.0357622432664774
GO:0045859regulation of protein kinase activity0.0360899418582341
GO:0043549regulation of kinase activity0.0365624667764168
GO:0051338regulation of transferase activity0.0370275569021061
GO:0043085positive regulation of catalytic activity0.0380758925119667
GO:0019932second-messenger-mediated signaling0.0395469873936715
GO:0051239regulation of multicellular organismal process0.0405592445225359
GO:0016044membrane organization and biogenesis0.0412676483960112
GO:0006954inflammatory response0.0419652184692328
GO:0007610behavior0.0420846488799162
GO:0022414reproductive process0.0433287996253402
GO:0005125cytokine activity0.0437158255262933
GO:0000074regulation of progression through cell cycle0.0493613408533506
GO:0051726regulation of cell cycle0.049835479474263
GO:0009887organ morphogenesis0.0498936231862632
GO:0031325positive regulation of cellular metabolic process0.0499508811830772



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
adult organism1.07e-12114
hemopoietic organ1.91e-117
immune organ1.91e-117
spleen7.46e-113
gastrointestinal system mesentery7.46e-113
stomach region7.46e-113
mesentery7.46e-113
gastrointestinal system serosa7.46e-113
mesentery of stomach7.46e-113
gut mesentery7.46e-113
dorsal mesentery7.46e-113
dorsal mesogastrium7.46e-113
peritoneal cavity7.46e-113
spleen primordium7.46e-113
blood2.22e-0715
haemolymphatic fluid2.22e-0715
organism substance2.22e-0715
Disease
Ontology termp-valuen
lymphoma2.13e-0810
hematologic cancer6.18e-0751
immune system cancer6.18e-0751


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)
MA0003.10.00040238
MA0004.111.2345
MA0006.10.279119
MA0007.10.265481
MA0009.10.395891
MA0014.10.00277835
MA0017.12.99133
MA0019.12.91722
MA0024.10.312615
MA0025.10.508683
MA0027.11.93196
MA0028.10.032054
MA0029.10.327543
MA0030.10.318663
MA0031.10.270046
MA0038.13.39844
MA0040.10.332103
MA0041.10.0940493
MA0042.10.0792314
MA0043.11.02525
MA0046.10.386991
MA0048.10.915538
MA0050.10.0796249
MA0051.10.136135
MA0052.10.335128
MA0055.10.828339
MA0056.10
MA0057.12.06674
MA0058.120.4269
MA0059.16.04104
MA0060.10.00694078
MA0061.14.04258
MA0063.10
MA0066.12.65769
MA0067.10.673046
MA0068.10.0455946
MA0069.10.383853
MA0070.10.374777
MA0071.10.1171
MA0072.10.371146
MA0073.11.696e-05
MA0074.12.62648
MA0076.10.0525452
MA0077.10.364942
MA0078.10.197204
MA0081.10.0465806
MA0083.10.40206
MA0084.10.847335
MA0087.10.369175
MA0088.11.26589
MA0089.10
MA0090.10.0579073
MA0091.10.0865076
MA0092.16.0767
MA0093.114.38
MA0095.10
MA0098.10
MA0100.14.3091
MA0101.11.2308
MA0103.19.58
MA0105.13.84914
MA0106.10.163029
MA0107.13.5716
MA0108.20.267801
MA0109.10
MA0111.10.490476
MA0113.10.173209
MA0114.11.169
MA0115.10.603788
MA0116.12.5408
MA0117.10.427006
MA0119.10.0412526
MA0122.11.99005
MA0124.10.566745
MA0125.10.493194
MA0130.10
MA0131.10.2093
MA0132.10
MA0133.10
MA0135.10.420972
MA0136.10.142619
MA0139.10.00355142
MA0140.10.115685
MA0141.11.52412
MA0142.12.76951
MA0143.11.57513
MA0144.10.144799
MA0145.12.37335
MA0146.10.443429
MA0147.16.922
MA0148.10.0971411
MA0149.10.110599
MA0062.20.004042
MA0035.20.11531
MA0039.20.00370508
MA0138.20.575161
MA0002.20.361695
MA0137.20.136268
MA0104.23.40818
MA0047.20.155654
MA0112.21.33369
MA0065.20.163186
MA0150.10.44969
MA0151.10
MA0152.10.119196
MA0153.10.478697
MA0154.10.737639
MA0155.10.000754999
MA0156.10.0345163
MA0157.10.227782
MA0158.10
MA0159.13.10997
MA0160.11.14983
MA0161.10
MA0162.10.00415725
MA0163.11.71831
MA0164.10.181076
MA0080.20.838393
MA0018.26.37996
MA0099.20.119388
MA0079.25.55621e-08
MA0102.20.88257
MA0258.11.02444
MA0259.12.16494
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
POLR2A#5430322.147453176558072.38288969218142e-112.83124705986046e-09



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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