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{{Coexpression_clusters
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1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.455568,MA0163.1;1.84145,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;3.14419,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C3792_Renal_Alveolar_anaplastic_acute_testicular_lymphoma_diffuse
|gostat_on_coexpression_clusters=GO:0005685!snRNP U1!0.00847744498676387!6626$GO:0005684!U2-dependent spliceosome!0.0211911169354966!6626$GO:0030532!small nuclear ribonucleoprotein complex!0.0353107296901619!6626$GO:0000375!RNA splicing, via transesterification reactions!0.0494022677164302!6626$GO:0000398!nuclear mRNA splicing, via spliceosome!0.0494022677164302!6626$GO:0000377!RNA splicing, via transesterification reactions with bulged adenosine as nucleophile!0.0494022677164302!6626
|id=C3792
|ontology_enrichment_celltype=CL:0000066!3.29e-25!254;CL:0000012!5.73e-21!682;CL:0000548!1.39e-20!679;CL:0000004!1.39e-20!679;CL:0000255!1.39e-20!679;CL:0000003!3.72e-12!722;CL:0002321!3.75e-12!248;CL:0000220!1.54e-11!246;CL:0000063!1.46e-10!578;CL:0000144!4.07e-09!625;CL:0000076!1.17e-07!62;CL:0000133!6.65e-07!59;CL:0000333!8.50e-07!41;CL:0002319!8.95e-07!25
|ontology_enrichment_disease=DOID:162!2.40e-43!235;DOID:14566!1.14e-40!239;DOID:0050686!1.28e-21!137;DOID:2531!1.22e-20!51;DOID:0060083!1.22e-20!51;DOID:0050687!1.44e-20!143;DOID:305!1.68e-17!106;DOID:1240!1.00e-16!39;DOID:8692!4.96e-13!31
|ontology_enrichment_uberon=
}}

Latest revision as of 12:33, 17 September 2013


Full id: C3792_Renal_Alveolar_anaplastic_acute_testicular_lymphoma_diffuse



Phase1 CAGE Peaks

Hg19::chr19:41256764..41256825,+p3@SNRPA
Hg19::chr20:42295713..42295738,+p2@MYBL2
Hg19::chr20:42295745..42295765,+p1@MYBL2


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:0005685snRNP U10.00847744498676387
GO:0005684U2-dependent spliceosome0.0211911169354966
GO:0030532small nuclear ribonucleoprotein complex0.0353107296901619
GO:0000375RNA splicing, via transesterification reactions0.0494022677164302
GO:0000398nuclear mRNA splicing, via spliceosome0.0494022677164302
GO:0000377RNA splicing, via transesterification reactions with bulged adenosine as nucleophile0.0494022677164302



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>

Cell Type
Ontology termp-valuen
epithelial cell4.37e-26253
animal cell7.64e-18679
eukaryotic cell7.64e-18679
embryonic cell1.52e-12250
native cell1.35e-09722
squamous epithelial cell1.66e-0763
meso-epithelial cell6.43e-0745
lining cell7.75e-0758
barrier cell7.75e-0758
Uber Anatomy
Ontology termp-valuen
trunk region element4.23e-07101
Disease
Ontology termp-valuen
cancer2.60e-44235
disease of cellular proliferation6.50e-42239
organ system cancer6.84e-22137
cell type cancer1.05e-21143
hematologic cancer7.94e-2051
immune system cancer7.94e-2051
carcinoma4.70e-18106
leukemia8.58e-1639
myeloid leukemia3.68e-1231


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
MA0004.11.93041
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.18.34001
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
MA0055.12.37507
MA0056.10
MA0057.10.333427
MA0058.11.70328
MA0059.10.714521
MA0060.12.13518
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.668628
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.11.31954
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.11.55117
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
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
MA0117.13.02823
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
MA0146.15.33893
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.25.50873
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.11.84145
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.23.14419
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
E2F1#186934.907389214879320.008460985347239390.0325340322035394
E2F4#1874312.66806031528440.0004917987006298980.00437057220005837
E2F6#187635.017155731697390.00791769806886330.0322158512004836
ELF1#199734.258097958807540.01295179875054610.0462215243365209
IRF1#365937.63716375356390.002244692747297240.0128049741006651
MAX#414936.452555509007120.003721913834265510.0186468847230574
MXI1#460139.96157162875930.001011470541259020.00720186609343816
MYC#460935.22228187160940.007020843755740150.0294442396902279
NFKB1#479035.488063424193840.006049381815655430.0269581578530994
PAX5#507936.669565531177830.003370290999677260.0172883016559574
POU2F2#545239.106124057742520.001324165192682130.00882148935118511
SIN3A#2594235.408884726815140.006318961977991520.0276683745606011
SP1#666735.69838137814090.005403962701712170.0246434573663487
USF1#739136.361499277207960.00388404057290560.0190238387372175
YY1#752834.911170749853860.008441455341808260.0329317976333761
ZEB1#6935211.25895467836260.01010222676646330.0378160021957942



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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