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Coexpression cluster:C4143: Difference between revisions

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{{Coexpression_clusters
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splicing!0.0024019489850783!9360;10199$GO:0006396!RNA processing!0.00566423892359164!9360;10199$GO:0016018!cyclosporin A binding!0.00566423892359164!9360$GO:0031981!nuclear lumen!0.00566423892359164!9360;10199$GO:0031974!membrane-enclosed lumen!0.00693705742595231!9360;10199$GO:0043233!organelle lumen!0.00693705742595231!9360;10199$GO:0005732!small nucleolar ribonucleoprotein complex!0.00693705742595231!10199$GO:0044428!nuclear part!0.00719345594856585!9360;10199$GO:0008144!drug binding!0.00719345594856585!9360$GO:0031202!RNA splicing factor activity, transesterification mechanism!0.00744489806851175!10199$GO:0044452!nucleolar part!0.0120616571778071!10199$GO:0016363!nuclear matrix!0.0126734263056732!9360$GO:0006364!rRNA processing!0.0170965459175916!10199$GO:0016072!rRNA metabolic process!0.0170965459175916!10199$GO:0016607!nuclear speck!0.0176895637176626!9360$GO:0003755!peptidyl-prolyl cis-trans isomerase activity!0.0176895637176626!9360$GO:0016859!cis-trans isomerase activity!0.0176895637176626!9360$GO:0016604!nuclear body!0.018885880737988!9360$GO:0042254!ribosome biogenesis and assembly!0.018885880737988!10199$GO:0005730!nucleolus!0.0266486946639436!10199$GO:0042277!peptide binding!0.0319735175896541!9360$GO:0022613!ribonucleoprotein complex biogenesis and assembly!0.0329026406580026!10199$GO:0044446!intracellular organelle part!0.0329026406580026!9360;10199$GO:0044422!organelle part!0.0329026406580026!9360;10199$GO:0016070!RNA metabolic process!0.0329026406580026!9360;10199$GO:0016853!isomerase activity!0.0389244521400519!9360$GO:0006457!protein 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A0114.1;1.35563,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;0.273764,MA0146.1;0.107247,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;1.9924,MA0035.2;0.894194,MA0039.2;0.195278,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.264678,MA0065.2;0.760954,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.149099,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.0373086,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C4143_Mast_acute_hepatoblastoma_embryonic_rhabdomyosarcoma_testicular_cord
|gostat_on_coexpression_clusters=GO:0008380!RNA splicing!0.0024019489850783!9360;10199$GO:0006396!RNA processing!0.00566423892359164!9360;10199$GO:0016018!cyclosporin A binding!0.00566423892359164!9360$GO:0031981!nuclear lumen!0.00566423892359164!9360;10199$GO:0031974!membrane-enclosed lumen!0.00693705742595231!9360;10199$GO:0043233!organelle lumen!0.00693705742595231!9360;10199$GO:0005732!small nucleolar ribonucleoprotein complex!0.00693705742595231!10199$GO:0044428!nuclear part!0.00719345594856585!9360;10199$GO:0008144!drug binding!0.00719345594856585!9360$GO:0031202!RNA splicing factor activity, transesterification mechanism!0.00744489806851175!10199$GO:0044452!nucleolar part!0.0120616571778071!10199$GO:0016363!nuclear matrix!0.0126734263056732!9360$GO:0006364!rRNA processing!0.0170965459175916!10199$GO:0016072!rRNA metabolic process!0.0170965459175916!10199$GO:0016607!nuclear speck!0.0176895637176626!9360$GO:0003755!peptidyl-prolyl cis-trans isomerase activity!0.0176895637176626!9360$GO:0016859!cis-trans isomerase activity!0.0176895637176626!9360$GO:0016604!nuclear body!0.018885880737988!9360$GO:0042254!ribosome biogenesis and assembly!0.018885880737988!10199$GO:0005730!nucleolus!0.0266486946639436!10199$GO:0042277!peptide binding!0.0319735175896541!9360$GO:0022613!ribonucleoprotein complex biogenesis and assembly!0.0329026406580026!10199$GO:0044446!intracellular organelle part!0.0329026406580026!9360;10199$GO:0044422!organelle part!0.0329026406580026!9360;10199$GO:0016070!RNA metabolic process!0.0329026406580026!9360;10199$GO:0016853!isomerase activity!0.0389244521400519!9360$GO:0006457!protein folding!0.0411644597921784!9360
|id=C4143
|ontology_enrichment_celltype=CL:0000542!1.56e-12!53;CL:0000051!1.56e-12!53;CL:0000838!4.24e-12!52;CL:0000037!4.70e-08!172;CL:0000566!4.70e-08!172;CL:0000988!5.60e-07!182;CL:0000945!8.83e-07!24;CL:0000826!8.83e-07!24
|ontology_enrichment_disease=DOID:162!7.93e-33!235;DOID:14566!1.65e-31!239;DOID:2531!1.02e-20!51;DOID:0060083!1.02e-20!51;DOID:1240!2.03e-18!39;DOID:0050686!5.71e-18!137;DOID:8692!1.39e-16!31;DOID:0050687!5.45e-16!143;DOID:305!2.73e-11!106;DOID:3095!8.61e-07!22;DOID:2994!8.61e-07!22
|ontology_enrichment_uberon=
}}

Latest revision as of 12:40, 17 September 2013


Full id: C4143_Mast_acute_hepatoblastoma_embryonic_rhabdomyosarcoma_testicular_cord



Phase1 CAGE Peaks

Hg19::chr2:170440902..170440927,+p3@PPIG
Hg19::chr2:71357744..71357791,+p1@MPHOSPH10
Hg19::chr6:144164455..144164564,+p1@LTV1


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:0008380RNA splicing0.0024019489850783
GO:0006396RNA processing0.00566423892359164
GO:0016018cyclosporin A binding0.00566423892359164
GO:0031981nuclear lumen0.00566423892359164
GO:0031974membrane-enclosed lumen0.00693705742595231
GO:0043233organelle lumen0.00693705742595231
GO:0005732small nucleolar ribonucleoprotein complex0.00693705742595231
GO:0044428nuclear part0.00719345594856585
GO:0008144drug binding0.00719345594856585
GO:0031202RNA splicing factor activity, transesterification mechanism0.00744489806851175
GO:0044452nucleolar part0.0120616571778071
GO:0016363nuclear matrix0.0126734263056732
GO:0006364rRNA processing0.0170965459175916
GO:0016072rRNA metabolic process0.0170965459175916
GO:0016607nuclear speck0.0176895637176626
GO:0003755peptidyl-prolyl cis-trans isomerase activity0.0176895637176626
GO:0016859cis-trans isomerase activity0.0176895637176626
GO:0016604nuclear body0.018885880737988
GO:0042254ribosome biogenesis and assembly0.018885880737988
GO:0005730nucleolus0.0266486946639436
GO:0042277peptide binding0.0319735175896541
GO:0022613ribonucleoprotein complex biogenesis and assembly0.0329026406580026
GO:0044446intracellular organelle part0.0329026406580026
GO:0044422organelle part0.0329026406580026
GO:0016070RNA metabolic process0.0329026406580026
GO:0016853isomerase activity0.0389244521400519
GO:0006457protein folding0.0411644597921784



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><br>disease_data<br>

Cell Type
Ontology termp-valuen
nucleate cell3.68e-1155
lymphocyte1.27e-1053
common lymphoid progenitor1.27e-1053
lymphoid lineage restricted progenitor cell2.68e-1052
Disease
Ontology termp-valuen
cancer2.79e-32235
disease of cellular proliferation1.84e-31239
hematologic cancer1.40e-1951
immune system cancer1.40e-1951
leukemia3.67e-1839
organ system cancer4.88e-18137
cell type cancer2.29e-16143
myeloid leukemia2.42e-1631
carcinoma6.11e-12106
germ cell and embryonal cancer6.89e-0722
germ cell cancer6.89e-0722


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)
MA0003.10.401049
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.12.67616
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
MA0060.12.13518
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
MA0073.10.0185922
MA0074.10.935474
MA0076.12.91768
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
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
MA0114.11.35563
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
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.9924
MA0035.20.894194
MA0039.20.195278
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
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.0373086
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
BCLAF1#9774214.43509840674790.006201147435546130.0273902151415099
BRCA1#672213.45615376214920.007119807716084560.0296320075739282
CCNT2#90536.336201576962630.003930750035764890.0190445167463931
CEBPB#105137.971147625824820.001974187055288560.0115449981447607
CHD2#1106310.34402283411690.0009033701102746880.00661434877642864
E2F1#186934.907389214879320.008460985347239390.0326156885055304
E2F6#187635.017155731697390.00791769806886330.0323064724415539
ELF1#199734.258097958807540.01295179875054610.0463371098146164
ELK4#2005210.8237877723120.01091284719516480.0402034233382417
GABPB1#255337.067683836182170.002832212825417420.0154429088061904
GTF2F1#2962312.73966087675770.0004835525047438590.004347601587719
IRF1#365937.63716375356390.002244692747297240.0128365255344126
JUND#372736.994663941871030.002921845042734990.0157069474170372
MAX#414936.452555509007120.003721913834265510.0186926164432246
MEF2A#4205212.4954872730960.008235029478029740.0324918112450301
MEF2C#4208227.54090299508270.001729119938369690.0106491070434835
MXI1#460139.96157162875930.001011470541259020.00721317663766139
MYC#460935.22228187160940.007020843755740150.0295106009178471
NFKB1#479035.488063424193840.006049381815655430.027008865742358
NFYB#4801211.17319550235760.01025467135054530.0381392265652789
NR3C1#290829.982015554115360.01278474365547170.046054975256409
REST#597839.650028716128020.001112636247114590.00769095353844733
SETDB1#9869226.8800174520070.001814468907964410.0108958899654379
SIN3A#2594235.408884726815140.006318961977991520.0277393161287654
SIX5#147912211.3911435703060.009873820081429030.0370806147243569
SP1#666735.69838137814090.005403962701712170.0247027820109475
TRIM28#10155212.39368336350830.008368344129438470.0329245241112987
USF1#739136.361499277207960.00388404057290560.0190721384829417



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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