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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=-0.297356432645478,

Latest revision as of 12:36, 17 September 2013


Full id: C3964_chronic_Mesenchymal_hepatocellular_hereditary_acute_rhabdomyosarcoma_Skeletal



Phase1 CAGE Peaks

Hg19::chr1:28844730..28844776,+p2@RCC1
Hg19::chr1:28844778..28844807,+p3@RCC1
Hg19::chr22:20105012..20105085,+p1@RANBP1


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

p.valueFDRnGenesnPathwayName
4.59498110789263e-050.02908623041296032194HIV Infection (Reactome):REACT_6185



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:0005083small GTPase regulator activity0.00884912319659774
GO:0005087Ran guanyl-nucleotide exchange factor activity0.00884912319659774
GO:0030695GTPase regulator activity0.00884912319659774
GO:0007090regulation of S phase of mitotic cell cycle0.00884912319659774
GO:0007052mitotic spindle organization and biogenesis0.00884912319659774
GO:0008536Ran GTPase binding0.00884912319659774
GO:0033261regulation of progression through S phase0.00904970673294687
GO:0042393histone binding0.00904970673294687
GO:0000084S phase of mitotic cell cycle0.00911647317396334
GO:0007051spindle organization and biogenesis0.00916982948411652
GO:0051320S phase0.00921343297182372
GO:0000790nuclear chromatin0.00924972184269641
GO:0005092GDP-dissociation inhibitor activity0.0102534655193447
GO:0000794condensed nuclear chromosome0.0102534655193447
GO:0007346regulation of progression through mitotic cell cycle0.0102534655193447
GO:0000082G1/S transition of mitotic cell cycle0.0102534655193447
GO:0000793condensed chromosome0.0147554015762654
GO:0044454nuclear chromosome part0.0170067703933241
GO:0007088regulation of mitosis0.0170067703933241
GO:0017016Ras GTPase binding0.0185651040629841
GO:0051329interphase of mitotic cell cycle0.018628663845914
GO:0031267small GTPase binding0.018628663845914
GO:0051325interphase0.0188654918799131
GO:0051020GTPase binding0.0189105199641022
GO:0000228nuclear chromosome0.0189105199641022
GO:0000226microtubule cytoskeleton organization and biogenesis0.0189105199641022
GO:0003682chromatin binding0.0210616528993315
GO:0016043cellular component organization and biogenesis0.0272424842678321
GO:0005088Ras guanyl-nucleotide exchange factor activity0.0274005387140235
GO:0007067mitosis0.0368278486951195
GO:0000087M phase of mitotic cell cycle0.0368278486951195
GO:0051301cell division0.0368278486951195
GO:0019899enzyme binding0.0412168034622221
GO:0000279M phase0.0412168034622221
GO:0005085guanyl-nucleotide exchange factor activity0.0412168034622221
GO:0007017microtubule-based process0.0412168034622221
GO:0000785chromatin0.0412168034622221
GO:0000278mitotic cell cycle0.0412168034622221
GO:0005096GTPase activator activity0.0420473751475497
GO:0000074regulation of progression through cell cycle0.0420473751475497
GO:0051726regulation of cell cycle0.0420473751475497
GO:0022403cell cycle phase0.0421833541290076
GO:0008047enzyme activator activity0.0494377287556743
GO:0006323DNA packaging0.0494377287556743
GO:0044427chromosomal part0.0494377287556743



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
animal cell1.74e-27679
eukaryotic cell1.74e-27679
epithelial cell8.27e-26253
native cell1.37e-16722
embryonic cell6.05e-15250
squamous epithelial cell6.34e-0863
kidney cell1.84e-0717
kidney epithelial cell1.84e-0717
epithelial cell of nephron2.07e-0715
somatic cell3.27e-07588
Uber Anatomy
Ontology termp-valuen
nephron epithelium2.07e-0715
renal tubule2.07e-0715
nephron tubule2.07e-0715
nephron2.07e-0715
uriniferous tubule2.07e-0715
nephrogenic mesenchyme2.07e-0715
segment of respiratory tract5.58e-0747
larynx6.22e-079
Disease
Ontology termp-valuen
cancer9.68e-34235
disease of cellular proliferation2.83e-32239
hematologic cancer8.99e-1851
immune system cancer8.99e-1851
organ system cancer1.20e-17137
cell type cancer1.37e-16143
carcinoma1.88e-16106
leukemia5.91e-1539
myeloid leukemia3.49e-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)
MA0003.13.22681
MA0004.11.93041
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
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
MA0055.10.190716
MA0056.10
MA0057.10.333427
MA0058.11.70328
MA0059.11.70014
MA0060.10.492218
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
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.12.626
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.11.55947
MA0103.10.628063
MA0105.11.5295
MA0106.10.986396
MA0107.11.36919
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.13.41476
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.12.7939
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.12.4174
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.10.707589
MA0147.12.37462
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.195278
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.20.731309
MA0065.22.13692
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.14.65556
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.0373086
MA0102.21.88331
MA0258.10.519674
MA0259.11.40979
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
CTCF#1066435.360256373075030.0064925092527670.0279697716392251
CTCFL#140690213.16431623931620.007433367036996010.0306814772942665
E2F6#187635.017155731697390.00791769806886330.0322560644645816
ELF1#199734.258097958807540.01295179875054610.0462721208807951
ETS1#211339.728760922202340.001085840092584840.00762995717079107
FOXA1#3169311.08141974938550.000734755275698670.00581782458216022
FOXA2#3170216.42030916844350.004810682352105480.0225919714992376
GABPB1#255337.067683836182170.002832212825417420.01542438730113
GTF2F1#2962312.73966087675770.0004835525047438590.00434386203706726
MAX#414936.452555509007120.003721913834265510.0186728615524261
MXI1#460139.96157162875930.001011470541259020.00720776281785965
MYC#460935.22228187160940.007020843755740150.0294785680230661
NANOG#79923329.24477848101273.99627955670032e-050.000738180828833083
NRF1#4899312.21027944771090.0005492172401020010.00471436667535242
SIN3A#2594235.408884726815140.006318961977991520.0277090343040457
SMC3#9126210.02995522995520.0126656379767470.0457569118493715
TAF7#6879311.43306940492390.0006690181981945830.00543578587219885
USF1#739136.361499277207960.00388404057290560.0190452750548706
YY1#752834.911170749853860.008441455341808260.0329736752232155
ZNF143#7702313.50087655222790.0004062804962997170.00389387251106232



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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