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{{Coexpression_clusters
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|full_id=C4725_Corneal_Keratinocyte_mesothelioma_Bronchial_Urothelial_papillotubular_Gingival
|id=C4725
}}

Latest revision as of 14:18, 17 September 2013


Full id: C4725_Corneal_Keratinocyte_mesothelioma_Bronchial_Urothelial_papillotubular_Gingival



Phase1 CAGE Peaks

Hg19::chr8:124194824..124194835,+p5@FAM83A
Hg19::chr8:124194875..124194920,+p2@FAM83A
Hg19::chr8:124194922..124194957,+p1@FAM83A


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

No GOStat results

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
endoderm-derived structure4.73e-24160
endoderm4.73e-24160
presumptive endoderm4.73e-24160
respiratory system5.57e-2074
respiratory tract6.24e-1954
digestive system5.99e-18145
digestive tract5.99e-18145
primitive gut5.99e-18145
segment of respiratory tract6.20e-1647
respiratory primordium9.28e-1538
endoderm of foregut9.28e-1538
subdivision of digestive tract2.48e-14118
foregut3.63e-1287
endo-epithelium2.64e-1182
epithelial bud7.50e-1137
orifice1.09e-1036
reproductive structure8.48e-1059
reproductive system8.48e-1059
upper respiratory tract1.90e-0919
epithelial fold3.50e-0947
anatomical space8.34e-0995
renal system8.88e-0948
thoracic cavity element8.95e-0934
thoracic cavity8.95e-0934
larynx9.99e-099
thoracic segment organ2.35e-0835
extraembryonic membrane2.42e-0814
membranous layer2.42e-0814
urinary system structure3.32e-0847
primordium5.09e-08160
respiratory system epithelium1.08e-0728
female organism1.64e-0741
organ part1.83e-07218
reproductive organ2.13e-0748
tracheobronchial tree3.42e-0715
lower respiratory tract3.42e-0715
urothelium3.69e-075
internal genitalia6.17e-0725
immaterial anatomical entity7.73e-07117
Disease
Ontology termp-valuen
carcinoma2.32e-20106
cell type cancer9.08e-14143
squamous cell carcinoma2.30e-1014
cancer8.35e-10235
disease of cellular proliferation3.55e-09239


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)
MA0003.12.61626
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
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.12.94978
MA0046.11.31611
MA0048.12.45333
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.11.06172
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
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
MA0081.11.70054
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.11.55947
MA0103.10.628063
MA0105.11.5295
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.12.36034
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
MA0139.11.96087
MA0140.13.41958
MA0141.12.84752
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.23.41713
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.23.77966
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.311277
MA0102.24.06575
MA0258.13.27997
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
CCNT2#90536.336201576962630.003930750035764890.0191225825873509
CEBPB#105137.971147625824820.001974187055288560.0115826145647594
CHD2#1106310.34402283411690.0009033701102746880.0066296866662201
E2F1#186934.907389214879320.008460985347239390.0327851017949889
E2F4#1874312.66806031528440.0004917987006298980.00439037221088007
E2F6#187635.017155731697390.00791769806886330.0324446372116771
EP300#203336.77394172622320.003216880500103790.016853161903704
FOS#235338.99795530889440.001372499272417130.00902092205865151
FOXA1#3169311.08141974938550.000734755275698670.00584307517236681
GATA1#2623313.56030814380040.0004009615963782630.00389544448038599
GATA2#2624312.7449317335540.0004829527704283790.00439059056326336
GATA3#2625327.2365163572064.94721007899563e-050.00085500856104621
GTF2F1#2962312.73966087675770.0004835525047438590.00436074087237233
HDAC2#3066313.41562023662630.0004140761399857210.00393643710030664
HMGN3#932438.178547723350590.001827766942164210.0109261148001081
JUN#3725312.51282919233630.0005103313992726250.00446498291100224
JUNB#3726330.61063265982113.4847716247536e-050.000682953769408222
JUND#372736.994663941871030.002921845042734990.0157718924135931
MAX#414936.452555509007120.003721913834265510.0187458024178653
MXI1#460139.96157162875930.001011470541259020.00723590464131454
MYC#460935.22228187160940.007020843755740150.0296166855564159
RAD21#5885310.35503389545630.0009004912073565420.00668893322938192
RFX5#5993312.04791082719510.0005717246050312580.00486914670348688
SMARCA4#65973156.7659033078882.58908533335753e-071.34194284432023e-05
SMARCB1#6598318.25271578115740.000164397760679890.00204131943022792
SMARCC1#6599343.66335931963151.20046018043203e-050.000302691600154855
SMARCC2#6601394.15537442689761.19621075407887e-064.86870829872342e-05
SMC3#9126315.04493284493280.0002935825420371870.00310936691084289
STAT1#6772320.70658749719920.0001125992441046670.00155387849564578
STAT2#6773365.26377118644073.59360517547754e-060.000118619636827338
STAT3#6774310.51946499715420.0008589184530415310.0064568188524584
TAL1#6886329.86861667744023.75103522793067e-050.000722927418656304
TFAP2A#7020316.5186343730450.0002218033880766340.00249514477028604
TFAP2C#7022310.80922860986020.0007916746575753130.0061901407174147
YY1#752834.911170749853860.008441455341808260.0331360277547588



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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