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Coexpression cluster:C2638: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2638_breast_bronchogenic_Amniotic_liver_endometrioid_Hepatocyte_serous
|id=C2638
}}

Latest revision as of 12:09, 17 September 2013


Full id: C2638_breast_bronchogenic_Amniotic_liver_endometrioid_Hepatocyte_serous



Phase1 CAGE Peaks

Hg19::chr22:19950047..19950056,+p9@COMT
Hg19::chr22:19950060..19950096,+p3@COMT
Hg19::chr22:19950097..19950117,+p5@COMT
Hg19::chr22:19950126..19950137,+p14@COMT


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>

Cell Type
Ontology termp-valuen
epithelial cell2.60e-25253
endodermal cell3.12e-1458
endo-epithelial cell5.61e-1442
embryonic cell4.62e-10250
epithelial cell of alimentary canal5.33e-0820
squamous epithelial cell8.15e-0763
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.11e-21160
endoderm1.11e-21160
presumptive endoderm1.11e-21160
anatomical cluster7.59e-20373
multi-tissue structure1.33e-19342
digestive system1.16e-17145
digestive tract1.16e-17145
primitive gut1.16e-17145
anatomical conduit2.33e-17240
multi-cellular organism9.57e-17656
organism subdivision7.16e-16264
subdivision of digestive tract5.36e-14118
epithelium8.91e-14306
cell layer4.06e-13309
anatomical system4.10e-13624
anatomical group7.55e-13625
organ system subdivision2.22e-12223
embryo2.38e-12592
developing anatomical structure2.15e-11581
organ part4.07e-11218
subdivision of trunk1.28e-09112
respiratory system1.38e-0974
embryonic structure1.40e-09564
endo-epithelium1.96e-0982
organ2.47e-09503
tube3.17e-09192
orifice3.63e-0936
foregut5.53e-0987
germ layer1.12e-08560
germ layer / neural crest1.12e-08560
embryonic tissue1.12e-08560
presumptive structure1.12e-08560
germ layer / neural crest derived structure1.12e-08560
epiblast (generic)1.12e-08560
immaterial anatomical entity1.71e-08117
trunk2.80e-08199
renal system4.17e-0848
oral opening4.33e-0822
head8.50e-0856
urinary system structure8.72e-0847
trunk region element8.86e-08101
anterior region of body1.68e-0762
craniocervical region1.68e-0762
mouth2.62e-0729
stomodeum2.62e-0729
thoracic segment of trunk2.67e-0752
exocrine gland5.36e-0731
exocrine system5.36e-0731
thoracic cavity element8.79e-0734
thoracic cavity8.79e-0734
Disease
Ontology termp-valuen
squamous cell carcinoma4.39e-0714


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)
MA0003.11.05935
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.13.53539
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.12.02223
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.111.6485
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.100363
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.12.31225
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.11.29536
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.12.95284
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.17.78226
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.569905
MA0146.13.58384
MA0147.10.46175
MA0148.12.93423
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.777367
MA0138.25.02795
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.21.99204
MA0112.20.187982
MA0065.21.7213
MA0150.11.53138
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.918944
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.22.00408
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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#1066445.360256373075030.001211145381643620.00818022456919604
EBF1#187948.9064668465690.00015887907472010.00199749267902884
ELF1#199744.258097958807540.003041525565781240.0161049426366166
HDAC2#3066413.41562023662633.0859005065161e-050.000627020161478667
HEY1#2346244.040111043105710.00375304636917980.0186303726294391
HMGN3#932448.178547723350590.0002234570284440470.00248299059407042
IRF1#365947.63716375356390.0002938853996185490.00307823661124878
MYC#460945.22228187160940.001344309395272740.00888484552163583
RAD21#5885410.35503389545638.6948481184721e-050.00129540833472911
SMC3#9126415.04493284493281.95092670935632e-050.000438461016996911
SP1#666745.69838137814090.0009482606065333980.00684797327380318
SP2#6668319.61514787038350.0002171004269245340.00248697504525297
TAF1#687243.343046285745290.008005664898701650.0322645533825539
ZNF263#1012748.221841637010680.0002187871180958320.00249262657650383



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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