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Coexpression cluster:C3876: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3876_colon_liver_Hepatocyte_choriocarcinoma_chorionic_Renal_serous
|id=C3876
}}

Latest revision as of 12:34, 17 September 2013


Full id: C3876_colon_liver_Hepatocyte_choriocarcinoma_chorionic_Renal_serous



Phase1 CAGE Peaks

Hg19::chr1:155100342..155100359,+p1@EFNA1
Hg19::chr1:155100366..155100377,+p2@EFNA1
Hg19::chr1:155100387..155100398,+p3@EFNA1


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
anatomical cluster1.10e-26373
organ system subdivision1.57e-22223
endoderm-derived structure4.95e-22160
endoderm4.95e-22160
presumptive endoderm4.95e-22160
subdivision of digestive tract1.14e-18118
anatomical conduit1.73e-18240
digestive system3.20e-18145
digestive tract3.20e-18145
primitive gut3.20e-18145
foregut8.84e-1687
organ part2.87e-15218
trunk region element5.65e-14101
organ3.65e-13503
adult organism6.77e-13114
multi-tissue structure7.11e-13342
tube1.47e-12192
endo-epithelium2.62e-1282
multi-cellular organism4.57e-11656
epithelium9.70e-11306
abdomen element2.25e-1054
abdominal segment element2.25e-1054
respiratory system3.08e-1074
cell layer3.17e-10309
anatomical system6.04e-10624
anatomical group7.16e-10625
subdivision of trunk9.99e-10112
immaterial anatomical entity2.72e-09117
exocrine gland3.09e-0931
exocrine system3.09e-0931
blood vessel endothelium3.48e-0918
endothelium3.48e-0918
cardiovascular system endothelium3.48e-0918
embryo3.72e-09592
respiratory primordium7.79e-0938
endoderm of foregut7.79e-0938
gland8.34e-0959
renal system1.01e-0848
urinary system structure1.43e-0847
respiratory tract2.33e-0854
developing anatomical structure3.34e-08581
primordium3.74e-08160
simple squamous epithelium4.92e-0822
abdominal segment of trunk9.36e-0860
abdomen9.36e-0860
gut epithelium2.00e-0754
epithelium of foregut-midgut junction3.53e-0725
anatomical boundary3.53e-0725
hepatobiliary system3.53e-0725
foregut-midgut junction3.53e-0725
septum transversum3.53e-0725
excretory tube3.85e-0716
kidney epithelium3.85e-0716
parenchyma5.66e-0715
nephron epithelium7.64e-0715
renal tubule7.64e-0715
nephron tubule7.64e-0715
nephron7.64e-0715
uriniferous tubule7.64e-0715
nephrogenic mesenchyme7.64e-0715
Disease
Ontology termp-valuen
carcinoma6.98e-19106
cell type cancer1.22e-16143


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
MA0004.10.826076
MA0006.11.5435
MA0007.10.804807
MA0009.11.3275
MA0014.13.14798
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
MA0058.10.716037
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
MA0073.119.7049
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
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
MA0114.10.549955
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
MA0146.13.00132
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.27.10722
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.20.264678
MA0065.21.39232
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.13.71118
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.11.43223
MA0163.11.84145
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.28.15771
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
E2F6#187635.017155731697390.00791769806886330.0322334321592739
EGR1#195834.988179094810140.008056488137383440.0320745459756867
HMGN3#932438.178547723350590.001827766942164210.0108738337609051
HNF4A#3172323.13229036295378.07584663437677e-050.00122842025436597
SIN3A#2594235.408884726815140.006318961977991520.0276869470556912
SMARCB1#6598318.25271578115740.000164397760679890.002030696360455
SMARCC2#6601394.15537442689761.19621075407887e-064.85357633819902e-05
ZBTB7A#5134137.35190930787590.002516255860282270.0140247222644903



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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