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{{Coexpression_clusters
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|coexpression_dpi_cluster_scores_median=0,-0.

Latest revision as of 12:39, 17 September 2013


Full id: C4117_Urothelial_small_Corneal_tubular_Smooth_cervical_pharyngeal



Phase1 CAGE Peaks

Hg19::chr2:110873370..110873379,-p3@MALL
Hg19::chr2:110873388..110873405,-p1@MALL
Hg19::chr2:110873422..110873434,-p2@MALL


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><br>


Uber Anatomy
Ontology termp-valuen
anatomical cluster2.81e-24373
anatomical system7.41e-23624
anatomical group1.46e-22625
anatomical conduit4.97e-22240
epithelium9.14e-22306
multi-cellular organism3.05e-21656
cell layer3.76e-21309
epithelial tube2.48e-17117
organism subdivision1.23e-16264
multi-tissue structure5.85e-16342
tube1.51e-15192
trunk2.46e-15199
vessel1.27e-1368
organ part4.20e-13218
splanchnic layer of lateral plate mesoderm4.48e-1383
vasculature9.14e-1378
vascular system9.14e-1378
anatomical space2.10e-1295
compound organ2.15e-1268
epithelial tube open at both ends3.27e-1259
blood vessel3.27e-1259
blood vasculature3.27e-1259
vascular cord3.27e-1259
simple squamous epithelium7.66e-1222
embryo1.27e-11592
endoderm-derived structure1.31e-11160
endoderm1.31e-11160
presumptive endoderm1.31e-11160
organ1.36e-11503
trunk region element3.46e-11101
renal system5.29e-1148
squamous epithelium7.24e-1125
urinary system structure7.86e-1147
developing anatomical structure8.48e-11581
blood vessel endothelium3.99e-1018
endothelium3.99e-1018
cardiovascular system endothelium3.99e-1018
subdivision of trunk4.88e-10112
immaterial anatomical entity6.28e-10117
unilaminar epithelium2.43e-09148
subdivision of digestive tract6.71e-09118
digestive system7.47e-09145
digestive tract7.47e-09145
primitive gut7.47e-09145
embryonic structure9.40e-09564
nephron epithelium1.10e-0815
renal tubule1.10e-0815
nephron tubule1.10e-0815
nephron1.10e-0815
uriniferous tubule1.10e-0815
nephrogenic mesenchyme1.10e-0815
circulatory system1.14e-08112
epithelial fold1.49e-0847
excretory tube1.63e-0816
kidney epithelium1.63e-0816
germ layer3.26e-08560
germ layer / neural crest3.26e-08560
embryonic tissue3.26e-08560
presumptive structure3.26e-08560
germ layer / neural crest derived structure3.26e-08560
epiblast (generic)3.26e-08560
cardiovascular system3.39e-08109
thoracic segment organ3.39e-0835
thoracic segment of trunk3.68e-0852
thoracic cavity element4.53e-0834
thoracic cavity4.53e-0834
intermediate mesoderm6.59e-0828
mesenchyme7.07e-08160
entire embryonic mesenchyme7.07e-08160
duct1.24e-0719
epithelial bud2.06e-0737
cortex of kidney2.96e-0712
renal parenchyma2.96e-0712
parenchyma3.16e-0715
tracheobronchial tree3.76e-0715
lower respiratory tract3.76e-0715
artery8.09e-0742
arterial blood vessel8.09e-0742
arterial system8.09e-0742
endo-epithelium8.27e-0782


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)
MA0003.11.0927
MA0004.10.826076
MA0006.10.639288
MA0007.11.88666
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
MA0041.11.97353
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
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
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.668628
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
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.11.36919
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
MA0139.11.96087
MA0140.10.894983
MA0141.10.712476
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
MA0035.20.894194
MA0039.21.15986
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
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
MA0162.11.43223
MA0163.10.387745
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.00160703
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#1066435.360256373075030.0064925092527670.0280021133119857
E2F1#186934.907389214879320.008460985347239390.0326060606132738
ESR1#2099330.76860329615453.43136389821584e-050.00067795727235294
MYC#460935.22228187160940.007020843755740150.0295070382698489



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.