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Coexpression cluster:C2724: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2724_Hep2_epitheloid_giant_Lymphatic_large_clear_Mesothelial
|id=C2724
|ontology_enrichment_celltype=CL:0000222!6.73e-25!119;CL:0000066!9.47e-19!254;CL:0000220!3.00e-17!246;CL:0002321!2.06e-16!248;CL:0000213!2.36e-15!57;CL:0000215!2.36e-15!57;CL:0002139!6.36e-13!24;CL:0002078!2.22e-12!44;CL:0000076!7.86e-12!62;CL:0000115!5.28e-11!35;CL:0000183!3.72e-10!59;CL:0000187!4.92e-10!54;CL:0000359!7.98e-10!32;CL:0000680!8.57e-10!57;CL:0000056!8.57e-10!57;CL:0000355!8.57e-10!57;CL:0000071!2.02e-09!18;CL:0002546!2.02e-09!18;CL:0000192!2.38e-09!42;CL:0000514!2.38e-09!42;CL:0000055!3.20e-08!180;CL:0000393!2.56e-07!60;CL:0000211!2.56e-07!60
|ontology_enrichment_disease=DOID:305!1.99e-08!106
|ontology_enrichment_uberon=UBERON:0000477!2.85e-31!286;UBERON:0003914!6.60e-29!118;UBERON:0000119!3.49e-25!312;UBERON:0000481!5.10e-25!347;UBERON:0004111!5.21e-25!241;UBERON:0000483!1.55e-24!309;UBERON:0003104!4.78e-24!238;UBERON:0009142!4.78e-24!238;UBERON:0002049!3.49e-23!79;UBERON:0007798!3.49e-23!79;UBERON:0000055!2.10e-22!69;UBERON:0004872!5.61e-22!84;UBERON:0000490!2.23e-20!138;UBERON:0001981!2.37e-20!60;UBERON:0007500!2.37e-20!60;UBERON:0004537!2.37e-20!60;UBERON:0006965!2.37e-20!60;UBERON:0000025!1.38e-19!194;UBERON:0000467!2.92e-18!625;UBERON:0005256!3.42e-18!143;UBERON:0000480!6.63e-18!626;UBERON:0000468!3.03e-17!659;UBERON:0002100!2.68e-16!216;UBERON:0001009!7.73e-16!113;UBERON:0004535!1.07e-15!110;UBERON:0001637!5.31e-15!42;UBERON:0003509!5.31e-15!42;UBERON:0004572!5.31e-15!42;UBERON:0000475!6.66e-14!365;UBERON:0000926!1.34e-13!448;UBERON:0004120!1.34e-13!448;UBERON:0006603!1.34e-13!448;UBERON:0002050!2.44e-13!605;UBERON:0005423!2.44e-13!605;UBERON:0000923!3.03e-13!604;UBERON:0005291!3.03e-13!604;UBERON:0006598!3.03e-13!604;UBERON:0002532!3.03e-13!604;UBERON:0004573!1.47e-12!33;UBERON:0004571!1.47e-12!33;UBERON:0000922!1.66e-12!612;UBERON:0001048!6.72e-11!168;UBERON:0000487!8.79e-11!22;UBERON:0006914!2.91e-10!25;UBERON:0000914!3.94e-10!83;UBERON:0002329!3.94e-10!83;UBERON:0003077!3.94e-10!83;UBERON:0003059!3.94e-10!83;UBERON:0007282!3.94e-10!83;UBERON:0009618!3.94e-10!83;UBERON:0007285!3.94e-10!83;UBERON:0001007!6.93e-10!155;UBERON:0001555!6.93e-10!155;UBERON:0007026!6.93e-10!155;UBERON:0001134!1.23e-09!61;UBERON:0002036!1.23e-09!61;UBERON:0003082!1.23e-09!61;UBERON:0000486!1.38e-09!82;UBERON:0002385!1.60e-09!63;UBERON:0001015!1.60e-09!63;UBERON:0000383!1.60e-09!63;UBERON:0004119!1.88e-09!169;UBERON:0000925!1.88e-09!169;UBERON:0006595!1.88e-09!169;UBERON:0001986!2.02e-09!18;UBERON:0004638!2.02e-09!18;UBERON:0004852!2.02e-09!18;UBERON:0004290!2.24e-09!70;UBERON:0003103!6.62e-09!69;UBERON:0000077!7.97e-09!130;UBERON:0004921!8.38e-09!129;UBERON:0004185!8.38e-09!129;UBERON:0000947!2.45e-08!21;UBERON:0010191!2.45e-08!21;UBERON:0000062!8.01e-08!511;UBERON:0001041!8.70e-08!98;UBERON:0001737!1.55e-07!9;UBERON:0000948!9.28e-07!24;UBERON:0005498!9.28e-07!24;UBERON:0004140!9.28e-07!24;UBERON:0009881!9.28e-07!24;UBERON:0004141!9.28e-07!24;UBERON:0003084!9.28e-07!24;UBERON:0007005!9.28e-07!24;UBERON:0004139!9.28e-07!24;UBERON:0004291!9.28e-07!24;UBERON:0007100!9.78e-07!27;UBERON:0005177!9.93e-07!107
}}

Latest revision as of 12:11, 17 September 2013


Full id: C2724_Hep2_epitheloid_giant_Lymphatic_large_clear_Mesothelial



Phase1 CAGE Peaks

Hg19::chr3:149087248..149087262,-p3@TM4SF1
Hg19::chr3:149087622..149087670,-p@chr3:149087622..149087670
-
Hg19::chr3:149089491..149089519,-p1@AK023364
Hg19::chr3:149095424..149095445,-p1@TM4SF1


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
epithelial tube3.24e-28117
anatomical cluster1.11e-22373
vasculature4.35e-2278
vascular system4.35e-2278
vessel6.80e-2268
splanchnic layer of lateral plate mesoderm4.47e-2183
epithelial tube open at both ends5.21e-2059
blood vessel5.21e-2059
blood vasculature5.21e-2059
vascular cord5.21e-2059
anatomical conduit7.09e-20240
cell layer1.15e-18309
multi-tissue structure1.25e-18342
epithelium3.12e-18306
unilaminar epithelium3.41e-18148
mesenchyme3.32e-17160
entire embryonic mesenchyme3.32e-17160
circulatory system1.27e-16112
cardiovascular system1.94e-16109
tube3.25e-15192
artery8.55e-1542
arterial blood vessel8.55e-1542
arterial system8.55e-1542
trunk mesenchyme9.88e-15122
trunk7.70e-14199
organism subdivision2.84e-13264
systemic artery1.98e-1233
systemic arterial system1.98e-1233
anatomical system5.47e-12624
anatomical group9.02e-12625
simple squamous epithelium1.46e-1022
multi-cellular organism1.82e-10656
squamous epithelium2.41e-1025
epithelial vesicle1.02e-0978
skeletal muscle tissue2.80e-0962
striated muscle tissue2.80e-0962
myotome2.80e-0962
blood vessel endothelium3.37e-0918
endothelium3.37e-0918
cardiovascular system endothelium3.37e-0918
digestive system3.39e-09145
digestive tract3.39e-09145
primitive gut3.39e-09145
muscle tissue4.05e-0964
musculature4.05e-0964
musculature of body4.05e-0964
compound organ4.61e-0968
primordium5.85e-09160
multilaminar epithelium1.12e-0883
somite2.20e-0871
presomitic mesoderm2.20e-0871
presumptive segmental plate2.20e-0871
dermomyotome2.20e-0871
trunk paraxial mesoderm2.20e-0871
endoderm-derived structure2.23e-08160
endoderm2.23e-08160
presumptive endoderm2.23e-08160
aorta2.27e-0821
aortic system2.27e-0821
dense mesenchyme tissue2.88e-0873
subdivision of digestive tract3.10e-08118
paraxial mesoderm5.61e-0872
presumptive paraxial mesoderm5.61e-0872
larynx8.76e-089
foregut1.98e-0787
respiratory primordium7.48e-0738
endoderm of foregut7.48e-0738
primary circulatory organ9.08e-0727
heart9.83e-0724
primitive heart tube9.83e-0724
primary heart field9.83e-0724
anterior lateral plate mesoderm9.83e-0724
heart tube9.83e-0724
heart primordium9.83e-0724
cardiac mesoderm9.83e-0724
cardiogenic plate9.83e-0724
heart rudiment9.83e-0724
Disease
Ontology termp-valuen
carcinoma4.93e-09106


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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
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
MA0041.14.20801
MA0042.12.80052
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.946082
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.11.1497
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
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
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.11.75269
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.000248021
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
FOXA2#3170212.31523187633260.009361916285467240.0353501274427099



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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