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{{Coexpression_clusters
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|full_id=C2229_Amniotic_Placental_lung_thyroid_kidney_Small_testicular
|id=C2229
}}

Latest revision as of 12:01, 17 September 2013


Full id: C2229_Amniotic_Placental_lung_thyroid_kidney_Small_testicular



Phase1 CAGE Peaks

Hg19::chr12:6485300..6485325,-p5@SCNN1A
Hg19::chr12:6485336..6485354,-p4@SCNN1A
Hg19::chr12:6485371..6485382,-p11@SCNN1A
Hg19::chr12:6485398..6485410,-p12@SCNN1A


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 structure1.64e-19160
endoderm1.64e-19160
presumptive endoderm1.64e-19160
urinary system structure1.20e-1547
trunk region element3.87e-15101
renal system4.57e-1548
subdivision of digestive tract2.64e-14118
digestive system3.10e-14145
digestive tract3.10e-14145
primitive gut3.10e-14145
foregut2.05e-1387
respiratory system2.63e-1274
endo-epithelium2.75e-1282
immaterial anatomical entity2.84e-12117
respiratory tract2.06e-1154
anatomical space4.05e-1195
respiratory primordium8.83e-1138
endoderm of foregut8.83e-1138
epithelial bud2.24e-1037
nephron tubule epithelium7.38e-1010
multi-tissue structure8.94e-10342
cavitated compound organ1.07e-0931
kidney2.42e-0926
kidney mesenchyme2.42e-0926
upper urinary tract2.42e-0926
kidney rudiment2.42e-0926
kidney field2.42e-0926
subdivision of trunk2.49e-09112
organ4.18e-09503
organism subdivision4.38e-09264
thoracic cavity element5.94e-0934
thoracic cavity5.94e-0934
thoracic segment organ1.71e-0835
organ system subdivision2.12e-08223
anatomical cluster3.83e-08373
primordium4.08e-08160
excretory tube8.17e-0816
kidney epithelium8.17e-0816
embryo9.13e-08592
lung1.08e-0722
respiratory tube1.08e-0722
respiration organ1.08e-0722
pair of lungs1.08e-0722
lung primordium1.08e-0722
lung bud1.08e-0722
male organism1.87e-0722
male reproductive system1.87e-0722
segment of respiratory tract2.75e-0747
nephron epithelium5.15e-0715
renal tubule5.15e-0715
nephron tubule5.15e-0715
nephron5.15e-0715
uriniferous tubule5.15e-0715
nephrogenic mesenchyme5.15e-0715
male reproductive organ5.70e-0711
multi-cellular organism7.74e-07656
Disease
Ontology termp-valuen
carcinoma7.50e-22106
cell type cancer1.38e-13143
squamous cell carcinoma9.84e-0914
adenocarcinoma9.16e-0725


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)
MA0003.10.233555
MA0004.10.71247
MA0006.11.31813
MA0007.11.65296
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
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.841508
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
MA0088.10.536981
MA0089.10
MA0090.16.46308
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.11.29536
MA0105.10.656404
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.16.41429
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.12.8366
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.12.47057
MA0140.10.779643
MA0141.11.46638
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.11.08195
MA0146.10.221129
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.483275
MA0138.20.928035
MA0002.21.75253
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.23.12566
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
MA0159.12.03616
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.11.90765
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.20937
MA0102.21.75932
MA0258.13.84649
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#1066445.360256373075030.001211145381643620.00816122411210261
ESR1#2099430.76860329615451.11467714392546e-064.59415020656791e-05
HDAC2#3066413.41562023662633.0859005065161e-050.00062580264660201
NANOG#79923429.24477848101271.36586687657858e-065.32275263891756e-05
NR3C1#2908414.9730233311731.98868032687801e-050.000441999967352229
RAD21#5885410.35503389545638.6948481184721e-050.00129135557827803
TAF1#687243.343046285745290.008005664898701650.0321479404935213
TBP#690843.706770687096390.005296377814784350.0243656242885324
TFAP2A#7020416.5186343730451.34240829060362e-050.00032619771861878
TFAP2C#7022410.80922860986027.32289634782688e-050.00114421898813688



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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