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Coexpression cluster:C2162: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2162_gastric_Hepatocyte_Intestinal_liver_Prostate_breast_colon
|id=C2162
}}

Latest revision as of 12:00, 17 September 2013


Full id: C2162_gastric_Hepatocyte_Intestinal_liver_Prostate_breast_colon



Phase1 CAGE Peaks

Hg19::chr11:72492742..72492753,-p8@STARD10
Hg19::chr11:72492758..72492820,-p2@STARD10
Hg19::chr11:72492878..72492899,-p5@STARD10
Hg19::chr11:72492903..72492966,-p1@STARD10


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 cell9.38e-22253
endodermal cell2.83e-1558
endo-epithelial cell1.71e-1142
extraembryonic cell4.69e-0719
kidney cell8.49e-0717
kidney epithelial cell8.49e-0717
Uber Anatomy
Ontology termp-valuen
trunk region element4.32e-16101
endoderm-derived structure4.77e-15160
endoderm4.77e-15160
presumptive endoderm4.77e-15160
anatomical cluster1.13e-14373
multi-tissue structure2.02e-13342
anatomical conduit1.10e-12240
digestive system1.03e-11145
digestive tract1.03e-11145
primitive gut1.03e-11145
subdivision of trunk2.00e-11112
endo-epithelium2.33e-1182
adult organism3.19e-11114
abdomen element3.55e-1154
abdominal segment element3.55e-1154
subdivision of digestive tract4.38e-11118
renal system1.67e-1048
multi-cellular organism2.98e-10656
urinary system structure3.77e-1047
organ system subdivision4.65e-10223
organ8.87e-10503
epithelium1.17e-09306
immaterial anatomical entity1.66e-09117
embryo1.79e-09592
tube2.36e-09192
cell layer5.17e-09309
anatomical system5.72e-09624
developing anatomical structure5.86e-09581
anatomical group5.88e-09625
exocrine gland2.33e-0831
exocrine system2.33e-0831
organ part5.41e-08218
extraembryonic membrane6.53e-0814
membranous layer6.53e-0814
foregut7.73e-0887
gland7.79e-0859
epithelium of foregut-midgut junction1.28e-0725
anatomical boundary1.28e-0725
hepatobiliary system1.28e-0725
foregut-midgut junction1.28e-0725
septum transversum1.28e-0725
organism subdivision2.28e-07264
abdominal segment of trunk2.51e-0760
abdomen2.51e-0760
gut epithelium3.33e-0754
kidney4.76e-0726
kidney mesenchyme4.76e-0726
upper urinary tract4.76e-0726
kidney rudiment4.76e-0726
kidney field4.76e-0726
cavitated compound organ6.92e-0731
sac9.39e-0726
Disease
Ontology termp-valuen
carcinoma3.98e-07106


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)
MA0003.19.1772
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.115.6589
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
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.14.51896
MA0063.10
MA0066.11.92841
MA0067.11.53181
MA0068.12.31526
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.15.62637
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.13.07281
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.13.36866
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.14.0488
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.13665
MA0115.11.45393
MA0116.10.457606
MA0117.12.78257
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
MA0145.10.569905
MA0146.12.31379
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.29.51044
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.79838
MA0047.20.856092
MA0112.21.65877
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.11.84959
MA0153.11.30799
MA0154.10.229241
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.13.50007
MA0163.119.1646
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.211.2591
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
EGR1#195844.988179094810140.001615011500076050.0101291247932046
FOSL1#8061439.7135797163734.01511434669553e-071.93598581373285e-05
FOXA1#316938.311064812039090.002740138182109850.0150334782307927
ZBTB7A#5134147.35190930787590.000342223540015990.00345929968019067
ZNF143#7702413.50087655222793.00867915035614e-050.000619770102138155



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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