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Coexpression cluster:C2136: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2136_Alveolar_serous_Placental_Renal_amniotic_Small_Mammary
|id=C2136
}}

Latest revision as of 11:59, 17 September 2013


Full id: C2136_Alveolar_serous_Placental_Renal_amniotic_Small_Mammary



Phase1 CAGE Peaks

Hg19::chr11:560958..561046,+p1@RASSF7
Hg19::chr11:706174..706213,+p2@EPS8L2
Hg19::chr11:706215..706216,+p6@EPS8L2
Hg19::chr11:706219..706260,+p1@EPS8L2


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 structure3.68e-27160
endoderm3.68e-27160
presumptive endoderm3.68e-27160
digestive system4.46e-21145
digestive tract4.46e-21145
primitive gut4.46e-21145
subdivision of digestive tract1.06e-19118
trunk region element3.56e-17101
renal system3.61e-1648
subdivision of trunk4.25e-16112
urinary system structure5.34e-1647
organism subdivision8.24e-16264
immaterial anatomical entity3.96e-15117
endo-epithelium5.35e-1482
foregut1.55e-1387
respiratory system1.15e-1174
trunk2.77e-11199
anatomical space5.59e-1195
abdomen element5.87e-1154
abdominal segment element5.87e-1154
abdominal segment of trunk2.18e-1060
abdomen2.18e-1060
multi-tissue structure4.07e-10342
primordium6.93e-10160
organ part7.84e-10218
kidney9.62e-1026
kidney mesenchyme9.62e-1026
upper urinary tract9.62e-1026
kidney rudiment9.62e-1026
kidney field9.62e-1026
reproductive structure1.16e-0959
reproductive system1.16e-0959
respiratory tract2.40e-0954
organ2.49e-09503
cavitated compound organ3.32e-0931
gut epithelium5.01e-0954
extraembryonic membrane6.80e-0914
membranous layer6.80e-0914
gland1.16e-0859
exocrine gland1.53e-0831
exocrine system1.53e-0831
female organism2.80e-0841
anatomical cluster3.29e-08373
organ segment4.21e-0898
respiratory primordium4.96e-0838
endoderm of foregut4.96e-0838
reproductive organ8.28e-0848
epithelial bud1.44e-0737
nephron tubule epithelium1.66e-0710
excretory tube1.73e-0716
kidney epithelium1.73e-0716
orifice1.94e-0736
internal genitalia2.10e-0725
nephron epithelium3.67e-0715
renal tubule3.67e-0715
nephron tubule3.67e-0715
nephron3.67e-0715
uriniferous tubule3.67e-0715
nephrogenic mesenchyme3.67e-0715
segment of respiratory tract6.18e-0747
thoracic cavity element7.79e-0734
thoracic cavity7.79e-0734
Disease
Ontology termp-valuen
carcinoma1.01e-20106
cell type cancer4.25e-14143
adenocarcinoma2.60e-0825


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)
MA0003.14.74396
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.13.76953
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
MA0055.10.125954
MA0056.10
MA0057.10.69331
MA0058.10.605914
MA0059.10.604454
MA0060.12.70115
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.11.18043
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.02755
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.11.29536
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.13665
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
MA0146.14.2865
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.28.68914
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.21.09513
MA0150.12.59564
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.12.30186
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.18.56919
MA0163.15.3466
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.213.2809
MA0102.21.75932
MA0258.10.418966
MA0259.11.1888
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
E2F1#186944.907389214879320.001724022357361790.0106252313808868
E2F6#187645.017155731697390.00157802193473060.00994971219761706
EGR1#195844.988179094810140.001615011500076050.0101260842922761
HEY1#2346244.040111043105710.00375304636917980.0185545282722258



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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