Allele-Specific Effects of ecSOD in Bacterial Infection

2017 ◽  
Vol 112 ◽  
pp. 205
Author(s):  
Sujung Jun ◽  
Byung-Jin Kim ◽  
Timothy J Break ◽  
Rance E Berg ◽  
Harlan P Jones ◽  
...  
2018 ◽  
Vol 10 (1) ◽  
Author(s):  
Nikolay Kondratyev ◽  
Arkady Golov ◽  
Margarita Alfimova ◽  
Tatiana Lezheiko ◽  
Vera Golimbet

2021 ◽  
Vol 35 (S1) ◽  
Author(s):  
Priyanka Kumari ◽  
Ryan Friedman ◽  
Lira Pi ◽  
Annika Helverson ◽  
Sarah Curtis ◽  
...  

Genetics ◽  
1996 ◽  
Vol 144 (4) ◽  
pp. 1545-1557 ◽  
Author(s):  
Jon D Schnorr ◽  
Celeste A Berg

In Drosophila, the Ras1 gene is required downstream of receptor tyrosine kinases for correct eye development, embryonic patterning, wing vein formation, and border cell migration. Here we characterize a P-element allele of Ras1, Ras15703, that affects viability, eye morphogenesis, and early and late stages of oogenesis. Flies transheterozgyous for Ras15703 and existing EMS-induced Ras1 alleles are viable and exhibit a range of eye and eggshell defects. Differences in the severity of these phenotypes in different tissues suggest that there are allele-specific effects of Ras1 in development. Analysis of rescue constructs demonstrates that these differential phenotypes are due to loss of function in Ras1 alone and not due to effects on neighboring genes. Females mutant at the Ras1 locus lay eggs with reduced or missing dorsal eggshell structures. We observe dominant interactions between Ras1 mutants and other dorsoventral pathway mutants, including and Egfrtop and gurken. Ras1 is also epistatic to K10. Unlike Egfrtop and gurken mutants, however, Ras1 females are moderately fertile, laying eggs with ventralized eggshells that can hatch normal larvae. These results suggest that Ras1 may have a different requirement in the patterning of the eggshell axis than in the patterning of the embryonic axis during oogenesis.


Stroke ◽  
2015 ◽  
Vol 46 (1) ◽  
pp. 197-202 ◽  
Author(s):  
Sepiede Azghandi ◽  
Caroline Prell ◽  
Sander W. van der Laan ◽  
Manuela Schneider ◽  
Rainer Malik ◽  
...  

2019 ◽  
Author(s):  
Pawel F Przytycki ◽  
Mona Singh

SummaryIdentifying cancer-relevant mutations in noncoding regions is extremely challenging due to the large numbers of such mutations, their low levels of recurrence, and the general difficulty in interpreting their impact. To uncover genes that are dysregulated due to somatic mutations in cis, we build upon the concept of differential allele-specific expression (ASE) and introduce methods to identify genes within an individual’s cancer whose ASE differs from what is found in matched normal tissue. When applied to breast cancer tumor samples, our methods readily detect the known allele-specific effects of copy number variation and nonsense-mediated decay. Further, genes that are found to recurrently exhibit differential ASE across samples are cancer relevant. Genes with cis mutations are enriched for differential ASE, and we find 147 potentially functional noncoding mutations cis to genes that exhibit significant differential ASE. Overall, our results suggest that differential ASE is a promising means for discovering gene dysregulation within an individual due to cis noncoding mutations.


2018 ◽  
Vol 10 (1) ◽  
Author(s):  
Nikolay Kondratyev ◽  
Arkady Golov ◽  
Margarita Alfimova ◽  
Tatiana Lezheiko ◽  
Vera Golimbet

2021 ◽  
Author(s):  
Cynthia A Kalita ◽  
Alexander Gusev

Background: Expression quantitative trait loci (eQTLs) have been crucial in providing an understanding of how genetic variants influence gene expression. However, eQTLs are known to exert cell type specific effects, and existing methods to identify cell type specific QTLs in bulk data require large sample sizes. Results: Here, we propose DeCAF (DEconvoluted cell type Allele specific Function), a new method to identify cell-fraction (cf) QTLs in tumors by leveraging both allelic and total expression information. Applying DeCAF to RNA-seq data from TCGA, we identified 3,664 genes with cfQTLs (at 10% FDR) in 14 cell types, a 5.63x increase in discovery over conventional interaction-eQTL mapping. cfQTLs replicated in external cell type specific eQTL data and were more enriched for cancer risk than conventional eQTLs. The intersection of tumor-specific QTL effects (tsQTLs) with GWAS loci identified rs4765621 and SCARB1, which has been previously linked to renal cell carcinoma (RCC) progression and experimentally validated in tumors. Conclusions: Our new method, DeCAF, empowers the discovery of biologically meaningful cfQTLs from bulk RNA-seq data in moderately sized studies. Our study contributes to a better understanding of germline mechanisms underlying the anticancer immune response as well as cfQTLs contributing to cancer risk.


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