Large-scale analyses of human microbiomes reveal thousands of small, novel genes and their predicted functions

2019 ◽  
Author(s):  
Ganesh Kadamur
Keyword(s):  
2007 ◽  
Vol 7 (1) ◽  
pp. 30 ◽  
Author(s):  
Julian Ceron ◽  
Jean-François Rual ◽  
Abha Chandra ◽  
Denis Dupuy ◽  
Marc Vidal ◽  
...  
Keyword(s):  

Blood ◽  
1998 ◽  
Vol 92 (12) ◽  
pp. 4622-4631 ◽  
Author(s):  
William L. Stanford ◽  
Georgina Caruana ◽  
Katherine A. Vallis ◽  
Maneesha Inamdar ◽  
Michihiro Hidaka ◽  
...  

Abstract We have developed a large-scale, expression-based gene trap strategy to perform genome-wide functional analysis of the murine hematopoietic and vascular systems. Using two different gene trap vectors, we have isolated embryonic stem (ES) cell clones containing lacZreporter gene insertions in genes expressed in blood island and vascular cells, muscle, stromal cells, and unknown cell types. Of 79 clones demonstrating specific expression patterns, 49% and 16% were preferentially expressed in blood islands and/or the vasculature, respectively. The majority of ES clones that expressedlacZ in blood islands also expressed lacZ upon differentiation into hematopoietic cells on OP9 stromal layers. Importantly, the in vivo expression of the lacZ fusion products accurately recapitulated the observed in vitro expression patterns. Expression and sequence analysis of representative clones suggest that this approach will be useful for identifying and mutating novel genes expressed in the developing hematopoietic and vascular systems.


Blood ◽  
1998 ◽  
Vol 92 (12) ◽  
pp. 4622-4631 ◽  
Author(s):  
William L. Stanford ◽  
Georgina Caruana ◽  
Katherine A. Vallis ◽  
Maneesha Inamdar ◽  
Michihiro Hidaka ◽  
...  

We have developed a large-scale, expression-based gene trap strategy to perform genome-wide functional analysis of the murine hematopoietic and vascular systems. Using two different gene trap vectors, we have isolated embryonic stem (ES) cell clones containing lacZreporter gene insertions in genes expressed in blood island and vascular cells, muscle, stromal cells, and unknown cell types. Of 79 clones demonstrating specific expression patterns, 49% and 16% were preferentially expressed in blood islands and/or the vasculature, respectively. The majority of ES clones that expressedlacZ in blood islands also expressed lacZ upon differentiation into hematopoietic cells on OP9 stromal layers. Importantly, the in vivo expression of the lacZ fusion products accurately recapitulated the observed in vitro expression patterns. Expression and sequence analysis of representative clones suggest that this approach will be useful for identifying and mutating novel genes expressed in the developing hematopoietic and vascular systems.


2019 ◽  
Vol 35 (19) ◽  
pp. 3576-3583 ◽  
Author(s):  
Chong Wu ◽  
Wei Pan

Abstract Motivation Most trait-associated genetic variants identified in genome-wide association studies (GWASs) are located in non-coding regions of the genome and thought to act through their regulatory roles. Results To account for enriched association signals in DNA regulatory elements, we propose a novel and general gene-based association testing strategy that integrates enhancer-target gene pairs and methylation quantitative trait locus data with GWAS summary results; it aims to both boost statistical power for new discoveries and enhance mechanistic interpretability of any new discovery. By reanalyzing two large-scale schizophrenia GWAS summary datasets, we demonstrate that the proposed method could identify some significant and novel genes (containing no genome-wide significant SNPs nearby) that would have been missed by other competing approaches, including the standard and some integrative gene-based association methods, such as one incorporating enhancer-target gene pairs and one integrating expression quantitative trait loci. Availability and implementation Software: wuchong.org/egmethyl.html Supplementary information Supplementary data are available at Bioinformatics online.


2017 ◽  
Vol 27 ◽  
pp. S195 ◽  
Author(s):  
J. Böhm ◽  
R. Schneider ◽  
E. Malfatti ◽  
V. Schartner ◽  
X. Lornage ◽  
...  

1998 ◽  
Vol 140 (3) ◽  
pp. 461-483 ◽  
Author(s):  
Scott Erdman ◽  
Li Lin ◽  
Michael Malczynski ◽  
Michael Snyder

Yeast cells mate by an inducible pathway that involves agglutination, mating projection formation, cell fusion, and nuclear fusion. To obtain insight into the mating differentiation of Saccharomyces cerevisiae, we carried out a large-scale transposon tagging screen to identify genes whose expression is regulated by mating pheromone. 91,200 transformants containing random lacZ insertions were screened for β-galactosidase (β-gal) expression in the presence and absence of α factor, and 189 strains containing pheromone-regulated lacZ insertions were identified. Transposon insertion alleles corresponding to 20 genes that are novel or had not previously been known to be pheromone regulated were examined for effects on the mating process. Mutations in four novel genes, FIG1, FIG2, KAR5/ FIG3, and FIG4 were found to cause mating defects. Three of the proteins encoded by these genes, Fig1p, Fig2p, and Fig4p, are dispensible for cell polarization in uniform concentrations of mating pheromone, but are required for normal cell polarization in mating mixtures, conditions that involve cell–cell communication. Fig1p and Fig2p are also important for cell fusion and conjugation bridge shape, respectively. The fourth protein, Kar5p/Fig3p, is required for nuclear fusion. Fig1p and Fig2p are likely to act at the cell surface as Fig1:: β-gal and Fig2::β-gal fusion proteins localize to the periphery of mating cells. Fig4p is a member of a family of eukaryotic proteins that contain a domain homologous to the yeast Sac1p. Our results indicate that a variety of novel genes are expressed specifically during mating differentiation to mediate proper cell morphogenesis, cell fusion, and other steps of the mating process.


2019 ◽  
Vol 85 (10) ◽  
pp. S98
Author(s):  
Wen Zhang ◽  
Georgios Voloudakis ◽  
Veera Rajagopal ◽  
Eric Schadt ◽  
Johan Björkegren ◽  
...  

2019 ◽  
pp. g3.200995.2018
Author(s):  
Dorothea Schultheis ◽  
Matthias Weißkopf ◽  
Christoph Schaub ◽  
Salim Ansari ◽  
Van Anh Dao ◽  
...  

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