scholarly journals The protein repertoire in early vertebrate embryogenesis

2019 ◽  
Author(s):  
Leonid Peshkin ◽  
Alexander Lukyanov ◽  
Marian Kalocsay ◽  
Robert Michael Gage ◽  
DongZhuo Wang ◽  
...  
Keyword(s):  
Protein Expression ◽  
Stage Iv ◽  
List Type ◽  
Web Browser ◽  
Genome Wide ◽  
Human Genes ◽  
Early Organogenesis ◽  
Multi Media ◽  
Comprehensive Characterization

SummaryWe present an unprecedentedly comprehensive characterization of protein dynamics across early development inXenopus laevis, available immediately via a convenient Web portal. This resource allows interrogation of the protein expression data in conjunction with other data modalities such as genome wide mRNA expression. This study provides detailed data for absolute levels of ∼14K uniqueXenopusproteins representing homologues of ∼9K unique human genes – a rich resource for developmental biologists. The purpose of this manuscript is limited to presenting and releasing the data browser.HighlightsRelative protein expression from stage IV oocyte, blastula, gastrula, neurula, and early organogenesisBiological triplicates with confidence intervals on protein expression reflect certainty in dynamic patternsConvenient time-series Web-browser integrated with the multi-media Xenbase portalGene-symbol search and multi-gene protein/mRNA juxtaposition capabilities

scholarly journals A Comprehensive Characterization of Genome-Wide Copy Number Aberrations in Colorectal Cancer Reveals Novel Oncogenes and Patterns of Alterations

PLoS ONE ◽  
2012 ◽  
Vol 7 (7) ◽  
pp. e42001 ◽  
Author(s):  
Tao Xie ◽  
Giovanni d’ Ario ◽  
John R. Lamb ◽  
Eric Martin ◽  
Kai Wang ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Copy Number ◽  
Copy Number Aberrations ◽  
Genome Wide ◽  
Comprehensive Characterization

scholarly journals High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq.

2016 ◽  
Author(s):  
Rafal Gumienny ◽  
Dominik Jedlinski ◽  
Georges Martin ◽  
Arnau Vina-Villaseca ◽  
Mihaela Zavolan
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Expression Patterns ◽  
Ribonucleoprotein Complexes ◽  
Short Rnas ◽  
Genome Wide ◽  
The Many ◽  
Nucleolar Rnas ◽  
Comprehensive Characterization

Identification of long and short RNAs, their processing and expression patterns have been greatly facilitated by high-throughput sequencing. Frequently, these RNAs act as guides for ribonucleoprotein complexes that regulate the expression or processing of target RNAs. However, to determine the targets of the many newly discovered regulatory RNAs in high-throughput remains a challenge. To globally assign guide small nucleolar RNAs to site of 2'-O-ribose methylation in human cells, we here developed novel computational methods for the analysis of data that was generated with protocols designed to capture direct small RNA-target interactions and to identify the sites of 2'-O-ribose methylation genome-wide. We thereby determined that many "orphan" snoRNAs appear to guide 2'-O-ribose methylation at sites that are targeted by other snoRNAs and that snoRNAs can be reliably captured in interaction with many mRNAs, in which a subsequent 2'-O-methylation cannot be detected. Our study provides a reliable approach to the comprehensive characterization of snoRNA-target interactions in species beyond those in which these interactions have been traditionally studied and contribute to the rapidly developing field of "epitranscriptomics".

scholarly journals The genetic basis of cis-regulatory divergence between the subspecies of cultivated rice (Oryza sativa)

2019 ◽  
Author(s):  
Malachy T Campbell ◽  
Qian Du ◽  
Kan Liu ◽  
Sandeep Sharma ◽  
Chi Zhang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phenotypic Variability ◽  
Cultivated Rice ◽  
Regulatory Variation ◽  
Selective Pressures ◽  
Regulatory Variants ◽  
Genome Wide ◽  
Comprehensive Characterization ◽  
Transcriptome Level

AbstractCultivated rice consists of two subspecies, Indica and Japonica, that exhibit well-characterized differences at the morphological and genetic levels. However, the differences between these subspecies at the transcriptome level remains largely unexamined. Here, we provide a comprehensive characterization of transcriptome divergence and cis-regulatory variation within rice using transcriptome data from 91 accessions from a rice diversity panel (RDP1). The transcriptomes of the two subspecies of rice are highly divergent. The expression and genetic diversity was significantly lower within Japonica relative to Indica, which is consistent with the known population bottleneck during Japonica domestication. Moreover, 1,860 and 1,325 genes showed differences in heritability in the broad and narrow sense respectively, between the subspecies, which was driven largely by environmental and genetic effects rather than differences in phenotypic variability. We leveraged high-density genotypic data and transcript levels to identify cis-regulatory variants that may explain the genetic divergence between the subspecies. We identified significantly more eQTL that were specific to the Indica subspecies compared to Japonica, suggesting that the observed differences in expression and genetic variability also extends to cis-regulatory variation. We next explored the potential causes of this cis-regulatory divergence by assessing local genetic diversity for cis-eQTL. Local genetic diversity around subspecies-specific cis-eQTL was significantly lower than genome-wide averages in subspecies lacking the eQTL, suggesting that selective pressures may have shaped regulatory variation in each subspecies. This study provides the first comprehensive characterization of transcriptional and cis-regulatory variation in cultivated rice, and could be an important resource for future studies.

scholarly journals Comprehensive characterization of programmed death ligand structural rearrangements in B-cell non-Hodgkin lymphomas

Blood ◽  
2016 ◽  
Vol 128 (9) ◽  
pp. 1206-1213 ◽  
Author(s):  
Lauren C. Chong ◽  
David D. W. Twa ◽  
Anja Mottok ◽  
Susana Ben-Neriah ◽  
Bruce W. Woolcock ◽  
...  
Keyword(s):  
Protein Expression ◽  
B Cell ◽  
T Cell Activation ◽  
Cell Activation ◽  
Structural Rearrangements ◽  
Programmed Death ◽  
Key Points ◽  
Comprehensive Characterization ◽  
Capture Sequencing

Key Points Capture sequencing reveals that PDL SRs cluster into 2 discrete breakpoint regions. PDL SRs are significantly associated with increased protein expression and limit T-cell activation.

scholarly journals In silico genome-wide identification and comprehensive characterization of the BES1 gene family in soybean

Heliyon ◽  
2019 ◽  
Vol 5 (6) ◽  
pp. e01868 ◽  
Author(s):  
Qing Li ◽  
Luqin Guo ◽  
Hong Wang ◽  
Yu Zhang ◽  
Chengming Fan ◽  
...  
Keyword(s):  
Gene Family ◽  
In Silico ◽  
Genome Wide ◽  
Comprehensive Characterization

scholarly journals Genetic sequence analysis of inherited bleeding diseases

Blood ◽  
2013 ◽  
Vol 122 (20) ◽  
pp. 3423-3431 ◽  
Author(s):  
Flora Peyvandi ◽  
Tom Kunicki ◽  
David Lillicrap
Keyword(s):  
Hemophilia A ◽  
Genetic Diagnosis ◽  
Coagulation Factor ◽  
Standard Of Care ◽  
Bleeding Disorders ◽  
Genome Wide ◽  
Human Genes ◽  
Genes Encoding ◽  
Made In

Abstract The genes encoding the coagulation factor proteins were among the first human genes to be characterized over 25 years ago. Since then, significant progress has been made in the translational application of this information for the 2 commonest severe inherited bleeding disorders, hemophilia A and B. For these X-linked disorders, genetic characterization of the disease-causing mutations is now incorporated into the standard of care and genetic information is used for risk stratification of treatment complications. With electronic databases detailing >2100 unique mutations for hemophilia A and >1100 mutations for hemophilia B, these diseases are among the most extensively characterized inherited diseases in humans. Experience with the genetics of the rare bleeding disorders is, as expected, less well advanced. However, here again, electronic mutation databases have been developed and provide excellent guidance for the application of genetic analysis as a confirmatory approach to diagnosis. Most recently, progress has also been made in identifying the mutant loci in a variety of inherited platelet disorders, and these findings are beginning to be applied to the genetic diagnosis of these conditions. Investigation of patients with bleeding phenotypes without a diagnosis, using genome-wide strategies, may identify novel genes not previously recognized as playing a role in hemostasis.

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