scholarly journals An annotation database for chemicals of emerging concern in exposome research

2021 ◽  
Vol 152 ◽  
pp. 106511
Author(s):  
Jeroen Meijer ◽  
Marja Lamoree ◽  
Timo Hamers ◽  
Jean-Philippe Antignac ◽  
Sébastien Hutinet ◽  
...  
Keyword(s):  
Annotation Database

scholarly journals Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
John T. Lovell ◽  
Nolan B. Bentley ◽  
Gaurab Bhattarai ◽  
Jerry W. Jenkins ◽  
Avinash Sreedasyam ◽  
...  
Keyword(s):  
Tree Breeding ◽  
Pathogen Resistance ◽  
Perennial Crop ◽  
Crop Species ◽  
Annotation Database ◽  
Pan Genome ◽  
Genome Integration ◽  
Transformative Potential ◽  
Genome Assemblies ◽  
Quantitative Genomics

AbstractGenome-enabled biotechnologies have the potential to accelerate breeding efforts in long-lived perennial crop species. Despite the transformative potential of molecular tools in pecan and other outcrossing tree species, highly heterozygous genomes, significant presence–absence gene content variation, and histories of interspecific hybridization have constrained breeding efforts. To overcome these challenges, here, we present diploid genome assemblies and annotations of four outbred pecan genotypes, including a PacBio HiFi chromosome-scale assembly of both haplotypes of the ‘Pawnee’ cultivar. Comparative analysis and pan-genome integration reveal substantial and likely adaptive interspecific genomic introgressions, including an over-retained haplotype introgressed from bitternut hickory into pecan breeding pedigrees. Further, by leveraging our pan-genome presence–absence and functional annotation database among genomes and within the two outbred haplotypes of the ‘Lakota’ genome, we identify candidate genes for pest and pathogen resistance. Combined, these analyses and resources highlight significant progress towards functional and quantitative genomics in highly diverse and outbred crops.

scholarly journals ADeditome provides the genomic landscape of A-to-I RNA editing in Alzheimer’s disease

2021 ◽  
Author(s):  
Sijia Wu ◽  
Mengyuan Yang ◽  
Pora Kim ◽  
Xiaobo Zhou
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Rna Editing ◽  
Memory Loss ◽  
Brain Regions ◽  
Disease Stage ◽  
Mirna Regulation ◽  
Annotation Database ◽  
Functional Annotations ◽  
Genomic Landscape

Abstract A-to-I RNA editing, contributing to nearly 90% of all editing events in human, has been reported to involve in the pathogenesis of Alzheimer’s disease (AD) due to its roles in brain development and immune regulation, such as the deficient editing of GluA2 Q/R related to cell death and memory loss. Currently, there are urgent needs for the systematic annotations of A-to-I RNA editing events in AD. Here, we built ADeditome, the annotation database of A-to-I RNA editing in AD available at https://ccsm.uth.edu/ADeditome, aiming to provide a resource and reference for functional annotation of A-to-I RNA editing in AD to identify therapeutically targetable genes in an individual. We detected 1676 363 editing sites in 1524 samples across nine brain regions from ROSMAP, MayoRNAseq and MSBB. For these editing events, we performed multiple functional annotations including identification of specific and disease stage associated editing events and the influence of editing events on gene expression, protein recoding, alternative splicing and miRNA regulation for all the genes, especially for AD-related genes in order to explore the pathology of AD. Combing all the analysis results, we found 108 010 and 26 168 editing events which may promote or inhibit AD progression, respectively. We also found 5582 brain region-specific editing events with potentially dual roles in AD across different brain regions. ADeditome will be a unique resource for AD and drug research communities to identify therapeutically targetable editing events. Significance: ADeditome is the first comprehensive resource of the functional genomics of individual A-to-I RNA editing events in AD, which will be useful for many researchers in the fields of AD pathology, precision medicine, and therapeutic researches.

scholarly journals Network Pharmacology Study of The Mechanism of Anti-Pneumonia Action Mechanism of Gentiana Rhodantha Franch

2021 ◽  
Author(s):  
Jun Luo ◽  
Xiusheng Tang ◽  
Guotao Shu ◽  
Dongxin Tang ◽  
Jia Yu ◽  
...  
Keyword(s):  
Chinese Medicine ◽  
Signaling Pathway ◽  
High Throughput Sequencing ◽  
Biological Information ◽  
Network Pharmacology ◽  
Chemical Components ◽  
Sequencing Analysis ◽  
Data Set ◽  
Annotation Database ◽  
Functional Richness

Abstract Background: Serum dragon bile is a Chinese medicine used to treat pneumonia, but its mechanism of action is not clear. Meanwhile, due to the development of microarray and RNA‐sequencing technology, high-throughput sequencing analysis is being used increasingly, and it has been applied as an indispensable tool in many medical fields. Therefore, in this article, we want to employed the bioinformatics approach to explore the relevant pharmacological mechanism of dragon serum bile in the treatment of pneumonia through network pharmacology.Methods: In this paper, the active chemical composition and action target of serum dragon bile are obtained through the pharmacology database (TCMSP) of Chinese medicine system and the literature, and the data set of the intersection of active ingredient and disease target is established, and the protein interoperability network of serum gallbladder action target and pneumonia action target is analyzed by using protein interaction network (PPI). Using the Biological Information Annotation Database (DAVID) for gene ontology (GO) functional richness analysis and based on kyoto Gene and Genomics Encyclopedia (KEGG) pathogenic rich analysis, to predict the mechanism of the role of seroclon bile against pneumonia. Results: Through the network pharmacological prediction, it is shown that the main chemical components of serum dragon bile are quercetin, isoorientin, luteolin, Stigmasterol, vanillic acid, etc, all of which have anti-pneumonia effects. The anti-pneumonia effect of serum dragon bile is mainly regulated by pathways in cancer, Bradder cancer, TNF signaling pathway, Hepatitis B and Non-small cell lung cancer, among which the TNF signaling pathway is more associated with pneumonia. Conclusions: It is concluded from the network pharmacological prediction that serum dragon bile may play an anti-pneumonia role by promoting apoptosis, survival, immunity, etc. Its anti-pneumonia path is closely related to key targets IL6, FOS, CASP3 and AKT1. This study provides theoretical support for the follow-up study of the anti-pneumonia mechanism of serum gentian bile.

scholarly journals Maize microarray annotation database

Plant Methods ◽  
2011 ◽  
Vol 7 (1) ◽  
pp. 31 ◽  
Author(s):  
Nanette Coetzer ◽  
Alexander A Myburg ◽  
Dave K Berger
Keyword(s):  
Annotation Database

scholarly journals Mining potentially actionable kinase gene fusions in cancer cell lines with the KuNG FU database

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Alessio Somaschini ◽  
Sebastiano Di Bella ◽  
Carlo Cusi ◽  
Laura Raddrizzani ◽  
Antonella Leone ◽  
...  
Keyword(s):  
Cell Line ◽  
Cell Lines ◽  
Cancer Cell ◽  
Tumor Cell Line ◽  
Cancer Cell Lines ◽  
Clinical Samples ◽  
Gene Fusions ◽  
Kinase Gene ◽  
Annotation Database ◽  
Kung Fu

AbstractInhibition of kinase gene fusions (KGFs) has proven successful in cancer treatment and continues to represent an attractive research area, due to kinase druggability and clinical validation. Indeed, literature and public databases report a remarkable number of KGFs as potential drug targets, often identified by in vitro characterization of tumor cell line models and confirmed also in clinical samples. However, KGF molecular and experimental information can sometimes be sparse and partially overlapping, suggesting the need for a specific annotation database of KGFs, conveniently condensing all the molecular details that can support targeted drug development pipelines and diagnostic approaches. Here, we describe KuNG FU (KiNase Gene FUsion), a manually curated database collecting detailed annotations on KGFs that were identified and experimentally validated in human cancer cell lines from multiple sources, exclusively focusing on in-frame KGF events retaining an intact kinase domain, representing potentially active driver kinase targets. To our knowledge, KuNG FU represents to date the largest freely accessible homogeneous and curated database of kinase gene fusions in cell line models.

scholarly journals The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology

2012 ◽  
Vol 41 (D1) ◽  
pp. D1199-D1205 ◽  
Author(s):  
Dapeng Wang ◽  
Yan Xia ◽  
Xinna Li ◽  
Lixia Hou ◽  
Jun Yu
Keyword(s):  
Comparative Genomics ◽  
Evolutionary Biology ◽  
Rice Genome ◽  
Annotation Database

scholarly journals The UniProt-GO Annotation database in 2011

2011 ◽  
Vol 40 (D1) ◽  
pp. D565-D570 ◽  
Author(s):  
E. C. Dimmer ◽  
R. P. Huntley ◽  
Y. Alam-Faruque ◽  
T. Sawford ◽  
C. O'Donovan ◽  
...  
Keyword(s):  
Annotation Database ◽  
Go Annotation

scholarly journals NONCODEV5: a comprehensive annotation database for long non-coding RNAs

2017 ◽  
Vol 46 (D1) ◽  
pp. D308-D314 ◽  
Author(s):  
ShuangSang Fang ◽  
LiLi Zhang ◽  
JinCheng Guo ◽  
YiWei Niu ◽  
Yang Wu ◽  
...  
Keyword(s):  
Annotation Database ◽  
Non Coding Rnas

scholarly journals ExonSkipDB: functional annotation of exon skipping event in human

2019 ◽  
Author(s):  
Pora Kim ◽  
Mengyuan Yang ◽  
Ke Yiya ◽  
Weiling Zhao ◽  
Xiaobo Zhou
Keyword(s):  
Functional Annotation ◽  
Exon Skipping ◽  
Tissue Expression ◽  
The Cancer Genome Atlas ◽  
Multiple Cancer ◽  
Annotation Database ◽  
Reading Frame ◽  
Normal Tissues ◽  
Cancer Genome Atlas ◽  
Functional Features

AbstractExon skipping (ES) is reported to be the most common alternative splicing event due to loss of functional domains/sites or shifting of the open reading frame (ORF), leading to a variety of human diseases and considered therapeutic targets. To date, systematic and intensive annotations of ES events based on the skipped exon units in cancer and normal tissues are not available. Here, we built ExonSkipDB, the ES annotation database available at https://ccsm.uth.edu/ExonSkipDB/, aiming to provide a resource and reference for functional annotation of ES events in multiple cancer and tissues to identify therapeutically targetable genes in individual exon units. We collected 14 272 genes that have 90 616 and 89 845 ES events across 33 cancer types and 31 normal tissues from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx). For the ES events, we performed multiple functional annotations. These include ORF assignment of exon skipped transcript, studies of lost protein functional features due to ES events, and studies of exon skipping events associated with mutations and methylations based on multi-omics evidence. ExonSkipDB will be a unique resource for cancer and drug research communities to identify therapeutically targetable exon skipping events.

Sign in / Sign up

Export Citation Format

Share Document