Browse
Submit Data
Databases
API
Help

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

BRAD V3.0: an upgraded Brassicaceae database.

ABSTRACT: The Brassicaceae Database (BRAD version 3.0, BRAD V3.0; http://brassicadb.cn) has evolved from the former Brassica Database (BRAD V2.0), and represents an important community portal hosting genome information for multiple Brassica and related Brassicaceae plant species. Since the last update in 2015, the complex genomes of numerous Brassicaceae species have been decoded, accompanied by many omics datasets. To provide an up-to-date service, we report here a major upgrade of the portal. The Model-View-ViewModel (MVVM) framework of BRAD has been re-engineered to enable easy and sustainable maintenance of the database. The collection of genomes has been increased to 26 species, along with optimization of the user interface. Features of the previous version have been retained, with additional new tools for exploring syntenic genes, gene expression and variation data. In the 'Syntenic Gene @ Subgenome' module, we added features to view the sequence alignment and phylogenetic relationships of syntenic genes. New modules include 'MicroSynteny' for viewing synteny of selected fragment pairs, and 'Polymorph' for retrieval of variation data. The updated BRAD provides a substantial expansion of genomic data and a comprehensive improvement of the service available to the Brassicaceae research community.

SUBMITTER: Chen H

PROVIDER: S-EPMC8728314 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

NPInter v3.0: an upgraded database of noncoding RNA-associated interactions.

Project description:Despite the fact that a large quantity of noncoding RNAs (ncRNAs) have been identified, their functions remain unclear. To enable researchers to have a better understanding of ncRNAs' functions, we updated the NPInter database to version 3.0, which contains experimentally verified interactions between ncRNAs (excluding tRNAs and rRNAs), especially long noncoding RNAs (lncRNAs) and other biomolecules (proteins, mRNAs, miRNAs and genomic DNAs). In NPInter v3.0, interactions pertaining to ncRNAs are not only manually curated from scientific literature but also curated from high-throughput technologies. In addition, we also curated lncRNA-miRNA interactions fromin silicopredictions supported by AGO CLIP-seq data. When compared with NPInter v2.0, the interactions are more informative (with additional information on tissues or cell lines, binding sites, conservation, co-expression values and other features) and more organized (with divisions on data sets by data sources, tissues or cell lines, experiments and other criteria). NPInter v3.0 expands the data set to 491,416 interactions in 188 tissues (or cell lines) from 68 kinds of experimental technologies. NPInter v3.0 also improves the user interface and adds new web services, including a local UCSC Genome Browser to visualize binding sites. Additionally, NPInter v3.0 defined a high-confidence set of interactions and predicted the functions of lncRNAs in human and mouse based on the interactions curated in the database. NPInter v3.0 is available athttp://www.bioinfo.org/NPInter/Database URL:http://www.bioinfo.org/NPInter/.

| S-EPMC4834207 | biostudies-literature

Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources.

Project description:The Brassica database (BRAD) was built initially to assist users apply Brassica rapa and Arabidopsis thaliana genomic data efficiently to their research. However, many Brassicaceae genomes have been sequenced and released after its construction. These genomes are rich resources for comparative genomics, gene annotation and functional evolutionary studies of Brassica crops. Therefore, we have updated BRAD to version 2.0 (V2.0). In BRAD V2.0, 11 more Brassicaceae genomes have been integrated into the database, namely those of Arabidopsis lyrata, Aethionema arabicum, Brassica oleracea, Brassica napus, Camelina sativa, Capsella rubella, Leavenworthia alabamica, Sisymbrium irio and three extremophiles Schrenkiella parvula, Thellungiella halophila and Thellungiella salsuginea. BRAD V2.0 provides plots of syntenic genomic fragments between pairs of Brassicaceae species, from the level of chromosomes to genomic blocks. The Generic Synteny Browser (GBrowse_syn), a module of the Genome Browser (GBrowse), is used to show syntenic relationships between multiple genomes. Search functions for retrieving syntenic and non-syntenic orthologs, as well as their annotation and sequences are also provided. Furthermore, genome and annotation information have been imported into GBrowse so that all functional elements can be visualized in one frame. We plan to continually update BRAD by integrating more Brassicaceae genomes into the database. Database URL: http://brassicadb.org/brad/.

| S-EPMC4653866 | biostudies-other

dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Nonsynonymous and Splice-Site SNVs.

Project description:The purpose of the dbNSFP is to provide a one-stop resource for functional predictions and annotations for human nonsynonymous single-nucleotide variants (nsSNVs) and splice-site variants (ssSNVs), and to facilitate the steps of filtering and prioritizing SNVs from a large list of SNVs discovered in an exome-sequencing study. A list of all potential nsSNVs and ssSNVs based on the human reference sequence were created and functional predictions and annotations were curated and compiled for each SNV. Here, we report a recent major update of the database to version 3.0. The SNV list has been rebuilt based on GENCODE 22 and currently the database includes 82,832,027 nsSNVs and ssSNVs. An attached database dbscSNV, which compiled all potential human SNVs within splicing consensus regions and their deleteriousness predictions, add another 15,030,459 potentially functional SNVs. Eleven prediction scores (MetaSVM, MetaLR, CADD, VEST3, PROVEAN, 4× fitCons, fathmm-MKL, and DANN) and allele frequencies from the UK10K cohorts and the Exome Aggregation Consortium (ExAC), among others, have been added. The original seven prediction scores in v2.0 (SIFT, 2× Polyphen2, LRT, MutationTaster, MutationAssessor, and FATHMM) as well as many SNV and gene functional annotations have been updated. dbNSFP v3.0 is freely available at http://sites.google.com/site/jpopgen/dbNSFP.

| S-EPMC4752381 | biostudies-literature

Analysis of 272 Genetic Variants in the Upgraded Interactive FXI Web Database Reveals New Insights into FXI Deficiency.

Project description:Coagulation Factor XI (FXI) is a plasma glycoprotein composed of four apple (Ap) domains and a serine protease (SP) domain. FXI circulates as a dimer and activates Factor IX (FIX), promoting thrombin production and preventing excess blood loss. Genetic variants that degrade FXI structure and function often lead to bleeding diatheses, commonly termed FXI deficiency. The first interactive FXI variant database underwent initial development in 2003 at https://www.factorxi.org . Here, based on a much improved FXI crystal structure, the upgraded FXI database contains information regarding 272 FXI variants (including 154 missense variants) found in 657 patients, this being a significant increase from the 183 variants identified in the 2009 update. Type I variants involve the simultaneous reduction of FXI coagulant activity (FXI:C) and FXI antigen levels (FXI:Ag), whereas Type II variants result in decreased FXI:C yet normal FXI:Ag. The database updates now highlight the predominance of Type I variants in FXI. Analysis in terms of a consensus Ap domain revealed the near-uniform distribution of 81 missense variants across the Ap domains. A further 66 missense variants were identified in the SP domain, showing that all regions of the FXI protein were important for function. The variants clarified the critical importance of changes in surface solvent accessibility, as well as those of cysteine residues and the dimer interface. Guidelines are provided below for clinicians who wish to use the database for diagnostic purposes. In conclusion, the updated database provides an easy-to-use web resource on FXI deficiency for clinicians.

| S-EPMC8763576 | biostudies-literature

Brassicaceae

Project description:Various representative species from the mustard family (Brassicaceae). Raw sequence reads

| PRJNA806513 | ENA

Brassicaceae

Project description:Brassicaceae species transcriptome analysis

| PRJNA242124 | ENA

Brassicaceae

Project description:Brassicaceae Woodiness raw sequencing data

| PRJNA678873 | ENA

Brassicaceae

Project description:Brassicaceae's microbiome raw sequence reads

| PRJNA529542 | ENA

The Chicago Classification of esophageal motility disorders, v3.0.

Project description:The Chicago Classification (CC) of esophageal motility disorders, utilizing an algorithmic scheme to analyze clinical high-resolution manometry (HRM) studies, has gained acceptance worldwide.This 2014 update, CC v3.0, developed by the International HRM Working Group, incorporated the extensive clinical experience and interval publications since the prior (2011) version.Chicago Classification v3.0 utilizes a hierarchical approach, sequentially prioritizing: (i) disorders of esophagogastric junction (EGJ) outflow (achalasia subtypes I-III and EGJ outflow obstruction), (ii) major disorders of peristalsis (absent contractility, distal esophageal spasm, hypercontractile esophagus), and (iii) minor disorders of peristalsis characterized by impaired bolus transit. EGJ morphology, characterized by the degree of overlap between the lower esophageal sphincter and the crural diaphragm and baseline EGJ contractility are also part of CC v3.0. Compared to the previous CC version, the key metrics of interpretation, the integrated relaxation pressure (IRP), the distal contractile integral (DCI), and the distal latency (DL) remain unchanged, albeit with much more emphasis on DCI for defining both hypo- and hypercontractility. New in CC v3.0 are: (i) the evaluation of the EGJ at rest defined in terms of morphology and contractility, (ii) 'fragmented' contractions (large breaks in the 20-mmHg isobaric contour), (iii) ineffective esophageal motility (IEM), and (iv) several minor adjustments in nomenclature and defining criteria. Absent in CC v3.0 are contractile front velocity and small breaks in the 20-mmHg isobaric contour as defining characteristics.Chicago Classification v3.0 is an updated analysis scheme for clinical esophageal HRM recordings developed by the International HRM Working Group.

| S-EPMC4308501 | biostudies-literature

GlobSnow v3.0 Northern Hemisphere snow water equivalent dataset.

Project description:We describe the Northern Hemisphere terrestrial snow water equivalent (SWE) time series covering 1979-2018, containing daily, monthly and monthly bias-corrected SWE estimates. The GlobSnow v3.0 SWE dataset combines satellite-based passive microwave radiometer data (Nimbus-7 SMMR, DMSP SSM/I and DMSP SSMIS) with ground based synoptic snow depth observations using bayesian data assimilation, incorporating the HUT Snow Emission model. The original GlobSnow SWE retrieval methodology has been further developed and is presented in its current form in this publication. The described GlobSnow v3.0 monthly bias-corrected dataset was applied to provide continental scale estimates on the annual maximum snow mass and its trend during the period 1980 to 2018.

| S-EPMC8249486 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data