Atlas of Iberian water beetles (ESACIB database).
Ontology highlight
ABSTRACT:
SUBMITTER: Sanchez-Fernandez D
PROVIDER: S-EPMC4591726 | biostudies-other | 2015
REPOSITORIES: biostudies-other
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Project description:Hepatocellular carcinoma (HCC) is highly heterogeneous in nature and has been one of the most common cancer types worldwide. To ensure repeatability of identified gene expression patterns and comprehensively annotate the transcriptomes of HCC, we carefully curated 15 public HCC expression datasets that cover around 4000 clinical samples and developed the database HCCDB to serve as a one-stop online resource for exploring HCC gene expression with user-friendly interfaces. The global differential gene expression landscape of HCC was established by analyzing the consistently differentially expressed genes across multiple datasets. Moreover, a 4D metric was proposed to fully characterize the expression pattern of each gene by integrating data from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx). To facilitate a comprehensive understanding of gene expression patterns in HCC, HCCDB also provides links to third-party databases on drug, proteomics, and literatures, and graphically displays the results from computational analyses, including differential expression analysis, tissue-specific and tumor-specific expression analysis, survival analysis, and co-expression analysis. HCCDB is freely accessible at http://lifeome.net/database/hccdb.
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Project description:High-throughput small RNA (sRNA) sequencing technology enables an entirely new perspective for plant microRNA (miRNA) research and has immense potential to unravel regulatory networks. Novel insights gained through data mining in publically available rich resource of sRNA data will help in designing biotechnology-based approaches for crop improvement to enhance plant yield and nutritional value. Bioinformatics resources enabling meta-analysis of miRNA expression across multiple plant species are still evolving. Here, we report PmiRExAt, a new online database resource that caters plant miRNA expression atlas. The web-based repository comprises of miRNA expression profile and query tool for 1859 wheat, 2330 rice and 283 maize miRNA. The database interface offers open and easy access to miRNA expression profile and helps in identifying tissue preferential, differential and constitutively expressing miRNAs. A feature enabling expression study of conserved miRNA across multiple species is also implemented. Custom expression analysis feature enables expression analysis of novel miRNA in total 117 datasets. New sRNA dataset can also be uploaded for analysing miRNA expression profiles for 73 plant species. PmiRExAt application program interface, a simple object access protocol web service allows other programmers to remotely invoke the methods written for doing programmatic search operations on PmiRExAt database.Database URL:http://pmirexat.nabi.res.in.
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Project description:The coronavirus disease 19 (COVID-19) is a highly pathogenic viral infection of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), resulted in the global pandemic of 2020. A lack of therapeutic and preventive strategies has quickly posed significant threats to world health. A comprehensive understanding of SARS-CoV-2 evolution and natural selection, how it impacts host interaction, and phenotype symptoms is vital to develop effective strategies against the virus. The SARS2Mutant database (http://sars2mutant.com/) was developed to provide valuable insights based on millions of high-quality, high-coverage SARS-CoV-2 complete protein sequences. Users of this database have the ability to search for information on three amino acid substitution mutation strategies based on gene name, geographical zone, or comparative analysis. Each strategy is presented in five distinct formats which includes: (i) mutated sample frequencies, (ii) heat maps of mutated amino acid positions, (iii) mutation survivals, (iv) natural selections and (v) details of substituted amino acids, including their names, positions, and frequencies. GISAID is a primary database of genomics sequencies of influenza viruses updated daily. SARS2Mutant is a secondary database developed to discover mutation and conserved regions from the primary data to assist with design for targeted vaccine, primer, and drug discoveries.
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Project description:During a survey of genetic and species diversity patterns of leaf beetle (Coleoptera: Chrysomelidae) assemblages across the Iberian Peninsula we found a broad congruence between morphologically delimited species and variation in the cytochrome oxidase (cox1) gene. However, one species pair each in the genera Longitarsus Berthold and Pachybrachis Chevrolat was inseparable using molecular methods, whereas diagnostic morphological characters (including male or female genitalia) unequivocally separated the named species. Parsimony haplotype networks and maximum likelihood trees built from cox1 showed high genetic structure within each species pair, but no correlation with the morphological types and neither with geographic distributions. This contrasted with all analysed congeneric species, which were recovered as monophyletic. A limited number of specimens were sequenced for the nuclear 18S rRNA gene, which showed no or very limited variation within the species pair and no separation of morphological types. These results suggest that processes of lineage sorting for either group are lagging behind the clear morphological and presumably reproductive separation. In the Iberian chrysomelids, incongruence between DNA-based and morphological delimitations is a rare exception, but the discovery of these species pairs may be useful as an evolutionary model for studying the process of speciation in this ecological and geographical setting. In addition, the study of biodiversity patterns based on DNA requires an evolutionary understanding of these incongruences and their potential causes.
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Project description:BackgroundFor centuries roses have been selected based on a number of traits. Little information exists on the genetic and molecular basis that contributes to these traits, mainly because information on expressed genes for this economically important ornamental plant is scarce.ResultsHere, we used a combination of Illumina and 454 sequencing technologies to generate information on Rosa sp. transcripts using RNA from various tissues and in response to biotic and abiotic stresses. A total of 80714 transcript clusters were identified and 76611 peptides have been predicted among which 20997 have been clustered into 13900 protein families. BLASTp hits in closely related Rosaceae species revealed that about half of the predicted peptides in the strawberry and peach genomes have orthologs in Rosa dataset. Digital expression was obtained using RNA samples from organs at different development stages and under different stress conditions. qPCR validated the digital expression data for a selection of 23 genes with high or low expression levels. Comparative gene expression analyses between the different tissues and organs allowed the identification of clusters that are highly enriched in given tissues or under particular conditions, demonstrating the usefulness of the digital gene expression analysis. A web interface ROSAseq was created that allows data interrogation by BLAST, subsequent analysis of DNA clusters and access to thorough transcript annotation including best BLAST matches on Fragaria vesca, Prunus persica and Arabidopsis. The rose peptides dataset was used to create the ROSAcyc resource pathway database that allows access to the putative genes and enzymatic pathways.ConclusionsThe study provides useful information on Rosa expressed genes, with thorough annotation and an overview of expression patterns for transcripts with good accuracy.
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Project description:BACKGROUND:Alternative splicing is an important biological process whose precision must be tightly regulated during growth and development. Although there are species, disease (e.g. cancers), or study specific databases available in many organisms, no database exists in livestock animals specifically tailored for alternative splicing. DESCRIPTION:We present in this study the development and implementation of a database for alternative splicing atlas in livestock animals (ASlive.org). Using publicly available RNASeq data sets across many tissues, cell types, and biological conditions totaling 28.6 T bases, we built a database of alternative splicing events in five major livestock and poultry animal species (cattle, sheep, pigs, horses, and chickens). The database contains many types of information on alternative splicing events, including basic information such as genomic locations, genes, and event types, quantitative measurements of alternative splicing in the form of percent spliced in (PSI), overlap with known DNA variants, as well as orthologous events across different lineage groups. CONCLUSIONS:This database, the first of its kind in livestock animals, will provide a useful exploratory tool to assist functional annotation of animal genomes.
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Project description:BackgroundMicroarray technologies facilitate high-throughput gene expression analysis. However, the diversity of platforms for rice gene expression analysis hinders efficient analysis. Tools to broadly integrate microarray data from different platforms are needed.ResultsIn this study, we developed the Rice Oligonucleotide Array Database (ROAD, http://www.ricearray.org) to explore gene expression across 1,867 publicly available rice microarray hybridizations. The ROAD's user-friendly web interface and variety of visualization tools facilitate the extraction of gene expression profiles using gene and microarray element identifications. The ROAD supports meta-analysis of genes expressed in different tissues and at developmental stages. Co-expression analysis tool provides information on co-regulation between genes under general, abiotic and biotic stress conditions. Additionally, functional analysis tools, such as Gene Ontology and KEGG (Kyoto Encyclopedia of Genes and Genomes) Orthology, are embedded in the ROAD. These tools facilitate the identification of meaningful biological patterns in a list of query genes.ConclusionsThe Rice Oligonucleotide Array Database provides comprehensive gene expression profiles for all rice genes, and will be a useful resource for researchers of rice and other grass species.
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Project description:BackgroundMicroRNAs (miRNAs) regulate gene expression and have been targeted as indicators of environmental/toxicologic stressors. Using the data from our deep sequencing of miRNAs in an extensive sampling of rat tissues, we developed a database called RATEmiRs for the Rat Atlas of Tissue-specific and Enriched miRNAs to allow users to dynamically determine mature-, iso- and pre-miR expression abundance, enrichment and specificity in rat tissues and organs.ResultsIllumina sequencing count data from mapped reads and meta data from the miRNA body atlas consisting of 21 and 23 tissues (14 organs) of toxicologic interest from 12 to 13 week old male and female Sprague Dawley rats respectively, were managed in a relational database with a user-friendly query interface. Data-driven pipelines are available to tailor the identification of tissue-enriched (TE) and tissue-specific (TS) miRNAs. Data-driven organ-specific (OS) pipelines reveal miRNAs that are expressed predominately in a given organ. A user-driven approach is also available to assess the tissue expression of user-specified miRNAs. Using one tissue vs other tissues and tissue(s) of an organ vs other organs, we illustrate the utility of RATEmiRs to facilitate the identification of candidate miRNAs. As a use case example, RATEmiRs revealed two TS miRNAs in the liver: rno-miR-122-3p and rno-miR-122-5p. When liver is compared to just the brain tissues for example, rno-miR-192-5p, rno-miR-193-3p, rno-miR-203b-3p, rno-miR-3559-5p, rno-miR-802-3p and rno-miR-802-5p are also detected as abundantly expressed in liver. As another example, 55 miRNAs from the RATEmiRs query of ileum vs brain tissues overlapped with miRNAs identified from the same comparison of tissues in an independent, publicly available dataset of 10 week old male rat microarray data suggesting that these miRNAs are likely not age-specific, platform-specific nor pipeline-dependent. Lastly, we identified 10 miRNAs that have conserved tissue/organ-specific expression between the rat and human species.ConclusionsRATEmiRs provides a new platform for identification of TE, TS and OS miRNAs in a broad array of rat tissues. RATEmiRs is available at: https://www.niehs.nih.gov/ratemirs.
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