Database Resources for Functional Circular RNAs.

Circular RNA (or circRNA) is a type of single-stranded covalently closed circular RNA molecule and play important roles in diverse biological pathways. A comprehensive functionally annotated circRNA database will help to understand the circRNAs and their functions. CircFunBase is such a web-accessible database that aims to provide a high-quality functional circRNA resource including experimentally validated and computationally predicted functions. CircFunBase provides visualized circRNA-miRNA interaction networks. In addition, a genome browser is provided to visualize the genome context of circRNA. In this chapter, we illustrate examples of searching for circRNA and getting detailed information of circRNA. Moreover, other circRNA related databases are outlined.

Applications of Bioinformatics to Plant Biotechnology.

Bioinformatics encompasses many tools and techniques that today are essential for all areas of research in the biological sciences. New databases with a wealth of information about genomes, proteins, metabolites, and metabolic pathways appear almost daily. Particularly, for scientists who carry out research in plant biology, the amount of information has multiplied exponentially due to the large number of databases available for many individual plant species. In this sense, bioinformatics together with next generation sequencing and 'omics' approaches, can provide tools for plant breeding and the genetic engineering of plants. In addition, these technologies enable a better understanding of the processes and mechanisms that can lead to plants with increased tolerance to different abiotic stress conditions and resistance to pathogen attack, as well as the development of crop varieties with improved nutritional quality of seeds and fruits.

Mouse Genome Informatics (MGI): reflecting on 25 years.

From its inception in 1989, the mission of the Mouse Genome Informatics (MGI) resource remains to integrate genetic, genomic, and biological data about the laboratory mouse to facilitate the study of human health and disease. This mission is ever more feasible as the revolution in genetics knowledge, the ability to sequence genomes, and the ability to specifically manipulate mammalian genomes are now at our fingertips. Through major paradigm shifts in biological research and computer technologies, MGI has adapted and evolved to become an integral part of the larger global bioinformatics infrastructure and honed its ability to provide authoritative reference datasets used and incorporated by many other established bioinformatics resources. Here, we review some of the major changes in research approaches over that last quarter century, how these changes are reflected in the MGI resource you use today, and what may be around the next corner.

MyLabStocks: a web-application to manage molecular biology materials.

Laboratory stocks are the hardware of research. They must be stored and managed with mimimum loss of material and information. Plasmids, oligonucleotides and strains are regularly exchanged between collaborators within and between laboratories. Managing and sharing information about every item is crucial for retrieval of reagents, for planning experiments and for reproducing past experimental results. We have developed a web-based application to manage stocks commonly used in a molecular biology laboratory. Its functionalities include user-defined privileges, visualization of plasmid maps directly from their sequence and the capacity to search items from fields of annotation or directly from a query sequence using BLAST. It is designed to handle records of plasmids, oligonucleotides, yeast strains, antibodies, pipettes and notebooks. Based on PHP/MySQL, it can easily be extended to handle other types of stocks and it can be installed on any server architecture. MyLabStocks is freely available from: https://forge.cbp.ens-lyon.fr/redmine/projects/mylabstocks under an open source licence.

The NIH Roadmap Epigenomics Program data resource.

The NIH Roadmap Reference Epigenome Mapping Consortium is developing a community resource of genome-wide epigenetic maps in a broad range of human primary cells and tissues. There are large amounts of data already available, and a number of different options for viewing and analyzing the data. This report will describe key features of the websites where users will find data, protocols and analysis tools developed by the consortium, and provide a perspective on how this unique resource will facilitate and inform human disease research, both immediately and in the future.

Introduction to section III: resources for CFTR research.

This section of Cystic Fibrosis Protocols and Diagnosis focuses on resources available to facilitate the activities of the research community in the field of cystic fibrosis (CF). An overview of the protocols and resources described in subsequent chapters of this book section is provided, as well as how they can accelerate research in this area.

DBCAT: database of CpG islands and analytical tools for identifying comprehensive methylation profiles in cancer cells.

DBCAT (database of CpG islands and analytical tools, http://dbcat.cgm.ntu.edu.tw/ ), developed to characterize comprehensive DNA methylation profiles in human cancers, is a web-based application and methylation database containing several convenient tools for investigating epigenetic regulation in human diseases. To our knowledge, DBCAT is the first online methylation analytical tool, and is composed of three parts: a CpG island finder, a genome query browser, and a tool for analyzing methylation microarray data. The analytical tools can quickly identify genes with methylated regions from microarray data, compare the methylation status changes between different arrays, and provide functional analysis in addition to colocalizing transcription factor binding sites.

Online resources for the molecular contextualization of disease.

Searching online resources can provide medical researchers with an efficient means of gathering existing knowledge on the molecular causes of disease. The researcher may choose to explore the following areas, e.g., genetic mutations associated with the disease, function and cellular sub-localization of the associated protein(s) and their protein interaction partners. Using a small case study, examining the disease retinoblastoma, this chapter guides the reader through the relevant information contained within relevant databases. It is shown that the integration of online biological knowledge with genomic and proteomic experimental data provides insights into the understanding of diseases in their molecular context.

Web-based resources for clinical bioinformatics.

In the post-Human Genome Project era, awareness of the resources available through the internet is essential to both molecular biologists and clinicians. An overview of the main databases and analytical tools described in this chapter is important to understand the principles upon which hypotheses are generated, experiments are based and conclusions reached. Similarly, an introduction to the terminology of these resources often facilitates their use and adoption into practice. This chapter covers database resources such as NCBI/ Entrez, Ensembl and UCSC as well as analytical tools for sequence alignment, promoter analysis and molecular interactions.

Wheat EST resources for functional genomics of abiotic stress.

BACKGROUND: Wheat is an excellent species to study freezing tolerance and other abiotic stresses. However, the sequence of the wheat genome has not been completely characterized due to its complexity and large size. To circumvent this obstacle and identify genes involved in cold acclimation and associated stresses, a large scale EST sequencing approach was undertaken by the Functional Genomics of Abiotic Stress (FGAS) project. RESULTS: We generated 73,521 quality-filtered ESTs from eleven cDNA libraries constructed from wheat plants exposed to various abiotic stresses and at different developmental stages. In addition, 196,041 ESTs for which tracefiles were available from the National Science Foundation wheat EST sequencing program and DuPont were also quality-filtered and used in the analysis. Clustering of the combined ESTs with d2_cluster and TGICL yielded a few large clusters containing several thousand ESTs that were refractory to routine clustering techniques. To resolve this problem, the sequence proximity and "bridges" were identified by an e-value distance graph to manually break clusters into smaller groups. Assembly of the resolved ESTs generated a 75,488 unique sequence set (31,580 contigs and 43,908 singletons/singlets). Digital expression analyses indicated that the FGAS dataset is enriched in stress-regulated genes compared to the other public datasets. Over 43% of the unique sequence set was annotated and classified into functional categories according to Gene Ontology. CONCLUSION: We have annotated 29,556 different sequences, an almost 5-fold increase in annotated sequences compared to the available wheat public databases. Digital expression analysis combined with gene annotation helped in the identification of several pathways associated with abiotic stress. The genomic resources and knowledge developed by this project will contribute to a better understanding of the different mechanisms that govern stress tolerance in wheat and other cereals.

[Structure, use, and risks of biomaterial repositories of embryonal tumors]. / Biomaterialbanken für embryonale Tumoren: Struktur, Nutzen und Risiken.

Availability of statistically sufficient numbers of tumor samples and other biomaterials in high quality together with corresponding clinical data is crucial for biomedical research. Tumor repositories from individual scientists are mostly not sufficient to satisfy these criteria, especially since pediatric tumors are rare. In 2000 three centralized tumor repositories (neuroblastoma in Cologne, nephroblastoma in Würzburg, hepatoblastoma, brain tumors in Bonn) have been established by the "German Competence Net Pediatric Oncology und Hematology". The aim was to collect biomaterial including tumor samples, normal tissue, and blood in high quality for research and diagnostic purposes at a central institution. Informed consent of the parents or patients is a prerequisite for scientific use of the samples and is requested by the therapy trial. The samples are collected according to accepted standards and shipped in the specially designed Tumorbox. The tumor repository organizes the distribution of the samples to the cooperating diagnostic laboratories. The number of collected tumor samples has increased over the years. In 2000, samples from 200 patients were collected while the patient number increased to 321 in 2005. Over the years the tumor repositories collected more than 7,150 samples (fresh frozen tumor, fresh frozen normal tissue, and blood). Through links with clinical trial databases the samples can be connected with clinical data. 12 of 14 applications for tumor material to be used in specific scientific projects have been approved by an independent supervisory board. The establishment of central tumor repositories represents a major step for biomedical research activities and quality control in pediatric oncology.