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The ARE-mRNA database (ARED) reveals that ARE-mRNAs encode a wide repertoire of functionally diverse proteins belonging to different biological processes and important in several disease states. Cluster analysis was performed using the ARE sequences to demonstrate potential relationships between the type and number of ARE motifs, and the functional characteristics of the proteins. Sponsors: This database is supported by The King Faisal Specialist Hospital and Research Center. Keywords: mRNA, Database, Au-rich, Element, Biological, Disease, State, Cluster, Analysis, Motif, Functional, Characterstic, Protein,
Proper citation: AU-RICH ELEMENT-CONTAINING mRNA DATABASE (RRID:SCR_012978) Copy
http://bioinformatics.psb.ugent.be/webtools/rRNA/
Database compiles all complete or nearly complete SSU (small subunit) and LSU (large subunit) ribosomal RNA sequences. Sequences are provided in aligned format. Alignment takes into account secondary structure information derived by comparative sequence analysis of thousands of sequences. Additional information such as literature references, taxonomy, secondary structure modles and nucleotide variability maps, is also available.
Proper citation: European ribosomal RNA database (RRID:SCR_012735) Copy
http://swissmodel.expasy.org/repository
Database of annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL.
Proper citation: SWISS-MODEL Repository (RRID:SCR_013032) Copy
http://www.replicationdomain.org
ReplicationDomain is an online database resource for storing, sharing and visualizing DNA replication timing and transcription data, as well as other numerical epigenetic data types. Data is typically obtained from DNA microarrays or DNA sequencing. Our site has a user registration system that allows registered users to upload their own data sets. While non-registered users may freely view and download public data sets, registered users may upload their own data sets and view them privately, share them with other registered users, or make published data sets publicly available. In addition we have implemented additional mechanisms that allow users to restrict sharing of data sets to a user designated group of registered users. Further details on the database usage are in the User Guide Page, while data set details are in the Documentation Page. Replication timing data were obtained by hybridizing early and late replication intermediates to Nimblegen oligonucleotide arrays, as described in Hiratani et al [PLoS Biology (2008) 6: e245]. Briefly, replication intermediates are prepared from cells that are first pulse-labeled with BrdU and then sorted into early and late stages of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted (nascent) replication intermediates that were synthesized either early or late during S-phase. After unbiased amplification of recovered DNA, the samples are differentially labeled with Cy3 and Cy5 and hybridized to Nimblegen CGH arrays containing one oligonucleotide probe every 5.8 kb across the mouse genome (Nimblegen, 2006-07-26_MM8_WG_CGH). Raw data from two independent biological replicates in which the early and late replicating DNA were labeled reciprocally with Cy3 and Cy 5 (dye switch) are loess-normalized and scaled to have the same median-absolute deviation using the limma package (R/Bioconductor) and then averaged. Finally, the data are smoothed with a weighted moving average (loess: local polynomial smoothing).
Proper citation: Replication Domain (RRID:SCR_012941) Copy
Database access to information services, educational opportunities, and resources in print and electronic format to faculty, students, and researchers in the schools of the health sciences.
Proper citation: University of Pittsburgh, Health Sciences Library System (RRID:SCR_011975) Copy
http://omabrowser.org/cgi-bin/gateway.pl
A database that identifies orthologs among publicly available, complete genomes. It offers a comprehensive search and numerous display options for 4.7 million proteins from 1000 species. The main features are the orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed.
Proper citation: OMA Browser (RRID:SCR_011978) Copy
It serves as a gateway for clinicians, families and researchers who have an interest in or are affected by Batten disease or who wish to find out more. Information can be accessed via four main routes - Clinicians, Families, Researchers, Professional Support. The Clinical route describes Batten disease and includes details on diagnosis and diagnostic services. The Family route also describes Batten disease and lists support groups. The Research route includes the NCL Mutation Database, established in 1998, and other useful information. The Professional Support route includes details of coordinated initiatives to support those affected by Batten disease. A fifth route, Research Consortia, serves to meet research needs and currently act as a focus for collaborative efforts to identify the remaining human and animal NCL genes and facilitate functional approaches. An additional route, Creativity, has been launched to display creative items from families with Batten disease, and to celebrate life, in both its fullness and fragility.
Proper citation: NCL Resource - A gateway for Batten disease (RRID:SCR_012826) Copy
http://affymetrix.arabidopsis.info
The NASC International Affymetrix Service is a commercial website that provides transcripomics services for a fee. This data is available for any available species, any consortium chip, and any kind of experiment. The website also provides open source and free Xspecies software and techniques that can be (examples) used to perform GeneChip transcriptomics experiments on species for which no current Affymetrix chip exists.
Proper citation: NASCs International Affymetrix Service (RRID:SCR_012825) Copy
http://www.phac-aspc.gc.ca/msds-ftss/
Material Safety Data Sheets for chemical products are available to laboratory workers for most chemicals and reagents. However because many laboratory workers, whether in research, public health, teaching, etc., are exposed to not only chemicals but infectious substances as well, there was a large gap in the readily available safety literature for employees. These MSDS are produced for personnel working in the life sciences as quick safety reference material relating to infectious micro-organisms. The MSDS are organized to contain health hazard information such as infectious dose, viability (including decontamination), medical information, laboratory hazard, recommended precautions, handling information and spill procedures. The intent of these documents is to provide a safety resource for laboratory personnel working with these infectious substances. Because these workers are usually working in a scientific setting and are potentially exposed to much higher concentrations of these human pathogens than the general public, the terminology in these MSDS is technical and detailed, containing information that is relevant specifically to the laboratory setting. It is hoped along with good laboratory practices, these MSDS will help provide a safer, healthier environment for everyone working with infectious substances. The MSDS is ran by the Public Health Agency of Canada. The Public Health Agency of Canada (PHAC) is the main Government of Canada agency responsible for public health in Canada. PHACs primary goal is to strengthen Canadas capacity to protect and improve the health of Canadians and to help reduce pressures on the health-care system. To do this, the Agency is working to build an effective public health system that enables Canadians to achieve better health and well-being in their daily lives by promoting good health, helping prevent and control chronic diseases and injury, and protecting Canadians from infectious diseases and other threats to their health. PHAC is also committed to reducing health disparities between the most advantaged and disadvantaged Canadians. Because public health is a shared responsibility, the Public Health Agency of Canada works in close collaboration with all levels of government (provincial, territorial and municipal) to build on each others skills and strengths. The Agency also works closely with non-government organizations, including civil society and business, and other countries and international organizations like the World Health Organization (WHO) to share knowledge, expertise and experiences.
Proper citation: Material Safety Data Sheets for Infectious Substances of Canada (RRID:SCR_013003) Copy
Database of orthologous protein coding genes across vertebrates, arthropods, fungi, basal metazoans, and bacteria.
Proper citation: OrthoDB (RRID:SCR_011980) Copy
A database of ingredients in brand-name household products linked to health information from Material Safety Data Sheets (MSDS) provided by manufacturers. The database is designed to help answer the following typical questions: *What are the chemical ingredients and their percentage in specific brands? *Which products contain specific chemical ingredients? *Who manufactures a specific brand? How do I contact this manufacturer? *What are the acute and chronic effects of chemical ingredients in a specific brand? *What other information is available about chemicals in the toxicology-related databases of the National Library of Medicine? NLM and its Contractor (the Database Providers) do not test products nor investigate to determine if this information is complete or accurate.
Proper citation: Household Products Database (RRID:SCR_013006) Copy
THIS RESOURCE IS NO LONGER IN SERVICE,documented on August 16, 2019. Fugu genome is among the smallest vertebrate genomes and has proved to be a valuable reference genome for identifying genes and other functional elements such as regulatory elements in the human and other vertebrate genomes, and for understanding the structure and evolution of vertebrate genomes. This site presents version 4 of the Fugu genome, released in October 2004 by the International Fugu Genome Consortium. Fugu rubripes has a very compact genome, with less than 15 consisting of dispersed repetitive sequence, which makes it ideal for gene discovery. A draft sequence of the fugu genome was determined by the International Fugu Genome Consortium in 2002 using the ''whole-genome shotgun'' sequencing strategy. Fugu is the second vertebrate genome to be sequenced, the first being the human genome. This webpage presents the annotation made on the fourth assembly by the IMCB team using the Ensembl annotation pipeline. We are continuing with the gap filling work and linking of the scaffolds to obtain super-contigs.
Proper citation: Fugu Genome Project (RRID:SCR_013014) Copy
THIS RESOURCE IS NO LONGER IN SEVICE. Documented on August 19,2019.It hosts records of currently available essential genes among a wide range of organisms. For prokaryotes, DEG contains essential genes in more than 10 bacteria, such as E. coli, B. subtilis, H. pylori, S. pneumoniae, M. genitalium and H. influenzae, whereas for eukaryotes, DEG contains those in yeast, humans, mice, worms, fruit flies, zebra fish and the plant A. thaliana. Users can Blast query sequences against DEG, and can also search for essential genes by their functions and names. Essential gene products comprise excellent targets for antibacterial drugs. Essential genes in a bacterium constitute a minimal genome, forming a set of functional modules, which play key roles in the emerging field, synthetic biology.
Proper citation: DEG - Database of Essential Genes (RRID:SCR_012929) Copy
https://genome-cancer.ucsc.edu/
A suite of web-based tools to visualize, integrate and analyze cancer genomics and its associated clinical data. It is possible to display your own clinical data within one of their datasets.
Proper citation: UCSC Cancer Genomics Browser (RRID:SCR_011796) Copy
http://www.unil.ch/comparativegenometrics/
The Comparative Genometrics website displays for sequenced genomes, three different genometric analyses: the DNA walk and the GC and TA skews during the initial phase. Although primarily focused on prokaryotic chromosomes, the CG website posts genometric information on paradigm plasmids, phages, viruses, and organelles. The genometric analyses are available via phylogenetic tree or alphabetical list. It also offers small genome information, for mitochondria, chloroplasts, viruses, bacteriophages, and plasmids.
Proper citation: Comparative Genometrics (RRID:SCR_012920) Copy
A genomics database project is an academic research program to identify molecular features of cancers that predict response to anti-cancer drugs.
Proper citation: Genomics of Drug Sensitivity in Cancer (RRID:SCR_011956) Copy
Cybase is dedicated to the study of a fascinating new class of proteins that possess a cyclic backbone in which the N and C termini have been joined with a conventional amide bond. These recently characterized molecules have now been found in organisms from all kingdoms of life and given the current rate of discovery the number of sequences could soon number in the hundreds. Research in our lab is aimed at further characterizing cyclic proteins and adapting them for commercial and medicinal use. In particular we work on a class of cyclic protein named the cyclotides. These proteins are found in the plants of the Rubiaceae and Violaceae and our specific goals include: determining the role that cyclotides play in plants, discovering the mechanism of action of the wide range of biological activities displayed by the cyclotides (including anti-HIV, anti-bacterial and insecticidal activity), characterising the genetics of the cyclotides and further discovery of novel cyclotides.
Proper citation: Cybase (RRID:SCR_012925) Copy
http://cbbiweb.uthscsa.edu/KMethylomes/
Datbase and web-based system for visualization and analysis of genome-wide methylation data of human cancers.
Proper citation: Cancer Methylome System (RRID:SCR_012013) Copy
http://54.235.254.95/histonehits/
A database for histone mutations and their phenotypes.
Proper citation: Histone Systematic Mutation Database (RRID:SCR_012015) Copy
A database of CpG islands and analytical tools for identifying comprehensive methylation profiles in cancer cells.
Proper citation: DBCAT (RRID:SCR_012014) Copy
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