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http://www.pdgene.org/

The PDGene database aims to provide a comprehensive, unbiased and regularly updated collection of genetic association studies performed on Parkinson's disease (PD) phenotypes. Eligible publications are identified following systematic searches of scientific literature databases, as well as the table of contents of journals in genetics, neurology, and psychiatry. The database can be searched either by a variety of dropdown menus or by specific keywords. For each gene, summary overviews are provided displaying key characteristics for each publication, including links to genotype distributions of the polymorphisms studied, random-effects allelic meta-analyses, and funnel plots for an assessment of publication bias. The PDGene database, developed by Massachusetts General Hospital/Harvard Medical School, The Michael J. Fox Foundation and the Alzheimer Research Forum, is supported by a grant from The Michael J. Fox Foundation in partnership with the Alzheimer Research Forum.

Proper citation: PDGene - A database for Parkinsons disease genetic association studies (RRID:SCR_006666) Copy   

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http://www.broadinstitute.org/annotation/tetraodon/

This database have been funded by the National Human Genome Research Institute (NHGRI) to produce shotgun sequence of the Tetraodon nigriviridis genome. The strategy involves Whole Genome Shotgun (WGS) sequencing, in which sequence from the entire genome is generated. Whole genome shotgun libraries were prepared from Tetraodon genomic DNA obtained from the laboratory of Jean Weissenbach at Genoscope. Additional sequence data of approximately 2.5X coverage of Tetraodon has also been generated by Genoscope in plasmid and BAC end reads. Broad and Genoscope intend to pool their data and generate whole genome assemblies. Tetraodon nigroviridis is a freshwater pufferfish of the order Tetraodontiformes and lives in the rivers and estuaries of Indonesia, Malaysia and India. This species is 20-30 million years distant from Fugu rubripes, a marine pufferfish from the same family. The gene repertoire of T. nigroviridis is very similar to that of other vertebrates. However, its relatively small genome of 385 Mb is eight times more compact than that of human, mostly because intergenic and intronic sequences are reduced in size compared to other vertebrate genomes. These genome characteristics along with the large evolutionary distance between bony fish and mammals make Tetraodon a compact vertebrate reference genome - a powerful tool for comparative genetics and for quick and reliable identification of human genes.

Proper citation: Tetraodon nigroviridis Database (RRID:SCR_007123) Copy   

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https://www.msu.edu/~brains/brains/human/brainstem/index.html

In this atlas you can view axial sections stained for cell bodies or for nerve fibers, at six rostro-caudal levels of the human brain stem. The creators of the site encourage the use of the data and it is available freely, but ask that they be contacted before any use. This site contains a series of axial sections stained for cell bodies or fibers at six rostro-caudal levels of the human brain stem. Sections are labeled for approximately 50 structures and are searchable through a web interface. For each level, a fiber and cell stain is provided. Labels may be turned on or off.

Proper citation: Atlas of the Human Brain Stem (RRID:SCR_007275) Copy   

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http://blog.aids.gov/

The AIDS.gov blog serves as a forum to foster public discussion on using new media effectively in response to HIV/AIDS, as well as HIV/AIDS research and policies. Along with weekly new media posts, the blog features other AIDS.gov-authored posts, guest posts, cross-posts from the White House Office of National AIDS Policy blog and the CDC Health Protection Perspectives blog, PEPFAR blog, and posts from the National Institute of Allergies and Infectious Diseases'' (NIAID) Division of AIDS. A large number of Federal agencies and programs are engaged in HIV/AIDS prevention, testing, treatment, policy, and research efforts in the United States. AIDS.gov serves as a gateway for information about these Federal efforts, with a focus on domestic programs. Since the launch of AIDS.gov on December 1, 2006 (World AIDS Day), there has been a growing interest in using new media tools to disseminate information about HIV/AIDS and improve prevention, testing, treatment, and research outcomes. AIDS.gov created this blog to address that interest, and has since expanded content areas to include key US Government HIV/AIDS-related research and policy posts, among other topics.

Proper citation: AIDS.gov Blog (RRID:SCR_007156) Copy   

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http://senselab.med.yale.edu/cellpropdb

A repository for data regarding membrane channels, receptor and neurotransmitters that are expressed in specific types of cells. The database is presently focused on neurons but will eventually include other cell types, such as glia, muscle, and gland cells. This resource is intended to: * Serve as a repository for data on gene products expressed in different brain regions * Support research on cellular properties in the nervous system * Provide a gateway for entering data into the cannonical neuron forms in NeuronDB * Identify receptors across neuron types to aid in drug development * Serve as a first step toward a functional genomics of nerve cells * Serve as a teaching aid

Proper citation: Cell Properties Database (RRID:SCR_007285) Copy   

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http://genenest.molgen.mpg.de/

GeneNest is a comprehensive visualization of gene indices of several organisms. The aim of GeneNest is to represent each gene by a single cluster of ESTs and/or mRNAs. Further subdivision of a cluster into contigs may be caused by alternative splicing, genomic sequences, or artifacts like chimeric sequences. Consensus sequence derived from GeneNest contigs are a basis for mapping genes onto the genome, and for analysis of splice isoforms. Organisms included are human, mouse, arabidopsis, zebrafish, drosophila, and sheep. human, mouse, arabidopsis, zebrafish, drosophila, sheep, EST, mRNA, alternative splicing, genomic sequences

Proper citation: GeneNest (RRID:SCR_007677) Copy   

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http://superfly.ucsd.edu/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 23, 2013. Homophila utilizes the sequence information of human disease genes from the NCBI OMIM (Online Mendelian Inheritance in Man) database in order to determine if sequence homologs of these genes exist in the current Drosophila sequence database (FlyBase). Sequences are compared using NCBI's BLAST program. The database is updated weekly and can be searched by human disease, gene name, OMIM number, title, subtitle and/or allelic variant descriptions.

Proper citation: Homophila (RRID:SCR_007717) Copy   

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http://zlab.bu.edu/HugeSearch/nph-HugeSearch.cgi

The Human Gene Expression Index (HuGE Index) aims to provide a comprehensive database to further our understanding of the expression of human genes in normal human tissues. mRNA expression levels of thousands of genes are obtained using high-density oligonucleotide array technology and used to create a public database. The website also provides interactive tools for researchers to query and visualize data over the Internet. To facilitate data analysis, genes are alsocross-referenced with their annotation in the LocusLink database at NCBI.

Proper citation: Human Gene Expression Index (RRID:SCR_007726) Copy   

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http://statgen.ncsu.edu/asg/

Alternative splicing essentially increases the diversity of the transcriptome and has important implications for physiology, development and the genesis of diseases. This resource uses a different approach to investigate alternative splicing (instead of the conventional case-by case fashion) and integrates all transcripts derived from a gene into a single splicing graph. ASG is a database of splicing graphs for human genes, using transcript information from various major sources (Ensembl, RefSeq, STACK, TIGR and UniGene). Each transcript corresponds to a path in the graph, and alternative splicing is displayed by bifurcations. This representation preserves the relationships between different splicing variants and allows us to investigate systematically all possible putative transcripts. Web interface allows users to display the splicing graphs, to interactively assemble transcripts and to access their sequences as well as neighboring genomic regions. ASG also provide for each gene, an exhaustive pre-computed catalog of putative transcriptsin total more than 1.2 million sequences. It has found that ~65 of the investigated genes show evidence for alternative splicing, and in 5 of the cases, a single gene might produce over 100 transcripts.

Proper citation: Alternate splicing gallery (RRID:SCR_008129) Copy   

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http://natural.salk.edu/CREB/

CREB target gene database that uses a multi-layered approach to predict, validate and characterize CREB target genes. For each gene, the database tries to provide the following information: 1. CREB binding sites on the promoters 2. Promoter occupancy by CREB 3. Gene activation by cAMP in tissues CREB seems to occupy a large number of promoters in the genome (up to ~5000 in human), and the profiles for CREB promoter occupancy are very similar in different human tissues. However, only a small proportion of CREB occupied genes are induced by cAMP in any cell type, possibly reflecting the requirement of additional regulatory partners that assist in recruitment of the transcriptional apparatus. To use the database, choose the species, select the table you want to search, leave field (''All'') and type in the gene you want to search. A table listing the search results will be returned, followed by the description of the table. If no search result is returned, try the official gene symbol or gene ID (locuslink number) from NCBI Entrez Gene to search. Sponsors: This work was supported by National Institutes of Health Grants GM RO1-037828 (to M.M.) and DK068655 (to R.A.Y.).

Proper citation: CRE Binding-protein Target Gene Database (RRID:SCR_008027) Copy   

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http://cmbi.bjmu.edu.cn/cmbidata/cgf/CGF_Database/cytokine.medic.kumamoto-u.ac.jp/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. A collection of cDNA, gene and protein records of cytokines deposited in public databases provides various information about the cytokine members of vertebrates in other databases including NCBI GenBank, Swiss-Prot, UniGene, TIGR (The Institute for Genomic Research) Gene Indices, Ensembl, Entrez Gene, Mouse Genome Informatics (MGI) and Rat Genome Database (RGD). It also provides orthologous relationship of cytokine members and includes novel members identified in the databases.

Proper citation: Cytokine Family Database (RRID:SCR_008134) Copy   

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http://blocks.fhcrc.org/blocks/codehop.html

This COnsensus-DEgenerate Hybrid Oligonucleotide Primer (CODEHOP) strategy has been implemented as a computer program that is accessible over the World-Wide Web and is directly linked from the BlockMaker multiple sequence alignment site for hybrid primer prediction beginning with a set of related protein sequences. This is a new primer design strategy for PCR amplification of unknown targets that are related to multiply-aligned protein sequences. Each primer consists of a short 3' degenerate core region and a longer 5' consensus clamp region. Only 3-4 highly conserved amino acid residues are necessary for design of the core, which is stabilized by the clamp during annealing to template molecules. During later rounds of amplification, the non-degenerate clamp permits stable annealing to product molecules. The researchers demonstrate the practical utility of this hybrid primer method by detection of diverse reverse transcriptase-like genes in a human genome, and by detection of C5 DNA methyltransferase homologs in various plant DNAs. In each case, amplified products were sufficiently pure to be cloned without gel fractionation. Sponsors: This work was supported in part by a grant from the M. J. Murdock Charitable Trust and by a grant from NIH. S. P. is a Howard Hughes Medical Institute Fellow of the Life Sciences Research Foundation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

Proper citation: COnsensus-DEgenerate Hybride Oligonucleotide Primers (RRID:SCR_002875) Copy   

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http://coot.embl.de/g2d/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database of candidate genes for mapped inherited human diseases. Candidate priorities are automatically established by a data mining algorithm that extracts putative genes in the chromosomal region where the disease is mapped, and evaluates their possible relation to the disease based on the phenotype of the disorder. Data analysis uses a scoring system developed for the possible functional relations of human genes to genetically inherited diseases that have been mapped onto chromosomal regions without assignment of a particular gene. Methodology can be divided in two parts: the association of genes to phenotypic features, and the identification of candidate genes on a chromosonal region by homology. This is an analysis of relations between phenotypic features and chemical objects, and from chemical objects to protein function terms, based on the whole MEDLINE and RefSeq databases.

Proper citation: Candidate Genes to Inherited Diseases (RRID:SCR_008190) Copy   

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http://neibank.nei.nih.gov

An integrated resource for genomics and bioinformatics in vision research including expressed sequence tag (EST) data and sequence-verified cDNA clones for multiple eye tissues of several species, web-based access to human eye-specific SAGE data through EyeSAGE, and comprehensive, annotated databases of known human eye disease genes and candidate disease gene loci. All expression- and disease-related data are integrated in EyeBrowse, an eye-centric genome browser. NEIBank provides a comprehensive overview of current knowledge of the transcriptional repertoires of eye tissues and their relation to pathology. The data can be interrogated in several ways. Specific gene names can be entered into the search window. Alternatively, regions of the genome can be displayed. For example, entering two STS markers separated by a semicolon (e.g. RH18061;RH80175) allows the display of the entire chromosomal region associated with the mapping of a specific disease locus. ESTs for each tissue can then be displayed to help in the selection of candidate genes. In addition, sequences can be entered into a BLAST search and rapidly aligned on the genome, again showing eye derived ESTs for the same region. To see the same region at the full UCSC site, cut and paste the location from the position window of the genome browser. EyeBrowse includes a custom track display SAGE data for human eye tissues derived from the EyeSAGE project. The track shows the normalized sum of SAGE tag counts from all published eye-related SAGE datasets centered on the position of each identifiable Unigene cluster. This indicates relative activity of each gene locus in eye. Clicking on the vertical count bar for a particular location will bring up a display listing gene details and linking to specific SAGE counts for each eye SAGE library and comparisons with normalized sums for neural and non-neural tissues. To view or alter settings for the EyeSAGE track on EyeBrowse, click on the vertical gray bar at the left of the display. Other custom tracks display known eye disease genes and mapped intervals for candidate loci for retinal disease, cataract, myopia and cornea disease. These link back to further information at NEIBank.

Proper citation: NEIBank (RRID:SCR_007294) Copy   

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https://hirnetwork.org

Network helps to organize and support collaborative research related to loss of functional beta cell mass in Type 1 Diabetes (T1D). Project consists of four independent research initiatives: Consortium on Beta Cell Death and Survival (CBDS), Consortium on Human Islet Biomimetics (CHIB), Consortium on Modeling Autoimmune Interactions (CMAI), Consortium on Targeting and Regeneration (CTAR), and Human Pancreas Analysis Program (HPAP).

Proper citation: Human Islet Research Network (HIRN) (RRID:SCR_014393) Copy   

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http://metscape.ncibi.org

A software program that allows users to visualize and interpret human metabolim and expression profiling data by providing users with a bioinformatics framework. Its features include bulding and analyzing networks of genes and compounds, identifying enriched pathways from expression profiling data, and visualizing changes in metabolite data.

Proper citation: Metscape (RRID:SCR_014687) Copy   

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http://www.semel.ucla.edu/creativity/

The purpose of this center is to study the molecular, cellular, systems and cognitive mechanisms that result in cognitive enhancements and explain unusual levels of performance in gifted individuals, including extraordinary creativity. Additionally, by understating the mechanisms responsible for enhancements in performance we may be better suited to intervene and reverse disease states that result in cognitive deficits. One of the key topics addressed by the Center is the biological basis of cognitive enhancements, a topic that can be studied in human subjects and animal models. In the past much of the focus in the brain sciences has been on the study of brain mechanisms that degrade cognitive performance (for example, on mutations or other lesions that cause cognitive deficits). The Tennenbaum Center for the Biology of Creativity at UCLA enables an interdisciplinary team of leading scientists to advance knowledge about the biological bases of creativity. Starting with a pilot project program, a series of investigations was launched, spanning disciplines from basic molecular biology to cognitive neuroscience. Because the concept of creativity is multifaceted, initial efforts targeted refinement of the component processes necessary to generate novel, useful cognitive products. The identified core cognitive processes: 1.) Novelty Generation the ability to flexibly and adaptively generate products that are unique; 2.) Working Memory and Declarative Memory the ability to maintain, and then use relevant information to guide goal-directed performance, along with the capacity to store and retrieve this information; and 3.) Response Inhibition the ability to suppress habitual plans and substitute alternate actions in line with changing problem-solving demands. To study the basic mechanisms underlying these complex brain functions we use translational strategies. Starting from foundational studies in basic neuroscience, we forged an interdisciplinary strategy that permits the most advanced techniques for genetic manipulation and basic neurobiological research to be applied in close collaboration with human studies that converge on the same core cognitive processes. Our integrated research program aims to reveal the genetic architecture and fundamental brain mechanisms underlying creative cognition. The work holds enormous promise for both enhancing healthy cognitive performance and designing new treatments for diverse cognitive disorders. Sponsors: The Tennenbaum Center for the Biology of Creativity was inspired by the vision and generosity of Michael Tennenbaum.

Proper citation: Tennenbaum Center for the Biology of Creativity (RRID:SCR_000668) Copy   

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http://crbs.ucsd.edu/

CRBS is a UCSD organized research unit (ORU) that exists to provide human resources, high technology equipment, and administrative services to researchers engaged in fundamental research on cell structure and function relationships in central nervous system processes, cardiovascular networking, and muscular contraction through multiple scales and modalities. CRBS scientists investigate these processes through invention, refinement, and deployment of sophisticated technologies, especially: - High-powered electron microscopes that reveal three-dimensional cell structures - State-of-the-art X-ray crystallography and magnetic resonance analysis that provide detail on protein structures at high-resolution - Laser-scanning and confocal light microscopes that reveal molecules tagged with fluorescent markers as they traffic within cells and pass transfer signals within and between cells - High performance computing and grid-based integration of distributed data CRBS facilitates an interdisciplinary infrastructure in which people from biology, medicine, chemistry, and physics can work with those from computer science and information technologies in collaborative research. Researchers share interests in the study of complex biological systems at many scales, from the structures of enzymes, proteins, and the body's chemical communications network at atomic and molecular levels, to an organism's physiology, strength, and support at cellular and tissue levels. The CRBS infrastructure integrates resources for high-performance computing, visualization, and database technologies, and the grid-integration of large amounts of archival storage data. The California Institute for Telecommunications and Information Technology (Cal-IT2) and the San Diego Supercomputer Center (SDSC) are collaborators in simulating the activity of biological systems, analyzing the results, and organizing the growing storehouse of biological information. CRBS is an entity evolving as research evolves. It forges interactions with biotechnology and biocomputing companies for technology transfer. Interaction, collaboration, and multiscale research produce new perspectives, reveal fruitful research topics, lead to the development of new technologies and drugs, and train a new generation of researchers in biological systems. Sponsors: CRBS is supported by the University of California at San Diego.

Proper citation: Center for Research in Biological Systems (RRID:SCR_002666) Copy   

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http://stemcells.nih.gov/research/registry/

A listing of human embryonic cell lines that are eligible for use in NIH funded research. Those lines that carry disease-specific mutations are noted as such under the line name. Total Eligible Lines = 200. The purpose of the Registry is to provide investigators with: # a unique NIH Code for each cell line that must be used when applying for NIH funding and # contact information to facilitate investigators' acquisition of stem cells. Before submitting a new grant application and supporting materials for consideration of a human embryonic stem cell line, scientists may wish to see what lines are already under consideration: * Human embryonic stem cell lines submitted to NIH that are being reviewed to determine if they may be used in NIH-supported research, http://grants.nih.gov/stem_cells/registry/pending.htm President George W. Bush required that the name of the registry be changed in his Executive Order #13435, issued on June 20, 2007. As a result of this Executive Order, the former National Institutes of Health Human Embryonic Stem Cell Registry will now be called the National Institutes of Health Human Pluripotent Stem Cell Registry. The registry will now include both human embryonic stem cells that were derived consistent with the President's policy of August 9, 2001 and human pluripotent stem cells derived from non-embryonic sources.

Proper citation: NIH Human Pluripotent Stem Cell Registry (RRID:SCR_003149) Copy   

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http://www.icn.ucl.ac.uk/motorcontrol/imaging/suit.htm

High-resolution atlas template of the human cerebellum and brainstem, based on the anatomy of 20 young healthy individuals. The atlas is spatially unbiased, i.e. the location of each structure is equal to the expected location of that structure across individuals in MNI space. At the same time, the new template preserves the anatomical detail of cerebellar structures through a nonlinear atlas-generation algorithm. By using automated nonlinear normalization methods, a more accurate intersubject-alignment than current whole-brain methods can be achieved. The toolbox allows you to: * Automatically isolate cerebellar structures from the cerebral cortex based on an anatomical image * Achieve accurate anatomical normalization of cerebellar structures * Normalize functional imaging data for fMRI group analysis * Normalize focal cerebellar lesions for lesion-symptom mapping * Use Voxel-based morphometry (VBM) to determine patterns of cerebellar degeneration or growth * Use a probabilisitc atlas in SUIT space to assign locations to different cerebellar lobuli in an unbiased and informed way * Automatically define ROIs for specific cerebellar lobuli and summarize function and anatomical data * Improve normalization of the deep cerebellar nuclei using an ROI-driven normalization. The suit-toolbox requires Matlab (Version 6.5 and higher) and SPM. The newest version only supports SPM8, although it likely runs under SPM2 or 5 as well. A standalone version for the suit-toolbox is not planned. Usage of the isolation or normalization functions, however, does not require that the analysis is conducted under SPM.

Proper citation: Spatially unbiased atlas template of the cerebellum and brainstem (RRID:SCR_004969) Copy   

•   Source: SciCrunch Registry