Tools   Select Another Resource Report Type

http://www.biorag.org/index.php

Bio Resource for array genes is a free online resource for easy access to collective and integrated information from various public biological resources for human, mouse, rat, fly and c. elegans genes. The resource includes information about the genes that are represented in Unigene clusters. This resource provides interactive tools to selectively view, analyze and interpret gene expression patterns against the background of gene and protein functional information. Different query options are provided to mine the biological relationships represented in the underlying database. Search button will take you to the list of query tools available. This Bio resource is a platform designed as an online resource to assist researchers in analyzing results of microarray experiments and developing a biological interpretation of the results. This site is mainly to interpret the unique gene expression patterns found as biological changes that can lead to new diagnostic procedures and drug targets. This interactive site allows users to selectively view a variety of information about gene functions that is stored in an underlying database. Although there are other online resources that provide a comprehensive annotation and summary of genes, this resource differs from these by further enabling researchers to mine biological relationships amongst the genes captured in the database using new query tools. Thus providing a unique way of interpreting the microarray data results based on the knowledge provided for the cellular roles of genes and proteins. A total of six different query tools are provided and each offer different search features, analysis options and different forms of display and visualization of data. The data is collected in relational database from public resources: Unigene, Locus link, OMIM, NCBI dbEST, protein domains from NCBI CDD, Gene Ontology, Pathways (Kegg, Genmapp and Biocarta) and BIND (Protein interactions). Data is dynamically collected and compiled twice a week from public databases. Search options offer capability to organize and cluster genes based on their Interactions in biological pathways, their association with Gene Ontology terms, Tissue/organ specific expression or any other user-chosen functional grouping of genes. A color coding scheme is used to highlight differential gene expression patterns against a background of gene functional information. Concept hierarchies (Anatomy and Diseases) of MESH (Medical Subject Heading) terms are used to organize and display the data related to Tissue specific expression and Diseases. Sponsors: BioRag database is maintained by the Bioinformatics group at Arizona Cancer Center. The material presented here is compiled from different public databases. BioRag is hosted by the Biotechnology Computing Facility of the University of Arizona. 2002,2003 University of Arizona.

Proper citation: Bio Resource for Array Genes Database (RRID:SCR_000748) Copy   

•   Source: SciCrunch Registry

https://wiki.nci.nih.gov/display/cageneindex/Cancer+Gene+Index+End+User+Documentation

THIS RESOURCE IS NO LONGER IN SERVICE, documented on November 17, 2016. A database of genes that have been experimentally associated with human cancer diseases and/or pharmacological compounds, the evidence of these associations, and relevant annotations on the data.

Proper citation: Cancer Gene Index (RRID:SCR_001117) Copy   

•   Source: SciCrunch Registry

http://gemma-doc.chibi.ubc.ca/neurocarta/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Neurocarta is a knowledgebase that consolidates information on genes and phenotypes across multiple resources and allows tracking and exploring of the associations. The system enables automatic and manual curation of evidence supporting each association, as well as user-enabled entry of their own annotations. Phenotypes are recorded using controlled vocabularies such as the Disease Ontology to facilitate computational inference and linking to external data sources. The gene-to-phenotype associations are filtered by stringent criteria to focus on the annotations most likely to be relevant. Neurocarta is constantly growing and currently holds more than 30,000 lines of evidence linking over 6,800 genes to 1,800 different phenotypes. Neurocarta is a one-stop shop for researchers looking for candidate genes for any disorder of interest. In Neurocarta, they can review the evidence linking genes to phenotypes and filter out the evidence they're not interested in. In addition, researchers can enter their own annotations from their experiments and analyze them in the context of existing public annotations. Neurocarta's in-depth annotation of neurodevelopmental disorders makes it a unique resource for neuroscientists working on brain development.

Proper citation: Neurocarta (RRID:SCR_000617) Copy   

•   Source: SciCrunch Registry

http://aclame.ulb.ac.be/

A database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons. In addition to provide information on the full genomes and genetic entities, it aims at building a comprehensive classification of the functional modules of MGE's at the protein, gene, and higher levels. Prophinder, a tool dedicated to the detection of prophages in sequenced bacterial genomes, is available on ACLAME.

Proper citation: A Classification of Mobile genetic Elements (RRID:SCR_001694) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2039752/

It aims to help researchers to utilize information more efficiently from the published association data. This database is freely accessible only for academic users under the GNU GPL PADB indexes the sentences containing "associat*" or "case-control*" or "cohort*" or "meta-analysis" or "systematic review" or "odds ratio*" or "hazard ratio*" or "risk ratio*" or "relative risk*" from PubMed abstracts and automatically extracts the numeric values of odds ratios, hazard ratios, risk ratios and relative risks data when available. PADB automatically identifies HUGO official symbols of human genes using NCBI Entrez Gene data, and each gene is linked to the UCSC genome browser and International HapMap Project database. Furthermore, molecular pathways listed in BioCarta or KEGG databases can be accessed through the link using CGAP gene annotation data. Also, each record in PADB is linked to GAD or HPLD if it is available from those databases. Currently, (Last Update of Database Contents : Dec. 20, 2006) PADB indexes more than 1,500,000 abstracts including about 190,000 risk values ranging from 0.00001 to 4878.9 and 3,442 human genes related to 461 molecular pathways. Sponsors: This work was supported by the Brain Korea 21 Project for Medical Science, Yonsei University, Seoul, Korea and a faculty research grant of Yonsei University College of Medicine for 2006, Seoul, Korea.

Proper citation: Published Association Database (RRID:SCR_001841) Copy   

•   Source: SciCrunch Registry

http://5sage.gi.k.u-tokyo.ac.jp/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on October 30, 2012. A database that displays the observed frequencies of individual 5' end SAGE tags and previously unknown transcription start sites in the promoter regions, introns and intergenic regions of known genes. 5'SAGE will be useful for analyzing promoter regions and start site variation in different tissues, and is freely available.

Proper citation: 5 prime end Serial Analysis of Gene Expression Database (RRID:SCR_001680) Copy   

•   Source: SciCrunch Registry

http://spliceosomedb.ucsc.edu/

A database of proteins and RNAs that have been identified in various purified splicing complexes. Various names, orthologs and gene identifiers of spliceosome proteins have been cataloged to navigate the complex nomenclature of spliceosome proteins. Links to gene and protein records are also provided for the spliceosome components in other databases. To navigate spliceosome assembly dynamics, tools were created to compare the association of spliceosome proteins with complexes that form at specific stages of spliceosome assembly based on a compendium of mass spectrometry experiments that identified proteins in purified splicing complexes.

Proper citation: Spliceosome Database (RRID:SCR_002097) Copy   

•   Source: SciCrunch Registry

http://www.credrivermice.org/expression/

Database of microarray analysis of twelve major classes of fluorescent labeled neurons within the adult mouse forebrain that provide the first comprehensive view of gene expression differences. The publicly available datasets demonstrate a profound molecular heterogeneity among neuronal subtypes, represented disproportionately by gene paralogs, and begin to reveal the genetic programs underlying the fundamental divisions between neuronal classes including that between glutamatergic and GABAergic neurons. Five of the 12 populations were chosen from cingulate cortex and included several subtypes of GABAergic interneurons and pyramidal neurons. The remaining seven were derived from the somatosensory cortex, hippocampus, amygdala and thalamus. Using these expression profiles, they were able to construct a taxonomic tree that reflected the expected major relationships between these populations, such as the distinction between cortical interneurons and projection neurons. The taxonomic tree indicated highly heterogeneous gene expression even within a single region. This dataset should be useful for the classification of unknown neuronal subtypes, the investigation of specifically expressed genes and the genetic manipulation of specific neuronal circuit elements. Datasets: * Full: Here you can query gene expression results for the neuronal populations * Strain: Here you can query the same expression results accessed under the full checkbox, with one additional population (CT6-CG2) included as a control for the effects of mouse strain. This population is identical to CT6-CG (YFPH) except the neurons were derived from wild-type mice of three distinct strains: G42, G30, and GIN. * Arlotta: Here you can query the same expression results accessed under the full checkbox, with nine additional populations from the dataset of Arlotta et al., 2005. These populations were purified by FACS after retrograde labeling with fluorescent microspheres. Populations are designated by the prefix ACS for corticospinal neurons, ACC for corticocallosal neurons and ACT for corticotectal neurons, followed by the suffix E18 for gestational age 18 embryos, or P3, P6 and P14 for postnatal day 3, 6 and 14 pups. For each successful gene query the following information is returned: # Signal level line plot: Signal level is plotted on Y-axis (log base 2) for each sample. Samples include the thirty six representing the twelve populations profiled in Sugino et al. In addition, six samples from homogenized (=dissociated and but not sorted) cortex are included representing two different strains: G42-HO is homogenate from strain G42, GIN-HO is homogenate from stain GIN. # Signal level raster plots: Signal level is represented by color (dark red is low, bright red is high) for all samples. Color scale is set to match minimum (dark red) and maximum (bright yellow) signal levels within the displayed set of probe sets. # Scaled signal level raster plots: Same as 2) except color scale is adjusted separately for each gene according to its maximum and minimum signal level. # Table: Basic information about the returned probe sets: * Affymetrix affyid of probe set * NCBI gene symbol, NCBI gene name * NCBI geneID * P-value score from ANOVA for each gene is also given if available (_anv column). P-value represents the probability that there is no difference in the expression across cell types.

Proper citation: Mouse Neuronal Expression Database (RRID:SCR_002043) Copy   

•   Source: SciCrunch Registry

http://gfpweb.aecom.yu.edu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Database of expression patterns of C. elegans promoter::GFP constructs. A text description of the observed pattern is provided, indicating the stage(s) and tissue(s) in which GFP is expressed. Also available for some strains are the corresponding 2D and 3D images. Investigators may browse the entire list, search by gene name, tissue, stage, and pattern. Search results may be downloaded in .csv and .txt formats. All of the strains in the expression pattern database are displayed in the browse page. The records are organized by gene; information such as locus name, genomic location (WormBase), the presence of images and videos, and the actual expression pattern are shown in a tabular format.

Proper citation: Expression Patterns for C. elegans promoter GFP fusions (RRID:SCR_001619) Copy   

•   Source: SciCrunch Registry

https://cell-innovation.nig.ac.jp/GNP/index_e.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Integrated database of experiment data generated by participating research institutes and public databases relating to: 1) transcription starting position of human genes in the human genome, 2) conjunction to control region on transcriptional factors and the human genome 3) protein-protein interaction with a central focus on transcription factors organized for use in genome level research. Gene Search is the function to search the integrated database by using keywords and public IDs. The search results can be visualized by: * Genome Explorer : provides annotation of landmarks (genes, transcription start sites, etc.) aligned in accordance with their genome locations. * PPI Network : provides a graphical view of protein-protein interaction (PPI) network from the experimental data generated under the project and the public datasets. * Expression Profile : clusters genes by expression pattern and display the result with heatmap. The function provides genes which have relation of coregulation and anti-coregulation. * Comparison Viewer : This function gives the view to compare the genomic regions between human and mouse homologous genes. The viewer shows the distribution of transcription start sites (TSS) as the way of separable by tissues or time points with other landmarks on genome region. * Gene Stock : This is the function to save the gene list that you are interested until the session is closed.

Proper citation: Genome Network Platform (RRID:SCR_001737) Copy   

•   Source: SciCrunch Registry

http://srv00.recas.ba.infn.it/ASPicDB/

A database to access reliable annotations of the alternative splicing pattern of human genes, obtained by ASPic algorithm (Castrignano et al. 2006), and to the functional annotation of predicted isoforms. Users may select and extract specific sets of data related to genes, transcripts and introns fulfilling a combination of user-defined criteria. Several tabular and graphical views of the results are presented, providing a comprehensive assessment of the functional implication of alternative splicing in the gene set under investigation. ASPicDB also includes information on tissue-specific splicing patterns of normal and cancer cells, based on available EST data and their library source annotation.

Proper citation: ASPicDB (RRID:SCR_002102) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/astd/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The Alternative Splicing and Transcript Diversity (ASTD) database project is creating a database of alternative splice events and transcripts of genes from human, mouse and rat. Full length transcripts are generated with the aim of understanding the mechanism of alternative splicing on a genome-wide scale. The current release of the human genome consists of: 16715 genes, 14101 have more than one splice isoform, with an average of 5.6 splice patterns per gene. 10831 transcripts are annotated as full length with a transcription start site and a poly(A). The current release of the mouse genome consists of: 16491 genes, 13028 have more than one splice isoform, with an average of 4 splice patterns per gene. 6011 transcripts are annotated as full length with a transcription start site and a poly(A). The current release of the rat genome consists of: 10424 genes, 6344 have more than one splice isoform, with an average of 2.6 splice patterns per gene. 1250 transcripts are annotated as full length with a transcription start site and a poly(A). Sponsors: The ASTD project at EBI is supported by a grant from the EC: Eurasnet Network of Excellence (LSHG-CT-2005-518238). It was also supported by the ASD grant from the EC (QLRT-CT-2001-02062) until November 2005 and the ATD grant from the EC (LSHG-CT-2003-503329) until May 2007.

Proper citation: The Alternatve Splicing Database (RRID:SCR_001883) Copy   

•   Source: SciCrunch Registry

http://mus.well.ox.ac.uk/gscandb/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database / display tool of genome scans, with a web interface that lets the user view the data. It does not perform any analyses - these must be done by other software, and the results uploaded into it. The basic features of GSCANDB are: * Parallel viewing of scans for multiple phenotypes. * Parallel analyses of the same scan data. * Genome-wide views of genome scans * Chromosomal region views, with zooming * Gene and SNP Annotation is shown at high zoom levels * Haplotype block structure viewing * The positions of known Trait Loci can be overlayed and queried. * Links to Ensembl, MGI, NCBI, UCSC and other genome data browsers. In GSCANDB, a genome scan has a wide definition, including not only the usual statistical genetic measures of association between genetic variation at a series of loci and variation in a phenotype, but any quantitative measure that varies along the genome. This includes for example competitive genome hybridization data and some kinds of gene expression measurements.

Proper citation: WTCHG Genome Scan Viewer (RRID:SCR_001635) Copy   

•   Source: SciCrunch Registry

https://brd.cancer.gov/

Database to find literature, established protocols, and best practices for collecting, storing, and handling biological samples. Its main purpose is to help researchers improve the quality and reproducibility of biospecimen-based medical and genetic research. Provides a library of validated protocols that laboratories use to properly process human biospecimens (like blood or tissue) without degrading their molecular integrity. Offers procedural guidelines (BEBPs) backed by scientific literature to protect samples from pre-analytical variables (e.g., storage temperature, time-to-freezing). Catalogs thousands of peer-reviewed articles focused on biospecimen science.

Proper citation: Biospecimen Research Database (RRID:SCR_001944) Copy   

•   Source: SciCrunch Registry

http://hertellab.mmg.uci.edu/cgi-bin/HEXEvent/HEXEventWEB.cgi

A free database that provides a list of human internal exons and reports all their known splice events based on EST information from the UCSC Genome Browser. This list can be restricted by the user to either only a specific region in the genome (by specifying the chromosome, the strand and the start and end position), to a whole chromosome or to a group of genes. Furthermore, exons can be filtered according to their splicing type (constitutive exons, cassette exons and exons with one or more alternative 3' and/or 5' splice sites). In order to extract a customized set of exons, the user-specific definitions of exon types can be fixed. The user needs to specify in what fraction of ESTs an exon is allowed to be alternatively spliced in order to still be called constitutive. Furthermore, the user can restrict the set of requested cassette exons by a certain upper inclusion level, which, for instance, is useful when only looking for low-inclusion exons.

Proper citation: HEXEvent (RRID:SCR_002106) Copy   

•   Source: SciCrunch Registry

http://www.bacteriome.org

Database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase. Presently the resource offers access to two types of network: * A network of functional interactions derived through exploiting available functional genomic datasets within a Bayesian framework * Two networks of experimentally derived protein-protein interactions - a "core" network consisting of interactions deemed to be of "high quality"; and an "extended" network which extends the "core" network by including interactions for which experimental evidence is less strong.

Proper citation: Bacteriome.org (RRID:SCR_001934) Copy   

•   Source: SciCrunch Registry

http://www.genepaint.org/MapP56_01.htm

Abbreviated reference atlas for the P56 mouse. All sections were nissl stained and digitized. To assist in the initial identification of sites of gene expression sites, maps of brains are available for E15.5, P7 and the adult. These maps depict the boundaries of major brain regions (cortex, thalamus, striatum, globus pallidus, ventral striatum, septum, basal forebrain, hippocampus, midbrain, pons, medulla, cerebellum) and also show the more prominent nerve tracts. Maps are most efficiently used by placing the window depicting the map of interest next to the gene expression image. Browsing is permitted between planes of sectioning thus allowing the most appropriate plane to be selected. Abbreviations are found in a list accessed by clicking the see abbreviation link at the bottom of each map. Alternatively, passing the cursor directly across the abbreviation on the map will result in the appearance of the appropriate term in the rider on top of the map panel. The annotation of anatomical details such as brain nuclei is currently beyond the scope of the GenePaint database. Hence, such information on the anatomy of the brain and embryo should be obtained from published atlases of mouse anatomy (Kaufman, 1995; Paxinos and Franklin, 2001; Jacobowitz and Abbott, 1997; Schambra et al., 1992; Valverde1998).

Proper citation: GenePaint P56 Mouse Atlas (RRID:SCR_002788) Copy   

•   Source: SciCrunch Registry

http://mouse.brain-map.org/static/atlas

Allen Mouse Brain Atlas includes full color, high resolution anatomic reference atlas accompanied by systematic, hierarchically organized taxonomy of mouse brain structures. Enables interactive online exploration of atlas and to provide deeper level of 3D annotation for informatics analysis and viewing in Brain Explorer 3D viewer.

Proper citation: Allen Mouse Brain Reference Atlas (RRID:SCR_002978) Copy   

•   Source: SciCrunch Registry

https://dgrc.bio.indiana.edu/Home

Serves Drosophila research community by collecting and distributing DNA clones and vectors; collecting and distributing Drosophila cell lines; developing and testing genomics technologies for use in Drosophila and assisting members of the research community in their use.

Proper citation: Drosophila Genomics Resource Center (RRID:SCR_002845) Copy   

•   Source: SciCrunch Registry

http://www.chickest.udel.edu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. A chicken EST Web site has been created to provide access to the data, and a set of unique sequences has been deposited with GenBank. This site contains over 40,000 EST sequences from the chicken cDNA libraries in the University of Delaware collection. Users can perform keyword searches, BLAST nucleotide sequences against our database, view clusters of similar or overlapping clones, and order clones. The cDNA and gene sequences of many mammalian cytokines and their receptors are known. However, corresponding information on avian cytokines is limited due to the lack of cross-species activity at the functional level or strong homology at the molecular level. To improve the efficiency of identifying cytokines and novel chicken genes, a directionally cloned cDNA library from T-cell-enriched activated chicken splenocytes was constructed, and the partial sequence of 5251 clones was obtained. Sequence clustering indicates that 2357 (42%) of the clones are present as a single copy, and 2961 are distinct clones, demonstrating the high level of complexity of this library. Comparisons of the sequence data with known DNA sequences in GenBank indicate that approximately 25% of the clones match known chicken genes, 39% have similarity to known genes in other species, and 11% had no match to any sequence in the database. Several previously uncharacterized chicken cytokines and their receptors were present in our library. This collection provides a useful database for cataloging genes expressed in T cells and a valuable resource for future investigations of gene expression in avian immunology. Therefore, the Chick EST database was created.

Proper citation: UD Chick EST Project (RRID:SCR_002236) Copy   

•   Source: SciCrunch Registry