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http://kb.phenoscape.org/

Knowledgebase that uses ontologies to integrate phenotypic data from genetic studies of zebrafish with evolutionary variable phenotypes from the systematic literature of ostariophysan fishes. Users can explore the data by searching for anatomical terms, taxa, or gene names. The expert system enables the broad scale analysis of phenotypic variation across taxa and the co-analysis of these evolutionarily variable features with the phenotypic mutants of model organisms. The Knowledgebase currently contains 565,158 phenotype statements about 2,527 taxa, sourced from 57 publications, as well as 38,189 phenotype statements about 4,727 genes, retrieved from ZFIN. 2013-01-26.

Proper citation: Phenoscape Knowledgebase (RRID:SCR_002821) Copy   

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http://www.angis.org.au/Databases/Heart/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The aim of this locus-specific mutation database was to provide an online resource that contains summarized and updated information on familial hypertrophic cardiomyopathy (FHC)-associated mutations and related data, for researchers and clinicians. It also serves as a means of publishing previously unpublished data, which could be of value in understanding genotype/phenotype correlations. This database contains mutations in various genes known to cause familial hypertrophic cardiomyopathy, a genetic disorder associated with defects in the sarcomere [1]. Only gene symbols approved by HUGO are used and mutations are reported in accordance with guidelines recommended by the Mutation Database Initiative of HUGO and EBI.

Proper citation: Familial Hypertrophic Cardiomyopathy DNA Mutation Database (RRID:SCR_002346) Copy   

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http://dbtbs.hgc.jp/

Database of experimentally validated gene regulatory relations and the corresponding transcription factor binding sites upstream of Bacillus subtilis genes. The database allows the comparison of systematic experiments with individual experimental results in order to facilitate the elucidation of the complete B. subtilis gene regulatory network. The current version is constructed by surveying 947 references and contains the information of 120 binding factors and 1475 gene regulatory relations. For each promoter, all of its known cis-elements are listed according to their positions, while these cis-elements are aligned to illustrate the consensus sequence for each transcription factor. All probable transcription factors coded in the genome were classified using Pfam motifs. The DBTBS database was reorganized to show operons instead of individual genes as the building blocks of gene regulatory networks. It now contains 463 experimentally known operons, as well as their terminator sequences if identifiable. In addition, 517 transcriptional terminators were identified computationally. (De Hoon, M.J.L. et al., PLoS Comput. Biol. 1, e25 (2005)). A new section was added under "Motif conservation", which presents hexameric motifs found to be conserved to different extents between upstream intergenic regions of genus-specific subgroups of homologous proteins.

Proper citation: DBTBS (RRID:SCR_002345) Copy   

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http://eggnog.embl.de

A database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories). eggNOG's database currently counts 1.7 million orthologous groups in 3686 species, covering over 7.7 million proteins (built from 9.6 million proteins). (Jan 30, 2014)

Proper citation: eggNOG (RRID:SCR_002456) Copy   

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http://edas2.bioinf.fbb.msu.ru/

Databases of alternatively spliced genes with data on the alignment of proteins, mRNAs, and EST. It contains information on all exons and introns observed, as well as elementary alternatives formed from them. The database makes it possible to filter the output data by changing the cut-off threshold by the significance level. It contains splicing information on human, mouse, dog (not yet functional) and rat (not yet functional). For each database, users can search by keyword or by overall gene expression. They can also view genes based on chromosomal arrangement or other position in genome (exon, intron, acceptor site, donor site), functionality, position, conservation, and EST coverage. Also offered is an online Fisher test.

Proper citation: EDAS - EST-Derived Alternative Splicing Database (RRID:SCR_002449) Copy   

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http://cpdb.molgen.mpg.de

An integrative interaction database that integrates different types of functional interactions from heterogeneous interaction data resources. Physical protein interactions, metabolic and signaling reactions and gene regulatory interactions are integrated in a seamless functional association network that simultaneously describes multiple functional aspects of genes, proteins, complexes, metabolites, etc. With human, yeast and mouse complex functional interactions, it currently constitutes the most comprehensive publicly available interaction repository for these species. Different ways of utilizing these integrated interaction data, in particular with tools for visualization, analysis and interpretation of high-throughput expression data in the light of functional interactions and biological pathways is offered.

Proper citation: ConsensusPathDB (RRID:SCR_002231) Copy   

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http://fullmal.hgc.jp/index_ajax.html

FULL-malaria is a database for a full-length-enriched cDNA library from the human malaria parasite Plasmodium falciparum. Because of its medical importance, this organism is the first target for genome sequencing of a eukaryotic pathogen; the sequences of two of its 14 chromosomes have already been determined. However, for the full exploitation of this rapidly accumulating information, correct identification of the genes and study of their expression are essential. Using the oligo-capping method, this database has produced a full-length-enriched cDNA library from erythrocytic stage parasites and performed one-pass reading. The database consists of nucleotide sequences of 2490 random clones that include 390 (16%) known malaria genes according to BLASTN analysis of the nr-nt database in GenBank; these represent 98 genes, and the clones for 48 of these genes contain the complete protein-coding sequence (49%). On the other hand, comparisons with the complete chromosome 2 sequence revealed that 35 of 210 predicted genes are expressed, and in addition led to detection of three new gene candidates that were not previously known. In total, 19 of these 38 clones (50%) were full-length. From these observations, it is expected that the database contains approximately 1000 genes, including 500 full-length clones. It should be an invaluable resource for the development of vaccines and novel drugs. Full-malaria has been updated in at least three points. (i) 8934 sequences generated from the addition of new libraries added so that the database collection of 11,424 full-length cDNAs covers 1375 (25%) of the estimated number of the entire 5409 parasite genes. (ii) All of its full-length cDNAs and GenBank EST sequences were mapped to genomic sequences together with publicly available annotated genes and other predictions. This precisely determined the gene structures and positions of the transcriptional start sites, which are indispensable for the identification of the promoter regions. (iii) A total of 4257 cDNA sequences were newly generated from murine malaria parasites, Plasmodium yoelii yoelii. The genome/cDNA sequences were compared at both nucleotide and amino acid levels, with those of P.falciparum, and the sequence alignment for each gene is presented graphically. This part of the database serves as a versatile platform to elucidate the function(s) of malaria genes by a comparative genomic approach. It should also be noted that all of the cDNAs represented in this database are supported by physical cDNA clones, which are publicly and freely available, and should serve as indispensable resources to explore functional analyses of malaria genomes. Sponsors: This database has been constructed and maintained by a Grant-in-Aid for Publication of Scientific Research Results from the Japan Society for the Promotion of Science (JSPS). This work was also supported by a Special Coordination Funds for Promoting Science and Technology from the Science and Technology Agency of Japan (STA) and a Grant-in-Aid for Scientific Research on Priority Areas from the Ministry of Education, Science, Sports and Culture of Japan.

Proper citation: Full-Malaria: Malaria Full-Length cDNA Database (RRID:SCR_002348) Copy   

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http://rarge.gsc.riken.go.jp/dsmutant/

RIKEN Arabidopsis Transposon mutants is a series of mutant lines which have a Ds transposon in the genome of Arabidopsis thaliana Nssen ecotype (background by Fedoroff and Smith). This web page provides information on the mutants produced in our laboratory. Each mutant line is assigned by stipulated line codes (ex. 13-4480-1). We determined the flanking sequences of Ds insertion for each independent line. Transposon insertion sites of mutants were estimated by a BLASTN homology against the genome sequence database of Arabidopsis thaliana Columbia ecotype. The closest genes (predicted by AGI) to the transposon insertion sites were picked up. The results of the BLASTP homology search against the nr database of NCBI for the closest genes have been collected for keyword searches.

Proper citation: RIKEN Arabidopsis Transposon mutants (RRID:SCR_003230) Copy   

•   Source: SciCrunch Registry

http://genomequebec.mcgill.ca/PReMod

Database that describes more than 100,000 computational predicted transcriptional regulatory modules within the human genome. These modules represent the regulatory potential for 229 transcription factors families and are the first genome-wide / transcription factor-wide collection of predicted regulatory modules for the human genome. The algorithm used involves two steps: (i) Identification and scoring of putative transcription factor binding sites using 481 TRANSFAC 7.2 position weight matrices (PWMs) for vertebrate transcription factors. To this end, each non-coding position of the human genome was evaluated for its similarity to each PWM using a log-likelihood ratio score with a local GC-parameterized third-order Markov background model. Corresponding orthologous positions in mouse and rat genomes were evaluated similarly and a weighted average of the human, mouse, and rat log-likelihood scores at aligned positions (based on a Multiz (Blanchette et al. 2004) genome-wide alignment of these three species) was used to define the matrix score for each genomic position and each PWM. (ii) Detection of clustered putative binding sites. To assign a module score to a given region, the five transcription factors with the highest total scoring hits are identified, and a p-value is assigned to the total score observed of the top 1, 2, 3, 4, or 5 factors. The p-value computation takes into consideration the number of factors involved (1 to 5), their total binding site scores, and the length and GC content of the region under evaluation. Users can retrieve all information for a given region, a given PWM, a given gene and so on. Several options are given for textual output or visualization of the data.

Proper citation: PReMod (RRID:SCR_003403) Copy   

•   Source: SciCrunch Registry

http://www-bio3d-igbmc.u-strasbg.fr/ICDS/

Database of interrupted coding sequences detected by a similarity-based approach in complete prokaryotic genomes. The definition of each interrupted gene is provided as well as the ICDS genomic localization with the surrounding sequence. To facilitate the experimental characterization of ICDS, optimized primers are proposed for re-sequencing purposes. The database is accessible by BLAST search or by genome. 118 Genomes are available in the database.

Proper citation: Interrupted CoDing Sequence Database (RRID:SCR_002949) Copy   

•   Source: SciCrunch Registry

http://ratmap.gen.gu.se/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented September 2, 2016. Database for defining official rat gene symbols. It includes rat gene symbols from three major sources: the Rat Genome Database (RGD), Ensembl, and NCBI-Gene. All rat symbols are compared with official symbols from orthologous human genes as specified by the Human Gene Nomenclature Committee (HGNC). Based on the outcome of the comparisons, a rat gene symbol may be selected. Rat symbols that do not match a human ortholog undergo a strict procedure of comparisons between the different rat gene sources as well as with the Mouse Genome Database (MGD). For each rat gene this procedure results in an unambiguous gene designation. The designation is presented as a status level that accompanies every rat gene symbol suggested in the database. The status level describes both how a rat symbol was selected, and its validity. Rat Gene Symbol Tracker approves rat gene symbols by an automatic procedure. The rat genes are presented with links to RGD, Ensembl, NCBI Gene, MGI and HGNC. RGST ensures that each acclaimed rat gene symbol is unique and follows the guidelines given by the RGNC. To each symbol a status level associated, describing the gene naming process.

Proper citation: Rat Gene Symbol Tracker (RRID:SCR_003261) Copy   

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http://bioinfo.mbi.ucla.edu/ASAP/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on 8/12/13. Database to access and mine alternative splicing information coming from genomics and proteomics based on genome-wide analyses of alternative splicing in human (30 793 alternative splice relationships found) from detailed alignment of expressed sequences onto the genomic sequence. ASAP provides precise gene exon-intron structure, alternative splicing, tissue specificity of alternative splice forms, and protein isoform sequences resulting from alternative splicing. They developed an automated method for discovering human tissue-specific regulation of alternative splicing through a genome-wide analysis of expressed sequence tags (ESTs), which involves classifying human EST libraries according to tissue categories and Bayesian statistical analysis. They use the UniGene clusters of human Expressed Sequence Tags (ESTs) to identify splices. The UniGene EST's are clustered so that a single cluster roughly corresponds to a gene (or at least a part of a gene). A single EST represents a portion of a processed (already spliced) mRNA. A given cluster contains many ESTs, each representing an outcome of a series of splicing events. The ESTs in UniGene contain the different mRNA isoforms transcribed from an alternatively spliced gene. They are not predicting alternative splicing, but locating it based on EST analysis. The discovered splices are further analyzed to determine alternative splicing events. They have identified 6201 alternative splice relationships in human genes, through a genome-wide analysis of expressed sequence tags (ESTs). Starting with 2.1 million human mRNA and EST sequences, they mapped expressed sequences onto the draft human genome sequence and only accepted splices that obeyed the standard splice site consensus. After constructing a tissue list of 46 human tissues with 2 million human ESTs, they generated a database of novel human alternative splices that is four times larger than our previous report, and used Bayesian statistics to compare the relative abundance of every pair of alternative splices in these tissues. Using several statistical criteria for tissue specificity, they have identified 667 tissue-specific alternative splicing relationships and analyzed their distribution in human tissues. They have validated our results by comparison with independent studies. This genome-wide analysis of tissue specificity of alternative splicing will provide a useful resource to study the tissue-specific functions of transcripts and the association of tissue-specific variants with human diseases.

Proper citation: ASAP: the Alternative Splicing Annotation Project (RRID:SCR_003415) Copy   

•   Source: SciCrunch Registry

http://www.phi-base.org/

Database that catalogs experimentally verified pathogenicity, virulence and effector genes from fungal, Oomycete and bacterial pathogens, which infect animal, plant, fungal and insect hosts. It is an invaluable resource in the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. In collaboration with the FRAC team, it also includes antifungal compounds and their target genes. Each entry is curated by domain experts and is supported by strong experimental evidence (gene disruption experiments, STM etc), as well as literature references in which the original experiments are described. Each gene is presented with its nucleotide and deduced amino acid sequence, as well as a detailed description of the predicted protein's function during the host infection process. To facilitate data interoperability, genes have been annotated using controlled vocabularies and links to external sources (Gene Ontology terms, EC Numbers, NCBI taxonomy, EMBL, PubMed and FRAC).

Proper citation: PHI-base (RRID:SCR_003331) Copy   

•   Source: SciCrunch Registry

http://www.mitomap.org/

Database of polymorphisms and mutations of the human mitochondrial DNA. It reports published and unpublished data on human mitochondrial DNA variation. All data is curated by hand. If you would like to submit published articles to be included in mitomap, please send them the citation and a pdf.

Proper citation: MITOMAP - A human mitochondrial genome database (RRID:SCR_002996) Copy   

•   Source: SciCrunch Registry

http://www.netpath.org/

A manually curated resource of signal transduction pathways in humans. All pathways are freely available for download in BioPAX level 3.0, PSI-MI version 2.5 and SBML version 2.1 formats. The slim pathway models representing only core reactions in each pathway are available at NetSlim. All the NetPath pathway models are also submitted to WikiPathways., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: NetPath (RRID:SCR_003567) Copy   

•   Source: SciCrunch Registry

http://www.fruitfly.org

Database on the sequence of the euchromatic genome of Drosophila melanogaster In addition to genomic sequencing, the BDGP is 1) producing gene disruptions using P element-mediated mutagenesis on a scale unprecedented in metazoans; 2) characterizing the sequence and expression of cDNAs; and 3) developing informatics tools that support the experimental process, identify features of DNA sequence, and allow us to present up-to-date information about the annotated sequence to the research community. Resources * Universal Proteomics Resource: Search for clones for expression and tissue culture * Materials: Request genomic or cDNA clones, library filters or fly stocks * Download Sequence data sets and annotations in fasta or xml format by http or ftp * Publications: Browse or download BDGP papers * Methods: BDGP laboratory protocols and vector maps * Analysis Tools: Search sequences for CRMs, promoters, splice sites, and gene predictions * Apollo: Genome annotation viewer and editor September 15, 2009 Illumina RNA-Seq data from 30 developmental time points of D. melanogaster has been submitted to the Short Read Archive at NCBI as part of the modENCODE project. The data set currently contains 2.2 billion single-end and paired reads and over 201 billion base pairs.

Proper citation: Berkeley Drosophila Genome Project (RRID:SCR_013094) Copy   

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http://www.grt.kyushu-u.ac.jp/spad/

It is divided to four categories based on extracellular signal molecules (Growth factor, Cytokine, and Hormone) and stress, that initiate the intracellular signaling pathway. SPAD is compiled in order to describe information on interaction between protein and protein, protein and DNA as well as information on sequences of DNA and proteins. There are multiple signal transduction pathways: cascade of information from plasma membrane to nucleus in response to an extracellular stimulus in living organisms. Extracellular signal molecule binds specific intracellular receptor, and initiates the signaling pathway. Now, there is a large amount of information about the signaling pathway which controls the gene expression and cellular proliferation. We have developed an integrated database SPAD to understand the overview of signaling transduction.

Proper citation: Signaling Pathway Database (RRID:SCR_008243) Copy   

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http://interactome-cmp.ucsf.edu/

This database currently holds E-MAP scores (individual interactions and correlation coefficients) for budding yeast genes involved in the early secretory pathway and chromosome function (including DNA damage and repair, transcriptional control, chromosome segregation and telomere regulation). E-MAPs (Epistatic Mini Array Profiles) are formed by creating and quantifying high-density genetic interaction maps. With this method, observed double mutant colony sizes are compared to those that would be expected from a distribution of typical double mutant colonies of each strain. Each interaction is assigned a score, which indicates the magnitude of the difference from the expected value and the certainty of the score. Negative (or aggravating) scores (< -2.5) correspond to synthetic sick/lethal interactions while positive (or alleviating) scores (> +2.5) corresponds to epistatic or suppressor interactions.

Proper citation: Krogan Lab Interactome Database (RRID:SCR_008121) Copy   

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http://mrna.otago.ac.nz/

Database that provides access to mRNA sequences and associated regulatory elements that were processed from Genbank. These mRNA sequences include complete genomes, which are divided into 5-prime UTRs, 3-prime UTRs, initiation sequences, termination regions and full CDS sequences. This data can be searched for a range of properties including specific mRNA sequences, mRNA motifs, codon usage, RSCU values, information content, etc.

Proper citation: Transterm (RRID:SCR_008244) Copy   

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http://escience.invitrogen.com/ipath/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. LINNEA Pathways is a user-friendly comprehensive online resource for gene- or protein-based scientific research. It is based on a total of 248 signaling and metabolic human biological pathway maps created for Invitrogen by GeneGo. The current version of iPath features 225 maps displaying human regulatory and metabolic pathways established in experimental literature produced by MetaCore from GeneGo, Inc. The map objects (proteins, genes, EC functions, and compounds) are connected via metabolic transformations and physical protein interactions, which were assembled by the GeneGo team of experienced annotators, geneticists, and biochemists. The pathways are organized in a vertical fashion following the general signaling path from signaling molecules and membrane receptors, via signal transduction cascades, to transcription factors and their gene targets. Following the natural organization of cellular machinery with highly interconnected pathways and modules, many maps are linked together via hyperlinked box symbols. Such linkage allows the reconstruction of a big picture view of human cell biology., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Invitrogen iPath (RRID:SCR_008120) Copy   

•   Source: SciCrunch Registry