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Found 49 result(s)

Human protein-protein interaction network database search

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<<<!!!<<< This repository is no longer available. >>>!!!>>> A human interactome map. The sequencing of the human genome has provided a surprisingly small number of genes, indicating that the complex organization of life is not reflected in the gene number but, rather, in the gene products – that is, in the proteins. These macromolecules regulate the vast majority of cellular processes by their ability to communicate with each other and to assemble into larger functional units. Therefore, the systematic analysis of protein-protein interactions is fundamental for the understanding of protein function, cellular processes and, ultimately, the complexity of life. Moreover, interactome maps are particularly needed to link new proteins to disease pathways and the identification of novel drug targets.

DEG

Database of Essential Genes

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DEG hosts records of currently available essential genomic elements, such as protein-coding genes and non-coding RNAs, among bacteria, archaea and eukaryotes. 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.

Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer

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The information in the Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer relates cytogenetic changes and their genomic consequences, in particular gene fusions, to tumor characteristics, based either on individual cases or associations. All the data have been manually culled from the literature by Felix Mitelman in collaboration with Bertil Johansson and Fredrik Mertens.

Organelle Genome Megasequencing Program

OGMP

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The Organelle Genome Megasequencing Program (OGMP) provides mitochondrial, chloroplast, and mitochondrial plasmid genome data. OGMP tools allow direct comparison of OGMP and NCBI validated records. Includes GOBASE, a taxonomically broad organelle genome database that organizes and integrates diverse data related to mitochondria and chloroplasts.

STRING

Known and Predicted Protein-Protein Interactions

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STRING is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations; they are derived from four sources: - Genomic Context - High-throughput Experiments - (Conserved) Coexpression - Previous Knowledge STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable.

Plant Transcription Factor Database

PlantTFDB

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Species included in PlantTFDB 4.0 covers the main lineages of green plants. Therefore, PlantTFDB provides genomic TF repertoires across Viridiplantae. To provide comprehensive information for the TF family, a brief introduction and key references are presented for each family. Comprehensive annotations are made for each identified TF, including functional domains, 3D structures, gene ontology (GO), plant ontology (PO), expression information, expert-curated functional description, regulation information, interaction, conserved elements, references, and annotations in various databases such as UniProt, RefSeq, TransFac, STRING, and VISTA. By inferring orthologous groups and constructing phylogenetic trees, evolutionary relationships among identified TFs were inferred. In addition, PlantTFDB has a simple and user-friendly interface to allow users to query based on combined conditions or make sequence similarity search using BLAST. The new version PlantTFDB 5.0 has been incorporated into PlantRegMap http://plantregmap.gao-lab.org/.

ArachnoServer

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ArachnoServer is a manually curated database containing information on the sequence, three-dimensional structure, and biological activity of protein toxins derived from spider venom. Spiders are the largest group of venomous animals and they are predicted to contain by far the largest number of pharmacologically active peptide toxins (Escoubas et al., 2006). ArachnoServer has been custom-built so that a wide range of biological scientists, including neuroscientists, pharmacologists, and toxinologists, can readily access key data relevant to their discipline without being overwhelmed by extraneous information.

NCBI Structure

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The Structure database provides three-dimensional structures of macromolecules for a variety of research purposes and allows the user to retrieve structures for specific molecule types as well as structures for genes and proteins of interest. Three main databases comprise Structure-The Molecular Modeling Database; Conserved Domains and Protein Classification; and the BioSystems Database. Structure also links to the PubChem databases to connect biological activity data to the macromolecular structures. Users can locate structural templates for proteins and interactively view structures and sequence data to closely examine sequence-structure relationships.

DTU Bioinformatics

Center for Biological Sequence Analysis (formerly)

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<<<!!!<<< DTU Bioinformatics was closed on 31 December 2018 as part of a reorganization at DTU >>>!!!>>>

Reactome

a curated pathway database

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Reactome is a manually curated, peer-reviewed pathway database, annotated by expert biologists and cross-referenced to bioinformatics databases. Its aim is to share information in the visual representations of biological pathways in a computationally accessible format. Pathway annotations are authored by expert biologists, in collaboration with Reactome editorial staff and cross-referenced to many bioinformatics databases. These include NCBI Gene, Ensembl and UniProt databases, the UCSC and HapMap Genome Browsers, the KEGG Compound and ChEBI small molecule databases, PubMed, and Gene Ontology.

NetPath

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<<<!!!<<< This repository is no longer available. >>>!!!>>> NetPath is currently one of the largest open-source repository of human signaling pathways that is all set to become a community standard to meet the challenges in functional genomics and systems biology. Signaling networks are the key to deciphering many of the complex networks that govern the machinery inside the cell. Several signaling molecules play an important role in disease processes that are a direct result of their altered functioning and are now recognized as potential therapeutic targets. Understanding how to restore the proper functioning of these pathways that have become deregulated in disease, is needed for accelerating biomedical research. This resource is aimed at demystifying the biological pathways and highlights the key relationships and connections between them. Apart from this, pathways provide a way of reducing the dimensionality of high throughput data, by grouping thousands of genes, proteins and metabolites at functional level into just several hundreds of pathways for an experiment. Identifying the active pathways that differ between two conditions can have more explanatory power than just a simple list of differentially expressed genes and proteins.

Broad GDAC Firehose

Genome Data Analysis Center

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Born of the desire to systematize analyses from The Cancer Genome Atlas pilot and scale their execution to the dozens of remaining diseases to be studied, GDAC Firehose now sits atop terabytes of analysis-ready TCGA data and reliably executes thousands of pipelines per month. More information: https://broadinstitute.atlassian.net/wiki/spaces/GDAC/

Huntingtin Interaction Network

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<<<!!!<<< This repository is no longer available. >>>!!!>>> The main objective of our work is to understand the pathomechanisms of late onset neurodegenerative disorders such as Huntington's, Parkinson's, Alzheimer's and Machado Joseph disease and to develop causal therapies for them. The disease causing proteins of these illnesses have been identified, but their functions in the unaffected organism are mostly unknown. Here, we have developed a strategy combining library and matrix yeast two-hybrid screens to generate a highly connected PPI network for Huntington's disease (HD).

OrtholugeDB

The Ortholog Database

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OrtholugeDB contains Ortholuge-based orthology predictions for completely sequenced bacterial and archaeal genomes. It is also a resource for reciprocal best BLAST-based ortholog predictions, in-paralog predictions (recently duplicated genes) and ortholog groups in Bacteria and Archaea. The Ortholuge method improves the specificity of high-throughput orthology prediction.

IMGT/LIGM-DBI

International ImMunoGeneTics information system / Laboratoire d'ImmunoGénétique Moléculaire-Database

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IMGT/LIGM-DB is a comprehensive database of Immunoglobulins (IG) and T cell Receptors (TR) from human and other vertebrates, with translation for fully annotated sequences.

AlphaFold

AlphaFold Protein Structure Database

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AlphaFold DB provides open access to protein structure predictions for the human proteome and 20 other key organisms to accelerate scientific research.

National Biodiversity Information System of Mexico

Sistema Nacional de Información sobre Biodiversidad de México

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The National Biodiversity Information System (SNIB) of Mexico by the National Commission for the Knowledge and Use of Biodiversity (CONABIO). The SNIB is of strategic importance in a megadiversity country like Mexico, making it clear to CONABIO from the beginning that the SNIB should rely on the work of the multiplicity of institutions and national and foreign experts that for years have been dedicated to the study of biodiversity of Mexico. The creation of this system was expressed as a mandate for CONABIO in the General Law of Ecological Balance and Environmental Protection (LGEEPA Art. 80 fraction V). The participation of specialists in the generation of data and information for the SNIB is one of the various ways in which they collaborate with this system, since having an information system that allows the country to make informed decisions regarding its biodiversity requires that it be made up of data and information supported by a broad network of experts.

GeneCards

The Human Gene Database

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GeneCards is a searchable, integrative database that provides comprehensive, user-friendly information on all annotated and predicted human genes. It automatically integrates gene-centric data from ~125 web sources, including genomic, transcriptomic, proteomic, genetic, clinical and functional information.

cisRED

Databases of genome-wide regulatory module and element predictions

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<<<!!!<<< This repository is no longer available. >>>!!!>>>

Mammalian Transcriptomic Database

MTD

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MTD is focused on mammalian transcriptomes with a current version that contains data from humans, mice, rats and pigs. Regarding the core features, the MTD browses genes based on their neighboring genomic coordinates or joint KEGG pathway and provides expression information on exons, transcripts, and genes by integrating them into a genome browser. We developed a novel nomenclature for each transcript that considers its genomic position and transcriptional features.

ErythronDB

Erythron Database

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<<<!!!<<< The original ErythronDB site is now retired! Code for generating the web site is available here https://github.com/ErythronDB/erythrondb-docker. >>>!!!>>>

Cornell Activity Datasets: CAD-60 & CAD-120

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<<<!!!<<< The repository is no longer available. >>>!!!>>>

Mechanism and Catalytic Site Atlas

CSA (formerly)

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M-CSA is a database of enzyme reaction mechanisms. It provides annotation on the protein, catalytic residues, cofactors, and the reaction mechanisms of hundreds of enzymes. There are two kinds of entries in M-CSA. 'Detailed mechanism' entries are more complete and show the individual chemical steps of the mechanism as schemes with electron flow arrows. 'Catalytic Site' entries annotate the catalytic residues necessary for the reaction, but do not show the mechanism. The M-CSA (Mechanism and Catalytic Site Atlas) represents a unified resource that combines the data in both MACiE and the CSA

The Taenia solium Genome Project

T. solium Genome Project

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>>>!!!<<< 2021-08; The repository is no longer available. >>>!!!<<< Archived page of Taenia solium genome project see https://web.archive.org/web/20160309194611/http://www.taeniasolium.unam.mx/taenia

The MaxQuant DataBase

MaxQB

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MaxQB stores and displays collections of large proteomics projects and allows joint analysis and comparison. As a first dataset is contains proteome data of 11 different human cell lines. The 11 cell line proteomes together identify proteins expressed from more than half of all human genes. For each protein of interest, expression levels estimated by label-free quantification can be visualized across the cell lines. Similarly, the expression rank order and estimated amount of each protein within each proteome are plotted.