Open Directory - Science: Biology: Biochemistry and Molecular Biology: Biomolecules: Proteins and Enzymes: Proteomics: Databases

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Cancer Immunome Database - resource maintained by the Ludwig Institute for Cancer Research, Academy of Cancer Immunology and European Cancer Immunome Program. [requires free registration]
Ciliary Proteome Database - Assembles all existing ciliary and basal body proteomics data into an open resource for the scientific community with the ultimate aim of exploring further the role of the cilium in disease and the mechanisms underlying ciliary biology.
ExPASy: Swiss 2DPAGE - Two-dimensional polyacrylamide gel electrophoresis database, including manual for mapping proteomes of different phyla.
Human Protein Reference Database - HPRD offers a centralized platform to visualize domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. Includes map of pathways and FAQ maintained by Johns Hopkins University and the Institute of Bioinformatics.
JPSL: Joint ProteomicS Laboratory - At the Ludwig Institute for Cancer Research and the Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia. Proteomic databases, techniques and methods, staff, publications, news and conferences.
Orientations of Proteins in Membranes Database - OPM of transmembrane, monotopic, peripheral polypeptides and their spatial arrangement in situ of PDB entries. Includes classification, 3D imagesand contacts at the University of Michigan, Ann Arbor.
PHCI-2DPAGE Parasite Host Cell Interaction 2D-PAGE Database - 2D-PAGE database at the University of Aarhus, Denmark.
POGs/PlantRBP - Relational database that integrates data from rice, maize, and Arabidopsis by placing the complete Arabidopsis and rice proteomes, and the available maize sequences, into putative orthologous groups (POGS).
Plasma Proteome Database - Resource for human plasma proteins along with their isoforms, specific expression, disease, localization, post translational modification and SNP. Includes FAQ, query interface, or browsing by structure or function.
Protein Modification Resource - Freely accessible on-line systems biology resource devoted to commonly studied protein post-translational modifications.
Proteomics of Lactococcus lactis - Searchable database with references.
Rice Proteome Database - Provides information on rice proteomics, the database, protocols, proteome tools and rice genome tools.

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Description

Open Directory - Science: Biology: Biochemistry and Molecular Biology: Gene Expression: Databases

Online Genomics@ (20)
Proteomics@ (12)

See also:

Science: Biology: Bioinformatics: Software (93)
Science: Biology: Genetics: Eukaryotic: Databases and Maps (3)
Science: Biology: Genetics: Software (54)

Allen Brain Atlas - Database of gene expression patterns in the mouse brain.
ArrayExpress - Database of gene expression and other microarray data at the European Bioinformatics Institute (EBI), located at the Wellcome Trust Foundation in Cambridge, UK.
BATEx - Data base for gene expression data from plants.
European Nucleotide Archive (ENA) - Provides a comprehensive record of the world's nucleotide sequencing information. Contains databases of next generation sequencing reads, including RNA-seq data, submitted to the Sequence Read Archive (SRA). It also contains databases of sequence assemblies and annotations.
Exploring the Metabolic and Generic Control of Gene Expression - Database with the data for the experiments in the paper - DeRisi et. al. Science 278: 680-686. Includes text files that can be downloaded. The original paper requires a subscription fee.
Gene Expression Machine Learning Repository - A collection of gene expression datasets that can be used for benchmarking gene expression oriented machine learning algorithms.
Gene Expression Omnibus - Database of gene expression data from NCBI (National Center for Biotechnical Information). Includes a definable search by different characteristics.
Gene Expression in Tooth - Database on the expression of different genes in the developing tooth.
GeneExpress - Designed for analysis of genomic regulatory sequences of higher eukaryotes. Includes several databases and programs for visualization of the information contained. From the Laboratory of Theoretical Genetics of the Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Science in Novosibirsk (Russia).
GenePaint - Database of gene expression patterns in the mouse embryo. From Max-Planck-Institute for Biophysical Chemistry, Dept. Genes and Behavior, Göttingen, Germany
Genevestigator - Multi-organism microarray database and expression meta-analysis tool.
Genomics Portals - Integrative platform for analyzing a large collection of genome-scale datasets (more than 400 million data points).
IRESite: The Database of Experimentally Verified IRES Structures - This database contains information about the experimentally studied IRES (Internal Ribosome Entry Site) segments.
Kyoto Encyclopedia of Genes and Genomes (KEGG) - Graphical and hypertext-based information from Kanehisa Laboratories in the Bioinformatics Center of Kyoto University, Japan.
MERNA - A data base of metal binding sites of RNA, from the Holbrooke Laboratory, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Mirage - Information methodologies, tools, and technologies relating to the study of gene expression and signal transduction. From the Institute for Transcriptional Informatics (IFTI), USA.
Oncomine - Compendium of cancer transcriptome profiles with analysis engine.
Polbase - Repository of biochemical, genetic, and structural information about DNA polymerases.
RNase P Database - A compilation of RNase P sequences, sequence alignments, secondary structures, three-dimensional structures, and accessory information.
Ribosomal Database Project - From Center for Microbial Ecology, Michigan State University, USA
Rice Transcription Factor Database - RiceTFDB is a public database of rice genes involved in transcriptional control. From the University of Potsdam, Berlin, Germany.
Stanford Microarray Database - Data from microarray experiments, and the corresponding image files. From Stanford University, USA.
StemBase - A database containing gene expression data from human and mouse stem cells and their derivatives.
The Database of Rice Transcription Factors (DRTF) - Free of charge database of transcription factors of rice. From CBI, Peking University, China.
WormBase - Data bases on the genetics of C elegans and related nematodes.

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