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Biochemistry and Molecular Biology
Science: Biology: Bioinformatics: Software
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Science: Biology: Genetics: Software
Allen Brain Atlas
- Database of gene expression patterns in the mouse brain.
- Database of gene expression and other microarray data at the European Bioinformatics Institute (EBI), located at the Wellcome Trust Foundation in Cambridge, UK.
- Data base for gene expression data from plants.
The Database of Rice Transcription Factors (DRTF)
- Free of charge database of transcription factors of rice. From CBI, Peking University, China.
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 in Tooth
- Database on the expression of different genes in the developing tooth.
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.
- Database of gene expression patterns in the mouse embryo. From Max-Planck-Institute for Biophysical Chemistry, Dept. Genes and Behavior, Göttingen, Germany
- Multi-organism microarray database and expression meta-analysis tool.
- 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.
- Information methodologies, tools, and technologies relating to the study of gene expression and signal transduction. From the Institute for Transcriptional Informatics (IFTI), USA.
- Compendium of cancer transcriptome profiles with analysis engine.
- Repository of biochemical, genetic, and structural information about DNA polymerases.
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.
RNase P Database
- A compilation of RNase P sequences, sequence alignments, secondary structures, three-dimensional structures, and accessory information.
- A database containing gene expression data from human and mouse stem cells and their derivatives.
- Data bases on the genetics of C elegans and related nematodes.
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