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http://amazonia.montp.inserm.fr/
A web interface and associated tools for easy query of public human transcriptome data by keyword, through thematic pages with list annotations. Amazonia provides a thematic entry to public transcriptomes: users may for instance query a gene on a Stem Cells page, where they will see the expression of their favorite gene across selected microarray experiments related to stem cell biology. This selection of samples can be customized at will among the 6331 samples currently present in the database. Every transcriptome study results in the identification of lists of genes relevant to a given biological condition. In order to include this valuable information in any new query in the Amazonia database, they indicate for each gene in which lists it is included. This is a straightforward and efficient way to synthesize hundreds of microarray publications., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: AmaZonia: Explore the Jungle of Microarrays Results (RRID:SCR_008405) Copy
http://www.molecularbrain.org/
MolecularBrain is an attempt to collect, collates, analyze and present the microarray derived gene expression data from various brain regions side by side. Transcription Profile of any gene in Mouse (online) and Human Brain (not yet) can be accessed as a histogram along with links to access various aspects of that gene. The expression levels were calculated from microarray data deposited at GEO (Gene expression omnibus). The molecular brain database could be searched using the built in search tool with the terms Entrez GeneID, gene symbol, synonym or description. Gene information along with their expression values can be also accessed from the alphabetical list of gene symbols on the footer. The protocol and GEO sample information is available.
Proper citation: Molecular Brain: Transcription Profiles of Mouse and Human Brains (RRID:SCR_008689) Copy
http://neuromorphometrics.com/?page_id=23
Collection of neuroanatomically labeled MRI brain scans, created by neuroanatomical experts. Regions of interest include the sub-cortical structures (thalamus, caudate, putamen, hippocampus, etc), along with ventricles, brain stem, cerebellum, and gray and white matter and sub-divided cortex into parcellation units that are defined by gyral and sulcal landmarks.
Proper citation: Manually Labeled MRI Brain Scan Database (RRID:SCR_009604) Copy
http://www.niddk.nih.gov/research-funding/research-resources/Pages/default.aspx
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 29,2023. Registry listing NIDDK resources, such as reagents, data, and protocols. They are derived from publicly available information provided by NIDDK-funded investigators, projects, and publications.
Proper citation: NIDDK Research Resources (RRID:SCR_014372) Copy
https://www.embrys.jp/embrys/html/About.html
Data collection of gene expression patterns mapped in whole-mount mouse embryo (ICR strain) of mid-gestational stages (Embryonic Day 9.5, 10.5, 11.5), in which most striking dynamics in pattern formation and organogenesis is observed. Collection of gene expression patterns of transcription factors (TFs) and TF-related factors such as transcription cofactors. Genes were extracted from databases including RIKEN Transcription Factor Database and Panther Classification System.
Proper citation: EMBRYS (RRID:SCR_006689) Copy
Project aimed at making neuroimaging data sets of brain freely available to scientific community. By compiling and freely distributing neuroimaging data sets, future discoveries in basic and clinical neuroscience are facilitated.
Proper citation: Open Access Series of Imaging Studies (RRID:SCR_007385) Copy
Collection of transmembrane protein datasets containing experimentally derived topology information from the literature and from public databases. Web interface of TOPDB includes tools for searching, relational querying and data browsing, visualisation tools for topology data.
Proper citation: Topology Data Bank of Transmembrane Proteins (RRID:SCR_007964) Copy
https://epilepsy.uni-freiburg.de/freiburg-seizure-prediction-project
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 29,2025. Electroencephalogram (EEG) data recorded from invasive and scalp electrodes. The EEG database contains invasive EEG recordings of 21 patients suffering from medically intractable focal epilepsy. The data were recorded during an invasive pre-surgical epilepsy monitoring at the Epilepsy Center of the University Hospital of Freiburg, Germany. In eleven patients, the epileptic focus was located in neocortical brain structures, in eight patients in the hippocampus, and in two patients in both. In order to obtain a high signal-to-noise ratio, fewer artifacts, and to record directly from focal areas, intracranial grid-, strip-, and depth-electrodes were utilized. The EEG data were acquired using a Neurofile NT digital video EEG system with 128 channels, 256 Hz sampling rate, and a 16 bit analogue-to-digital converter. Notch or band pass filters have not been applied. For each of the patients, there are datasets called ictal and interictal, the former containing files with epileptic seizures and at least 50 min pre-ictal data. the latter containing approximately 24 hours of EEG-recordings without seizure activity. At least 24 h of continuous interictal recordings are available for 13 patients. For the remaining patients interictal invasive EEG data consisting of less than 24 h were joined together, to end up with at least 24 h per patient. An interdisciplinary project between: * Epilepsy Center, University Hospital Freiburg * Bernstein Center for Computational Neuroscience (BCCN), Freiburg * Freiburg Center for Data Analysis and Modeling (FDM).
Proper citation: Electroencephalogram Database: Prediction of Epileptic Seizures (RRID:SCR_008032) Copy
https://www.crossref.org/services/event-data/
Database of events about articles that is run by CrossRef. It allows users to view social media mentions, news publication references, annotations, and more.
Proper citation: Crossref EventData (RRID:SCR_016281) Copy
https://www.gem-beta.org/Public/Home.aspx
Database that contains behavioral and social science measures organized by theoretical constructs. GEM is designed to enable researchers to use common measures with the goal of exchanging harmonized data.
Proper citation: Grid-Enabled Measures Database (RRID:SCR_016043) Copy
C. elegans RNAi feeding library distributed by Source BioScience Ltd. Designed for genome wide study of gene function in C. elegans through loss of function studies.
Proper citation: C. elegans RNAi Collection (Ahringer) (RRID:SCR_017064) Copy
https://wiki.helsinki.fi/display/twineng/Twinstudy
Twin panel consists of three nationwide samples of Finnish twin pairs. Major studies include nicotine dependence, eating disorders and brain imaging and alcohol use.
Proper citation: Finnish Twin Cohort Study (RRID:SCR_017477) Copy
http://mirwalk.umm.uni-heidelberg.de/
Software tool to store the predicted and the experimentally validated microRNA (miRNA)-target interaction pairs. Predictions within the complete sequence of genes of human, mouse, and rat genomes. Integrates a comparative platform of miRNA-binding sites resulting from ten different prediction datasets.
Proper citation: miRWalk (RRID:SCR_016509) Copy
Software tool as an annotated database of protein phosphorylation sites in eukaryotes. Contains experimentally identified and conserved p-sites which were collected from phosphoproteomic studies.
Proper citation: EPSD Eukaryotic Phosphorylation Site Database (RRID:SCR_016514) Copy
http://www.nitrc.org/projects/asdb/
Database as an open science framework with a scientific data extracted from scientific literature about various altered states of consciousness assessed with questionnaires. Used to compare what experiences are elicited by different drugs and non-pharmacological methods that induce altered states to help to understand human consciousness functions. Is listed by Neuroimaging Informatics Tools.
Proper citation: Altered States Database (RRID:SCR_016350) Copy
Collection of publicly available data of curated receptors, ligands and their interactions. Integrates existing datasets that pertain to cellular communication and new manually reviewed information. Used to search for particular ligand or receptor or to interrogate single cell transcriptomics data.
Proper citation: CellPhoneDB (RRID:SCR_017054) Copy
Collection of open chromatin regions from sequencing data. Metadata as entire curated DNase-I hypersensitive sites (DHS) on the whole genome datasets and data specific to each chromosome.
Proper citation: Database of Open Chromatin Regions (RRID:SCR_016614) Copy
Open source object relational database system that uses and extends SQL language combined with many features that safely store and scale the most complicated data workloads. PostgreSQL runs on all major operating systems.
Proper citation: PostgreSQL (RRID:SCR_021067) Copy
http://www.informatics.jax.org/genes.shtml
Searchable database of mouse genes, DNA segments, cytogenetic markers and QTLs. MGI provides access to integrated data on mouse genes and genome features, from sequences and genomic maps to gene expression and disease models.
Proper citation: Genes, Genome Features and Maps (RRID:SCR_017524) Copy
Collection of transcription factor microRNA regulations. TransmiR v2.0 manually curated TF-miRNA regulations from publications during 2013-2017 and included ChIP-seq-derived TF-miRNA regulation data.
Proper citation: TransmiR (RRID:SCR_017499) Copy
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