The Gene Expression Omnibus (GEO - NCBI) is a public repository archiving and freely distributing microarray, next-generation sequencing, and other forms of high-throughput functional genomic data submitted by the scientific community. In addition to data storage, a collection of web-based interfaces and applications are available to help users query and download the experiments and gene expression patterns stored in GEO.
...continue to read
A major goal of the Encyclopedia of DNA Elements (ENCODE) is to annotate all functional elements of the human genome including protein-coding genes, pseudogenes, and non-coding transcribed loci and to catalog the products of transcription including splice isoforms and regulatory elements that control the cells and circumstances in which a gene is active.
...continue to read
Add to my favorites
Category: Gene information search, Gene expression
WashU Human Epigenome Browser allows: Epigenome
The browser currently hosts Human (and other species) Epigenome Atlas data produced by the Roadmap Epigenomics project,but lets users diverge from the strict genome-centric view of the UCSC browser to, for instance, view all genes (or promoters, or 3’ UTRs) in a given pathway side by side. “You can do lots of Google Maps-style operations, and you can look at your data in the context of their metadata.
...continue to read
Add to my favorites
expression, homology and other information on groups of genes
Category: Gene expression
Gene Sorter shows expression, homology and other information on groups of genes that can be related in many ways.
...continue to read
Morpheus (from Broad Institute) is a web-based versatile matrix visualization and analysis software. View your dataset as a heat map, and then explore the interactive tools in Morpheus. Cluster, create new annotations, search, filter, sort, display charts, and more.
...continue to read
The Gene Expression Omnibus (GEO - NCBI) is a public repository that archives and freely distributes microarray, next-generation sequencing, and other forms of high-throughput functional genomic data submitted by the scientific community. In addition to data storage, a collection of web-based interfaces and applications are available to help users query and download the experiments and gene expression patterns stored in GEO.
...continue to read
ArrayMining is a web-server for online automating microarray statistical analysis of gene and protein expression microarray data, designed as a supporting tool for investigation of the genetic components of diseases. By providing feature selection, clustering and prediction analysis, it performs five common gene expression analysis tasks:cross-study normalisation, feature selection, sample clustering, sample classification, network analysis, gene set analysis.
...continue to read
The Allen Mouse Brain Atlas is a comprehensive genome-wide map of the adult mouse brain revealing where each gene is expressed, or “turned on. A combination of RNA in situ hybridization data, detailed Reference Atlases and informatics analysis tools are integrated to provide a searchable digital atlas of gene expression. Together, these resources present a comprehensive online platform for exploration of the brain at the cellular and molecular level.
...continue to read
Add to my favorites
Category: Proteomics data analysis, Gene expression
GenPattern Proteomics allows: Broad
GenePatern allowr various data analyses for proteomics: MRM-MS; peptide signature prediction; PEPPeR algorhitms; detection and alignment features across runs in LC-MS; support for SELDI/MALDI data.
...continue to read
Add to my favorites
Category: Other topics, Gene expression
Roadmap Epigenomics Project allows: Epigenome
The NIH Roadmap Epigenomics Mapping Consortium was launched with the goal of producing a public resource of human epigenomic data to catalyze basic biology and disease-oriented research. The Consortium leverages experimental pipelines built around next-generation sequencing technologies to map DNA methylation, histone modifications, chromatin accessibility and small RNA transcripts in stem cells and primary ex vivo tissues selected to represent the normal counterparts of tissues and organ system
...continue to read
The Common Fund's Genotype-Tissue Expression (GTEx) program aims to map all sites in the human genome where sequence variation quantitatively affects gene expression and regulation in multiple tissues, providing valuable insights into the mechanisms of gene regulation and its disease-related perturbations.
...continue to read
Add to my favorites
Category: Gene expression, Biomedical communities
International Human Epigenome Consortium (IHEC) allows: Epigenome
The International Human Epigenome Consortium (IHEC) is a global consortium with the primary goal of providing free access to high-resolution reference human epigenome maps for normal and disease cell types to the research community.
...continue to read
FANTOM is a large international consortium led by Japanese RIKEN that releases the first comprehensive map of gene activity across the human body. FANTOM5 has been mapping which genes are active in virtually all cell types across the human body, and the regions which determine where the genes are read from the genome. An associated data processing and visualization web system, Zenbu, enables researchers to quickly and easily integrate, visualize and compare large amounts of genomic information r
...continue to read
COXPRESdb (coexpressed gene database) represents the coexpression relationship for human, mouse, rat, chicken, zebrafish, fly and nematoda. COXPRESdb can help researchers to clarify the functional and regulatory networks of genes in a broad array of animal species.
...continue to read
JBrowse is a fast and full-featured scalable genome browser built completely with JavaScript and HTML5. It can run on your desktop, or be embedded in your website (see Bues et al., Genome Biol 17, 66 (2016) doi:10.1186/s13059-016-0924-1).
...continue to read
xCell is a webtool that performs cell type enrichment analysis from gene expression data for 64 immune and stroma cell types. xCell is a gene signatures-based method learned from thousands of pure cell types from various sources. (Aran et al., Genome Biology 18:220. 2017).
...continue to read
OmicsPred is an open resource applied to genetic scores to predict multi-omic traits from genotype data, uncovering insights into disease biology (Xu et al., Nature https://doi.org/10.1038/s41586-023-05844-9, 2023; https://www.nature.com/articles/d41586-023-00721-x)
...continue to read
CZ CELLxGENE from The Chan Zuckerberg Initiative, is a free-to-use online data portal collecting free and open-source tools for finding, querying, analysing, downloading and publishing single-cell data. As of April 2024, it includes some 85 million single cells 248 and 1,317 data sets covering 844 cell types. Most of the data represent single-cell RNA sequencing information from healthy human tissues, but non-human and cell-line data, as well as molecular-profiling data obtained using spatial tr
...continue to readPage: 1
Biomedical search tools
Online genomic tools
Online proteomics tools
Calculators
Biomedical lab tools
Scientific writing/reading
Biomedical communities
Biomedical funding and jobs
Medical topics
Biomedical softwares