Useful Tools
- Molecular Biology Tools – A list of free online molecular biology tools all in one place.
Gene Expression
- Attie Lab Diabetes Database – Mouse diabetes and obesity gene expression atlas
- Attie DO500 HFD – Eight strains of mouse and multiple tissue datasets
- BioGPS – Mouse and human gene expression atlas
- CIRCA – Mouse circadian gene expression atlas
- CITGeneDB – A comprehensive database of human and mouse genes enhancing or suppressing Cold-induced thermogenesis, validated by perturbation experiments in mice
- D2H2: A platform that facilitates data-driven hypothesis generation for the diabetes and related metabolic disorder research community.
- MGI – Mouse genome annotation
- Joslin Gene Expression Database – [Username & password required]
- MORPHEUS – Versatile matrix visualization and analysis software – View your dataset as a heat map
- Genebridge – Gene-GO Correlation Across Expression Datasets
- GenePattern – Computational biology open-source software for the analysis of genomic data
- Genekitr – Gene Analysis Toolkit base on R language
- GTEx Portal – An ongoing effort to build a comprehensive public resource to study tissue-specific gene expression and regulation.
- PrimerBank – Primer design for QPCR
- T2D Knowledge Portal – Human genetic information linked to type 2 diabetes and related traits
- Adipose Tissue Knowledge Portal – A knowledge portal integrating clinical and experimental data from human adipose tissue
- CellAge – The database of cell senescence genes
- CMDKP – Common Metabolic Diseases Knowledge Portal
- MOSTA – Mouse Organogenesis Spatiotemporal Transcriptomic Atlas
- L1000 FireworksFWD – A web application that provides interactive visualization of over 16,000 drug and small-molecule induced gene expression signatures
Transcriptional/Epigenetic regulation
- DAVID – Database for Annotation, Visualization and Integrated Discovery
- Enrichr – Gene set enrichment analysis tools
- Cistrome – Predict transcription factors that regulate genes of interest
- Metascape – A Gene Annotation & Analysis Resource
Single-Cell Analyses
- Tabula Muris – A compendium of single cell transcriptome data from the model organism Mus musculus, containing nearly 100,000 cells from 20 organs and tissues
- Tabula Sapiens – Tabula Sapiens is a benchmark, first-draft human cell atlas of nearly 500,000 cells from 24 organs of 15 normal human subjects.
- VISION – Functional interpretation of single cell RNA-seq latent manifolds
- Cellenics – open-source platform to analyze single-cell RNA sequencing datasets
- Cellxgene – Scalable single-cell visualization for biomedical research
- Single Cell Portal – Single-cell research collection from the Broad Institute
Proteomics
- The Human Protein Atlas
- GPCRdb – G-protein coupled receptor database
- OPABAT – Proteomics Database of Outbred Mouse Strains
Metabolomics
- LIPID MAPS – Lipidomics gateway
- HMBD – Very detailed information on metabolites
- SMPDB – Integrates RNA-seq, lipidomics, and metabolomics data
- Atlas of Inflammation Resolution
- HMDB -Human Metabolome Database
- Metabolomics Workbench
- Metaboanalyst – Analyzing pathways and enrichment in metabolites
- ELITE Portal – Exceptional Logevity Translational Resources
Interactome
- STRING – Functional protein association networks
- BIOPLEX – Protein-Protein interactions
- HuRI – The Human Reference Protein Interactome Mapping Project
Protocol
Mouse Phenotyping
- IMPC – An international effort by 19 research institutions to identify the function of every protein-coding gene in the mouse genome
- CalR – A web application for indirect calorimetry analysis (Alex Banks Lab)
CRISPR
- CRISPR gRNA Design Tool – gRNA design for KO
- Cas9-Activators with SAM – CRISPR activation system (Feng Zhang Lab)
Multi-Omics
yhtsenglab.org 