Useful Links

Gene Expression

• BioGPS – Mouse and human gene expression atlas
• CIRCA – Mouse circadian gene expression atlas
• Attie Lab Diabetes Database – Mouse diabetes and obesity gene expression atlas
• MGI – Mouse genome annotation
• CITGeneDB – A comprehensive database of human and mouse genes enhancing or suppressing Cold-induced thermogenesis, validated by perturbation experiments in mice
• PrimerBank – Primer design for QPCR
• Cellxgene – Scalable single-cell visualization for biomedical research
• 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

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

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

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

Protocol

• Protocol.io

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

• Signaling Pathways Project