This page contains a collection of links that I find interesting and helpful for metabolomics and other omics research, especially if combined with genomics. This is my personal VIP bookmark list, newest entries listed first (more or less) [updated 12 October 2022].

Phenome-wide association studies (PheWAS) Resources : analyze many phenotypes compared to a single genetic variant https://phewascatalog.org/

Astra Zeneca PheWAS portal : access association data from Rare variant contribution to human disease in 281,104 UK Biobank exomes, Nature, 2021.

Astra Zeneca Proteogenomics Portal : access pQTL data from Influences of rare protein-coding genetic variants on the human plasma proteome in 50,829 UK Biobank participants, medRxiv, 2022.

VannoPortal : variant annotation to integrate variant annotations like allele frequency, linkage disequilibrium, evolutionary signature, disease/trait association, pathogenesis, allele imbalance, functional prediction and tissue/cell type-specificity (similar to phenoscanner and SNiPa)

omicscience.org : metabolomics and proteomics web servers developed by the Gabi Kastenmuller lab

genebass : gene-based association summary statistics – a resource of exome-based association statistics, encompasses 3,817 phenotypes with gene-based and single-variant testing across 281,852 individuals with exome sequence data from the UK Biobank

OMICSPRED: An atlas of genetic scores for prediction of multi-omics data – Genetic scores for metabolomics (Metabolon, Nightingale) and proteomics (Somalogic, Olink) data, trained on the INTERVAL cohort

Pan-ancestry genetic analysis of the UK Biobank – summary statistics a multi-ancestry analysis of 7,221 phenotypes, across 6 continental ancestry groups, for a total of 16,119 genome-wide association studies – updated phenotypes (Apr 2022) here

LDLink – a suite of web-based applications designed to easily and efficiently interrogate linkage disequilibrium in population groups.

Glycostore – much about glycan structures (collection)

Explore data from UK Biobank provided by the Neale Lab:

METABOLIC ATLAS – THE ATLAS FOR EXPLORATION OF METABOLISM

The Human Blood Atlas – single cell type information on genome-wide RNA expression profiles of human protein-coding genes covering various B- and T-cells, monocytes, granulocytes and dendritic cells.

EpiGraphDB – pQTL browser to perform MR PheWAS of protein effects on traits

Enrichr – an amazingly easy and comprehensive tool to compute gene-set enrichment.

g:Profiler – functional enrichment analysis

Gene CoDis – a gene set enrichment tool.

Global Biobank Engine – browse metaanalyzed GWAS data using the UK Biobank chip; this site also has a nice visualization of genomic correlation between UKB phenotypes

FINNGEN GWAS (PheWeb, example)

BioBank Japan PheWeb

Atlas of GWAS Summary Statistics

Neale Lab GWAS (example)

Neale Lab UKB SNP-Heritability Browser (Insights from estimates of SNP-heritability for >2,000 traits and disorders in UK Biobank)

Oxford Big GWAS (example)

Gene Atlas GWAS (example)

UKBiobank ICD PheWeb: Analysis of 1403 ICD-based traits using SAIGE (top hits)

GWASbot Twitter account (TWITTER)

An atlas of polygenic burden associations across the human phenome (link)

ExPASy Bioinformatics Portal – a *really* extensive list of web-servers and data-bases

ExPASy is the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools (i.e., resources) in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc. (see Categories in their menu). On this portal you find resources from many different SIB groups as well as external institutions.

ARCHS4 provides access to gene counts from HiSeq 2000 and HiSeq 2500 platforms for human and mouse experiments from GEO and SRA.This is a great resource to investigate metabolically active genes [try NAT8 to find that it is specifically expressed in liver, and FADS1 to see its ubiquitous expression pattern] – the paper is here

pGWAS server

“Annotated pQTLs – for details see here“

mGWAS server

“Annotated mQTLs – for details see here“

SNiPA

“Annotated SNPs – for details see here“

Qtlizer

“Annotated SNPs – similar to SNiPA”

PhenoScanner

“Annotated SNPs – similar to SNiPA”

BIOS QTL browser

“This web page accompanies the manuscripts titled ‘Disease variants alter transcription factor levels and methylation of their binding sites’, by Bonder et al. and ‘Identification of context-dependent expression quantitative trait loci in whole blood’, by Zhernakova et al, both have been published to Nature Genetics. You can query our independent eQTL, meQTL and eQTMs on this server.”

gnomAD genome aggregation database

“The v2 data set (GRCh37/hg19) provided on this website spans 125,748 exome sequences and 15,708 whole-genome sequences from unrelated individuals sequenced as part of various disease-specific and population genetic studies.”

GTEx Portal

“The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation. This project will collect and analyze multiple human tissues from donors who are also densely genotyped, to assess genetic variation within their genomes. By analyzing global RNA expression within individual tissues and treating the expression levels of genes as quantitative traits, variations in gene expression that are highly correlated with genetic variation can be identified as expression quantitative trait loci, or eQTLs.”

The Human Protein Atlas

“The Human Protein Atlas utilizes an antibody-based approach, using both in-house generated antibodies, as well as commercial antibodies from different providers. Antibodies are used for immunofluorescence staining on cell lines for determination of spatial distribution at a subcellular level, as well as for immunohistochemistry on tissue microarrays for distribution of the protein expression in normal and cancer tissues. The open access database contains millions of high-resolution images, released together with application-specific validation performed for each antibody. The database has been developed in a gene-centric manner with the inclusion of all human genes predicted from genome efforts. Search functionalities allow for complex queries regarding protein expression profiles, protein classes, and chromosome location.”

The Small Molecule Pathway Database

“SMPDB (The Small Molecule Pathway Database) is an interactive, visual database containing more than 618 small molecule pathways found in humans. More than 70% of these pathways (>433) are not found in any other pathway database. SMPDB is designed specifically to support pathway elucidation and pathway discovery in metabolomics, transcriptomics, proteomics and systems biology.”

KEGG Mapper – Search&Color Pathway

“Search&Color Pathway is an advanced version of the KEGG pathway mapping tool, where given objects (genes, proteins, compounds, glycans, reactions, drugs, etc.) are searched against KEGG pathway maps and found objects are marked in any background and foreground colors.” (see also Color Pathway; this is is an extension of the Search&Color Pathway tool, allowing multiple coloring of a selected pathway map).

R-packages and other interesting software packages

  • Highcharter: an R wrapper for the Highcharts javascript charting libray
  • Keras: an R wrapper for the Keras deep learning library (works with tensorflow)
  • Pheweb: A tool to build multi-phenotype GWAS browsers

Kidney Interactive Transcriptomics