About COReD

COReD is a gene-centered evidence platform for respiratory-virus host-factor evaluation and discovery.

The database links clinical scRNA-seq, Host Genetics(GWAS), perturbation screens and animal infection models through gene-level pages and a clickable Evidence Matrix.

Its purpose is transparent, context-aware evidence review before experimental prioritization: users can examine where evidence appears, across which viruses, tissues, cell types and model systems, without reducing biologically distinct evidence types to a single opaque score.

Search a gene View evidence matrix How to use COReD

Gene-centered evidence review

Starts from a candidate host-factor gene and links independent evidence across clinical, genetic, perturbation and animal-model contexts.

Cross-study clinical scRNA-seq harmonization

Harmonizes patient datasets by anatomical site, disease grouping and common cell-type annotation to support cross-study host-factor evaluation.

Four linked evidence layers

Connects clinical scRNA-seq, Host Genetics(GWAS), perturbation screens and animal infection models through module-level pages.

What COReD Provides

Evidence layer	Current data scale	User action	Output
Clinical scRNA-seq	2,534 samples / 85 studies	Gene, cell-type, tissue and disease-group search; DE analysis	Expression context, cell-type context and differential genes
Host Genetics(GWAS)	SARS-CoV-2 / influenza / RSV	Regional gene-level review	Association evidence near candidate genes
Perturbation Screens	35 screens / 19 studies	KO/KD/OE evidence review	Functional perturbation evidence
Animal Models	289 samples / 45 datasets	Animal tissue and organism evidence review	Infection-model expression context
Evidence Matrix	Linked analyzable genes	Filter and sort matrix-wide evidence	Viral breadth and tissue and cell-type context

What COReD contains

COReD organizes heterogeneous public datasets around the question a user most often starts with: what evidence supports a candidate respiratory-virus host factor? Gene-centered pages connect clinical single-cell expression context, regional host-genetic associations, perturbation-screen evidence and animal infection-model expression patterns. The Evidence Matrix then provides a compact view of evidence availability, viral spectrum breadth and tissue and cell-type context across analyzable genes.

COReD therefore emphasizes transparent, context-aware evidence review rather than a universal weighted ranking score across biologically distinct evidence types.

Cross-study harmonization and analysis

COReD does not simply present clinical single-cell datasets as separate studies. Within each anatomical site, datasets from different studies are organized under a common cell-type framework. Clinical metadata and severity groupings are manually reviewed and harmonized using predefined criteria.

This organization enables users to construct and analyse large cross-study cohorts, rather than being restricted to study-by-study exploration. Candidate genes identified from these analyses can then be evaluated through the host genetics, perturbation screens, animal infection models and Evidence Matrix modules.

Positioning among related resources

Existing viral infection, respiratory atlas and COVID-focused databases provide valuable but different types of information. COReD has a narrower and complementary purpose: supporting respiratory-virus host-factor evaluation by combining harmonized patient single-cell context with genetic, perturbational and animal-model evidence in a gene-centered workflow.

Resource category	Representative resources	Primary contribution	COReD's complementary contribution
Viral or COVID single-cell resources	scMOVIR; SCovid	Single-cell atlases and exploration of infection-associated cellular states	Adds harmonized cross-study clinical cohorts and connects candidate genes to host genetics, perturbation screens and animal infection models
Respiratory reference atlases	Human Lung Cell Atlas (HLCA); LungMAP	Reference maps of lung and respiratory-tissue cell populations	Focuses specifically on infection-associated host-factor evaluation rather than comprehensive tissue annotation
COVID-focused transcriptomic or multi-omic resources	COVID19db; COMBATdb	Disease-focused molecular datasets and analytical resources for SARS-CoV-2 or COVID-19	Extends evaluation across multiple respiratory viruses and organizes evidence through a gene-centered, four-layer workflow
Broad virus-host resources	MVIP	Multi-virus or virus-host multi-omics exploration	Adds harmonized patient single-cell context and a respiratory-virus-focused evidence-review workflow

These resources are complementary rather than interchangeable. COReD's distinctive contribution is the combination of: (i) harmonized, analysis-ready clinical single-cell cohorts; (ii) gene-centered linkage to host genetics, perturbation screens and animal infection models; and (iii) a clickable Evidence Matrix for transparent comparison of evidence availability, viral breadth and tissue and cell-type context.

Representative resources are listed to clarify database positioning. Their inclusion does not imply that COReD replaces the corresponding atlas-level, disease-focused or virus-host resources.

Maintenance statement

COReD will be maintained at the same URL for at least five years and updated as new respiratory-virus host-factor datasets become available.