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. 2022 Jul 8;13(8):665–681.e4. doi: 10.1016/j.cels.2022.06.006

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© 2022 The Authors

Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.

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System-wide transcriptomics profile in COVID-19 patients identified dysregulated immune and metabolic pathways

(A) Sample distribution using normalized transcriptomics data (log₂ counts per million) of all protein-coding genes through UMAP, colored by cohort.

(B) Volcano plot visualizing gene expression changes in SARS-CoV-2-infected individuals (mild [n = 26] and severe [n = 11] in comparison with healthy individuals [HC, n = 21]). The top five significantly regulated genes are labeled.

(C) Volcano plot visualizing gene expression changes in SARS-CoV-2-infected individuals with severe COVID-19 (n = 11) in comparison with mild disease (n = 26). The top five significantly regulated genes are labeled.

(D) Heatmap visualizing expression pattern (Z score transformed log₂ counts per million) and log₂ scaled fold change values of significantly regulated genes in pairwise comparisons (adj. p < 0.05 and log₂-fold change > 1.5). Column annotation represents patient groups, and pairwise differential expression comparisons and rows represent genes.

(E) Heatmap visualizing significantly regulated Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways (adj. p < 0.05) in SARS-CoV-2-infected individuals (mild [n = 26] and severe [n = 11] in comparison with healthy individuals [HC, n = 21]) and COVID-19 patients with severe disease (n = 11) in comparison with patients with mild disease (n = 26). The color scale represents negative log₁₀ scaled adjusted p values of different directionality regulation classes. The non-directional p values are computed from the gene statistics disregarding the direction of expression. Mix-direction down and mix-direction up p values were computed by considering the segment of the gene statistics that are downregulated and upregulated, respectively. Distinct-directional p values were calculated using expression direction along with gene statistics. The distinct-direction up p values is exclusively influenced by the upregulation of genes. By contrast, distinct-direction down p values is influenced by downregulation of genes and not influenced by upregulation and downregulation together.