TBSignatureProfiler: Profile RNA-Seq Data Using TB Pathway Signatures

COVIDsignatures

R Documentation

A list of published/pre-print COVID-19 signatures.

Description

A set of 47 COVID-19 gene signatures from various single-cell and bulk RNA-seq publications and preprint manuscripts from early- to mid-2020. This set of signatures uses gene symbols.

Usage

COVIDsignatures

Format

list

Details

Signature names are composed of the last name of the primary author, followed by the type of sequencing data from which the signature was derived, the tissue from which the signature was derived, and ending with a reference to the cell type, infection status, or disease to which the signature belongs, as defined in the original publication.

Note that in some cases signatures will be positive identifiers of COVID-19 as positive markers of immune cell clusters are often provided for single-cell RNA-seq data; this should be taken into account when creating ROC curves and computing any AUC or disease risk estimates.

Source

Wilk_sc_PBMC_monocytes_up: Wilk, A.J., Rustagi, A., Zhao, N.Q. et al. 2020. "A single-cell atlas of the peripheral immune response in patients with severe COVID-19." Nature Medicine 26 (7): 1070-1076. https://doi.org/10.1038/s41591-020-0944-y
Wilk_sc_PBMC_monocytes_up: Wilk, A.J., Rustagi, A., Zhao, N.Q. et al. 2020. "A single-cell atlas of the peripheral immune response in patients with severe COVID-19." Nature Medicine 26 (7): 1070-1076. https://doi.org/10.1038/s41591-020-0944-y
Wilk_sc_PBMC_monocytes_down: Wilk, A.J., Rustagi, A., Zhao, N.Q. et al. 2020. "A single-cell atlas of the peripheral immune response in patients with severe COVID-19." Nature Medicine 26 (7): 1070-1076. https://doi.org/10.1038/s41591-020-0944-y
Wilk_sc_PBMC_NK_cells_up: Wilk, A.J., Rustagi, A., Zhao, N.Q. et al. 2020. "A single-cell atlas of the peripheral immune response in patients with severe COVID-19." Nature Medicine 26 (7): 1070-1076. https://doi.org/10.1038/s41591-020-0944-y
Wilk_sc_PBMC_NK_cells_down: Wilk, A.J., Rustagi, A., Zhao, N.Q. et al. 2020. "A single-cell atlas of the peripheral immune response in patients with severe COVID-19." Nature Medicine 26 (7): 1070-1076. https://doi.org/10.1038/s41591-020-0944-y
Wilk_sc_PBMCs_ISG_signature: Wilk, A.J., Rustagi, A., Zhao, N.Q. et al. 2020. "A single-cell atlas of the peripheral immune response in patients with severe COVID-19." Nature Medicine 26 (7): 1070-1076. https://doi.org/10.1038/s41591-020-0944-y
Wilk_sc_PBMC_activated_granulocytes: Wilk, A.J., Rustagi, A., Zhao, N.Q. et al. 2020. "A single-cell atlas of the peripheral immune response in patients with severe COVID-19." Nature Medicine 26 (7): 1070-1076. https://doi.org/10.1038/s41591-020-0944-y
Huang_sc_PBMC_IFN_signature: Wilk, A.J., Rustagi, A., Zhao, N.Q. et al. 2020. "Blood single cell immune profiling reveals the interferon-MAPK pathway mediated adaptive immune response for COVID-19." medRxiv.org: https://doi.org/10.1101/2020.03.15.20033472
Wen_sc_PBMC_monocytes: Wen, W., Su, W., Tang, H. et al. 2020. "Immune cell profiling of COVID-19 patients in the recovery stage by single-cell sequencing." Cell Discovery 6 (31). https://doi.org/10.1038/s41421-020-0168-9
Wen_sc_PBMC_NK_cells: Wen, W., Su, W., Tang, H. et al. 2020. "Immune cell profiling of COVID-19 patients in the recovery stage by single-cell sequencing." Cell Discovery 6 (31). https://doi.org/10.1038/s41421-020-0168-9
Wen_sc_PBMC_CD4_T_cells: Wen, W., Su, W., Tang, H. et al. 2020. "Immune cell profiling of COVID-19 patients in the recovery stage by single-cell sequencing." Cell Discovery 6 (31). https://doi.org/10.1038/s41421-020-0168-9
Wen_sc_PBMC_CD8_T_cells: Wen, W., Su, W., Tang, H. et al. 2020. "Immune cell profiling of COVID-19 patients in the recovery stage by single-cell sequencing." Cell Discovery 6 (31). https://doi.org/10.1038/s41421-020-0168-9
Wen_sc_PBMC_B_cells: Wen, W., Su, W., Tang, H. et al. 2020. "Immune cell profiling of COVID-19 patients in the recovery stage by single-cell sequencing." Cell Discovery 6 (31). https://doi.org/10.1038/s41421-020-0168-9
Xiong_bulk_PBMC_gene_signature_up: Xiong Y, Liu Y, Cao L, et al. 2020. "Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients." Emerging Microbes & Infections 9 (1):761-770. https://doi/org/10.1080/22221751.2020.1747363
Xiong_bulk_PBMC_gene_signature_down: Xiong Y, Liu Y, Cao L, et al. 2020. "Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients." Emerging Microbes & Infections 9 (1):761-770. https://doi/org/10.1080/22221751.2020.1747363
Xiong_sc_PBMC_cytokines_up: Xiong Y, Liu Y, Cao L, et al. 2020. "Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients." Emerging Microbes & Infections 9 (1):761-770. https://doi/org/10.1080/22221751.2020.1747363
Xiong_sc_PBMC_cytokines_down: Xiong Y, Liu Y, Cao L, et al. 2020. "Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients." Emerging Microbes & Infections 9 (1):761-770. https://doi/org/10.1080/22221751.2020.1747363
Liao_sc_BALF_G1_macrophages: Liao, M., Liu, Y., Yuan, J. et al. 2020. "Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19." Nature Medicine 26 (6): 842-844. https://doi.org/10.1038/s41591-020-0901-9
Liao_sc_BALF_G1_2_macrophages: Liao, M., Liu, Y., Yuan, J. et al. 2020. "Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19." Nature Medicine 26 (6): 842-844. https://doi.org/10.1038/s41591-020-0901-9
Liao_sc_BALF_G2_macrophages: Liao, M., Liu, Y., Yuan, J. et al. 2020. "Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19." Nature Medicine 26 (6): 842-844. https://doi.org/10.1038/s41591-020-0901-9
Liao_sc_BALF_G3_macrophages: Liao, M., Liu, Y., Yuan, J. et al. 2020. "Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19." Nature Medicine 26 (6): 842-844. https://doi.org/10.1038/s41591-020-0901-9
Liao_sc_BALF_G4_macrophages: Liao, M., Liu, Y., Yuan, J. et al. 2020. "Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19." Nature Medicine 26 (6): 842-844. https://doi.org/10.1038/s41591-020-0901-9
Liao_sc_BALF_CD8_T_cells_up: Liao, M., Liu, Y., Yuan, J. et al. 2020. "Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19." Nature Medicine 26 (6): 842-844. https://doi.org/10.1038/s41591-020-0901-9
Liao_sc_BALF_CD8_T_cells_down: Liao, M., Liu, Y., Yuan, J. et al. 2020. "Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19." Nature Medicine 26 (6): 842-844. https://doi.org/10.1038/s41591-020-0901-9
Hadjadj_nanostring_WB_gene_signature_up: Hadjadj J, Yatim N, Barnabei L, et al. 2020. "Impaired type I interferon activity and inflammatory responses in severe COVID-19 patients." Science 369 (6504): 718-724. https://doi.org/10.1126/science.abc6027
Hadjadj_nanostring_WB_gene_signature_down: Hadjadj J, Yatim N, Barnabei L, et al. 2020. "Impaired type I interferon activity and inflammatory responses in severe COVID-19 patients." Science 369 (6504): 718-724. https://doi.org/10.1126/science.abc6027
Hadjadj_nanostring_WB_ISG_signature: Hadjadj J, Yatim N, Barnabei L, et al. 2020. "Impaired type I interferon activity and inflammatory responses in severe COVID-19 patients." Science 369 (6504): 718-724. https://doi.org/10.1126/science.abc6027
Hadjadj_nanostring_WB_mild_moderate_up: Hadjadj J, Yatim N, Barnabei L, et al. 2020. "Impaired type I interferon activity and inflammatory responses in severe COVID-19 patients." Science 369 (6504): 718-724. https://doi.org/10.1126/science.abc6027
Hadjadj_nanostring_WB_mild_moderate_down: Hadjadj J, Yatim N, Barnabei L, et al. 2020. "Impaired type I interferon activity and inflammatory responses in severe COVID-19 patients." Science 369 (6504): 718-724. https://doi.org/10.1126/science.abc6027
Hadjadj_nanostring_WB_severe_up: Hadjadj J, Yatim N, Barnabei L, et al. 2020. "Impaired type I interferon activity and inflammatory responses in severe COVID-19 patients." Science 369 (6504): 718-724. https://doi.org/10.1126/science.abc6027
Hadjadj_nanostring_WB_severe_down: Hadjadj J, Yatim N, Barnabei L, et al. 2020. "Impaired type I interferon activity and inflammatory responses in severe COVID-19 patients." Science 369 (6504): 718-724. https://doi.org/10.1126/science.abc6027
Hadjadj_nanostring_critical_up: Hadjadj J, Yatim N, Barnabei L, et al. 2020. "Impaired type I interferon activity and inflammatory responses in severe COVID-19 patients." Science 369 (6504): 718-724. https://doi.org/10.1126/science.abc6027
Hadjadj_nanostring_critical_down: Hadjadj J, Yatim N, Barnabei L, et al. 2020. "Impaired type I interferon activity and inflammatory responses in severe COVID-19 patients." Science 369 (6504): 718-724. https://doi.org/10.1126/science.abc6027
Wei_sc_PBMC_inactivated_monocytes: Wei et al. 2020. "Viral Invasion and Type I Interferon Response Characterize the Immunophenotypes during COVID-19 Infection." SSRN: https://dx.doi.org/10.2139/ssrn.3555695
Wei_sc_PBMC_classical_monocytes: Wei et al. 2020. "Viral Invasion and Type I Interferon Response Characterize the Immunophenotypes during COVID-19 Infection." SSRN: https://dx.doi.org/10.2139/ssrn.3555695
Wei_sc_PBMCs_T_cells: Wei et al. 2020. "Viral Invasion and Type I Interferon Response Characterize the Immunophenotypes during COVID-19 Infection." SSRN: https://dx.doi.org/10.2139/ssrn.3555695
Wei_sc_PBMC_B_cells: Wei et al. 2020. "Viral Invasion and Type I Interferon Response Characterize the Immunophenotypes during COVID-19 Infection." SSRN: https://dx.doi.org/10.2139/ssrn.3555695
Silvin_sc_WB_combined_signature: Silvin A, Chapuis N, Dunsmore G, et al. 2020. "Elevated Calprotectin and Abnormal Myeloid Cell Subsets Discriminate Severe from Mild COVID-19." Cell 182 (6): 1401-1418.E18. https://doi.org/10.1016/j.cell.2020.08.002
Silvin_sc_WB_monocytes_up: Silvin A, Chapuis N, Dunsmore G, et al. 2020. "Elevated Calprotectin and Abnormal Myeloid Cell Subsets Discriminate Severe from Mild COVID-19." Cell 182 (6): 1401-1418.E18. https://doi.org/10.1016/j.cell.2020.08.002
Silvin_sc_WB_monocytes_down: Silvin A, Chapuis N, Dunsmore G, et al. 2020. "Elevated Calprotectin and Abnormal Myeloid Cell Subsets Discriminate Severe from Mild COVID-19." Cell 182 (6): 1401-1418.E18. https://doi.org/10.1016/j.cell.2020.08.002
Silvin_sc_WB_neutrophils_up: Silvin A, Chapuis N, Dunsmore G, et al. "Elevated Calprotectin and Abnormal Myeloid Cell Subsets Discriminate Severe from Mild COVID-19." Cell 182 (6): 1401-1418.E18. https://doi.org/10.1016/j.cell.2020.08.002
Silvin_sc_WB_neutrophils_down: Silvin A, Chapuis N, Dunsmore G, et al. "Elevated Calprotectin and Abnormal Myeloid Cell Subsets Discriminate Severe from Mild COVID-19." Cell 182 (6): 1401-1418.E18. https://doi.org/10.1016/j.cell.2020.08.002
Arunachalam_bulk_PBMC_blood_modules: Arunachalam PS, Wimmers F, Mok CKP, et al. 2020. "Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans." Science 369 (6508): 1210-1220. https://doi.org/10.1126/science.abc6261
Arunachalam_bulk_PBMC_covid_combined: Arunachalam PS, Wimmers F, Mok CKP, et al. 2020. "Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans." Science 369 (6508): 1210-1220. https://doi.org/10.1126/science.abc6261
Arunachalam_bulk_PBMC_moderate: Arunachalam PS, Wimmers F, Mok CKP, et al. 2020. "Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans." Science 369 (6508): 1210-1220. https://doi.org/10.1126/science.abc6261
Arunachalam_bulk_PBMC_severe: Arunachalam PS, Wimmers F, Mok CKP, et al. 2020. "Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans." Science 369 (6508): 1210-1220. https://doi.org/10.1126/science.abc6261
Arunachalam_bulk_PBMC_intensive_care: Arunachalam PS, Wimmers F, Mok CKP, et al. 2020. "Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans." Science 369 (6508): 1210-1220. https://doi.org/10.1126/science.abc6261
Dunning_bulk_WB_flu: Dunning J, Blankley S, Hoang LT, et al. 2018. "Progression of whole-blood transcriptional signatures from interferon-induced to neutrophil-associated patterns in severe influenza." Nature Immunology 19 (6): 625-635. https://doi.org/10.1038/s41590-018-0111-5