These genes were taken from table S2 and represent genes that are upregulated in human bronchial epithelial (NHBE) cells after SARS-CoV2 infection. Gene symbols were converted to HGNC identifiers. These genes represent those differentially expressed with an adjusted p-value of p<0.01 and a fold change limit of 1.5. Values given are log fold change. SARS-CoV2 is the virus that causes COVID-19.
These genes were taken from table S2 and represent genes that are downregulated in human bronchial epithelial (NHBE) cells after SARS-CoV2 infection. Gene symbols were converted to HGNC identifiers. These genes represent those differentially expressed with an adjusted p-value of p<0.01 and a fold change limit of 1.5. Values given are log fold change. SARS-CoV2 is the virus that causes COVID-19.
These genes were taken from table S2 and represent genes that are upregulated in 2B4 cells lines after SARS-CoV1 infection and are also differentially regulated in bronchial epithelial cells after SARS-CoV2 infection. Gene symbols were converted to HGNC identifiers. These genes represent those differentially expressed with an adjusted p-value of p<0.01. Values given are log fold change.
These genes were taken from table S2 and represent genes that are downregulated in 2B4 cells lines after SARS-CoV1 infection and are also differentially regulated in bronchial epithelial cells after SARS-CoV2 infection. Gene symbols were converted to HGNC identifiers. These genes represent those differentially expressed with an adjusted p-value of p<0.01. Values given are log fold change.
The GEO2R tool was used to analyze microarray data from mice either mock-infected or infected with SARS-CoV1. The Gene sets used in the analysis were from GSE59185. GEO2R was used with default parameters. Genes with an adjusted p-value of <0.05 and a log fold change <-1.0 are included in this set. EntrezGene identifiers or sequence identifiers were converted to MGI identifiers. Genes that could not be converted were omitted. If a gene was represented more than once, the largest fold-change was chosen.
Authors:
Jose A Regla-Nava, Jose L Nieto-Torres, Jose M Jimenez-Guardeño, Raul Fernandez-Delgado, Craig Fett, Carlos Castaño-RodrÃguez, Stanley Perlman, Luis Enjuanes, Marta L DeDiego
This gene set describes genes that are up-regulated by the host transcriptional response to SARS-CoV-2 infection in normal human bronchial epithelium cells (NHBE). COVID-19 is the disease caused by SARS-CoV-2 virus. We define up-regulated as those genes that show a (log 2 fold change) of >=2. These data are from the supplementary materials associated with the publication.
Authors:
Daniel Blanco-Melo, Benjamin E Nilsson-Payant, Wen-Chun Liu, Skyler Uhl, Daisy Hoagland, Rasmus Møller, Tristan X Jordan, Kohei Oishi, Maryline Panis, David Sachs, Taia T Wang, Robert E Schwartz, Jean K Lim, Randy A Albrecht, Benjamin R tenOever
This gene set describes genes that are up-regulated by the host transcriptional response to SARS-CoV-2 infection in human lung adenocarcinoma epithelial cells derived from pleural effusion (Calu3). COVID-19 is the disease caused by SARS-CoV-2 virus. We define up-regulated as those genes that show a (log 2 fold change) of >=2. These data are from the supplementary materials associated with the publication.
Authors:
Daniel Blanco-Melo, Benjamin E Nilsson-Payant, Wen-Chun Liu, Skyler Uhl, Daisy Hoagland, Rasmus Møller, Tristan X Jordan, Kohei Oishi, Maryline Panis, David Sachs, Taia T Wang, Robert E Schwartz, Jean K Lim, Randy A Albrecht, Benjamin R tenOever
This gene set describes genes that are up-regulated by the host transcriptional response to SARS-CoV-2 infection in human adenocarcinomic alveolar basal epithelial (A549) cells. COVID-19 is the disease caused by SARS-CoV-2 virus. We define up-regulated as those genes that show a (log 2 fold change) of >=2. These data are from the supplementary materials associated with the publication.
Authors:
Daniel Blanco-Melo, Benjamin E Nilsson-Payant, Wen-Chun Liu, Skyler Uhl, Daisy Hoagland, Rasmus Møller, Tristan X Jordan, Kohei Oishi, Maryline Panis, David Sachs, Taia T Wang, Robert E Schwartz, Jean K Lim, Randy A Albrecht, Benjamin R tenOever
The GEO2R tool was used to analyze microarray data from lungs of mice either mock-infected or infected with SARS-CoV1. The Gene sets used in the analysis were from GSE59185. GEO2R was used with default parameters. Genes with an adjusted p-value of <0.05 and a log fold change >1.0 are included in this set. EntrezGene identifiers or sequence identifiers were converted to MGI identifiers. Genes that could not be converted were omitted. If a gene was represented more than once, the largest fold-change was chosen.
Authors:
Jose A Regla-Nava, Jose L Nieto-Torres, Jose M Jimenez-Guardeño, Raul Fernandez-Delgado, Craig Fett, Carlos Castaño-RodrÃguez, Stanley Perlman, Luis Enjuanes, Marta L DeDiego
This gene set represents host genes that are required for SARS-CoV-2 infection. The genes were identified by a CRISPR screen in alveolar basal epithelial carcinoma cells. This set represents the top 100 scoring genes at a low multiplicity of infection, moi 0.01. Gene symbols of ranked genes in supplemental table 1 were converted to HGNC identifiers. Symbols that could not be unambiguously converted were omitted from the set.
Authors:
Zharko Daniloski, Tristan X Jordan, Hans-Hermann Wessels, Daisy A Hoagland, Silva Kasela, Mateusz Legut, Silas Maniatis, Eleni P Mimitou, Lu Lu, Evan Geller, Oded Danziger, Brad R Rosenberg, Hemali Phatnani, Peter Smibert, Tuuli Lappalainen, Benjamin R tenOever, Neville E Sanjana
This gene set represents host genes that are required for SARS-CoV-2 infection. The genes were identified by a CRISPR screen in alveolar basal epithelial carcinoma cells and necessity was confirmed using other methods. This set represents the top 100 scoring genes at a high multiplicity of infection, moi 0.3. Gene symbols of ranked genes in supplemental table 1 were converted to HGNC identifiers. Symbols that could not be unambiguously converted were omitted from the set.
Authors:
Zharko Daniloski, Tristan X Jordan, Hans-Hermann Wessels, Daisy A Hoagland, Silva Kasela, Mateusz Legut, Silas Maniatis, Eleni P Mimitou, Lu Lu, Evan Geller, Oded Danziger, Brad R Rosenberg, Hemali Phatnani, Peter Smibert, Tuuli Lappalainen, Benjamin R tenOever, Neville E Sanjana
These genes were taken from table S2 and represent genes that are upregulated in human liver Huh cells after Ebola virus infection and are also differentially regulated in bronchial epithelial cells after SARS-CoV2 infection. Gene symbols were converted to HGNC identifiers. These genes represent those differentially expressed with an adjusted p-value of p<0.01. Values given are log fold change.
These genes were taken from table S2 and represent genes that are downregulated in human liver Huh cells after Ebola virus infection and are also differentially regulated in bronchial epithelial cells after SARS-CoV2 infection. Gene symbols were converted to HGNC identifiers. These genes represent those differentially expressed with an adjusted p-value of p<0.01. Values given are log fold change.
These genes were taken from table S2 and represent genes that are upregulated in human blood after H1N1 virus infection and are also differentially regulated in bronchial epithelial cells after SARS-CoV2 infection. Gene symbols were converted to HGNC identifiers. These genes represent those differentially expressed with an adjusted p-value of p<0.01. Values given are log fold change.
These genes were taken from table S2 and represent genes that are downregulated in human blood after H1N1 virus infection and are also differentially regulated in bronchial epithelial cells after SARS-CoV2 infection. Gene symbols were converted to HGNC identifiers. These genes represent those differentially expressed with an adjusted p-value of p<0.01. Values given are log fold change.
Up in human epithelial airway cells after MERS-CoV infection
Description:
These genes were taken from table S2 and represent genes that are upregulated in human epithelial airway cells after MERS-CoV infection and are also differentially regulated in bronchial epithelial cells after SARS-CoV2 infection. Gene symbols were converted to HGNC identifiers. These genes represent those differentially expressed with an adjusted p-value of p<0.01. Values given are log fold change.
Down in human epithelial airway cells after MERS-CoV infection
Description:
These genes were taken from table S2 and represent genes that are downregulated in human epithelial airway cells after MERS-CoV infection and are also differentially regulated in bronchial epithelial cells after SARS-CoV2 infection. Gene symbols were converted to HGNC identifiers. These genes represent those differentially expressed with an adjusted p-value of p<0.01. Values given are log fold change.
This gene set describes genes that are up-regulated in post-mortem lung samples from COVID-19-positive patients relative to biopsied healthy lung tissue from uninfected individuals. COVID-19 is the disease caused by SARS-CoV-2 virus. We define up-regulated as those genes that show a (log 2 fold change) of >=2. These data are from the supplementary materials associated with the publication. Note: the following HGNC id is part of this data set but was not recognized HGNC:13378.
Authors:
Daniel Blanco-Melo, Benjamin E Nilsson-Payant, Wen-Chun Liu, Skyler Uhl, Daisy Hoagland, Rasmus Møller, Tristan X Jordan, Kohei Oishi, Maryline Panis, David Sachs, Taia T Wang, Robert E Schwartz, Jean K Lim, Randy A Albrecht, Benjamin R tenOever
Gene Ontology (GO) gene set. This set contains genes that have been annotated to the GO term "Sar guanyl-nucleotide exchange factor activity", which is defined as "Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Sar family. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase." This gene set was automatically constructed using annotation and ontology data provided by GO and only includes annotations with experimental and curatorial evidence codes (EXP, IDA, IPI, IMP, IGI, IEP, TAS, IC). The transitive closure of this term is taken into account using is_a and part_of relationships. For more information: The Gene Ontology Consortium (GOC), http://geneontology.org This gene set was generated using the GeneWeaver GO loader v. 0.2.8.
Authors:
M Ashburner, CA Ball, JA Blake, D Botstein, H Butler, JM Cherry, AP Davis, K Dolinski, SS Dwight, JT Eppig, MA Harris, DP Hill, L Issel-Tarver, A Kasarskis, S Lewis, JC Matese, JE Richardson, M Ringwald, GM Rubin, G Sherlock
Gene Ontology (GO) gene set. This set contains genes that have been annotated to the GO term "Sar guanyl-nucleotide exchange factor activity", which is defined as "Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Sar family. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase." This gene set was automatically constructed using annotation and ontology data provided by GO and only includes annotations with experimental and curatorial evidence codes (EXP, IDA, IPI, IMP, IGI, IEP, TAS, IC). The transitive closure of this term is taken into account using is_a and part_of relationships. For more information: The Gene Ontology Consortium (GOC), http://geneontology.org This gene set was generated using the GeneWeaver GO loader v. 0.2.8.
Authors:
M Ashburner, CA Ball, JA Blake, D Botstein, H Butler, JM Cherry, AP Davis, K Dolinski, SS Dwight, JT Eppig, MA Harris, DP Hill, L Issel-Tarver, A Kasarskis, S Lewis, JC Matese, JE Richardson, M Ringwald, GM Rubin, G Sherlock
Genes significantly upregulated (p < 0.05) in bronchoalveolar lavage fluid (BALF) from SARS-CoV2 patients compared to healthy donors. Genes were taken from the BALF DEGs tab of Supplementary File 1 with value = "Up" in "Tag" column. Values are log2 fold change. Genes were entered as base Ensemble IDs. The following gene identifiers were not in GeneWeaver at the time of loading: ENSG00000285704, ENSG00000227081, ENSG00000264895, ENSG00000233762, ENSG00000277534, ENSG00000279166, ENSG00000264853, ENSG00000213197, ENSG00000287085, ENSG00000218175, ENSG00000279133, ENSG00000244313, ENSG00000229119, ENSG00000185641, ENSG00000259600, ENSG00000287613, ENSG00000242299, ENSG00000228655, ENSG00000279483, ENSG00000286545, ENSG00000236439, ENSG00000234287, ENSG00000251076, ENSG00000286830, ENSG00000253339, ENSG00000272211, ENSG00000244398, ENSG00000250461, ENSG00000185495, ENSG00000219023, ENSG00000228793, ENSG00000274173, ENSG00000279544, ENSG00000217130, ENSG00000231856, ENSG00000258752, ENSG00000178715, ENSG00000218426, ENSG00000227615, ENSG00000281383, ENSG00000214530.
Authors:
Yong Xiong, Yuan Liu, Liu Cao, Dehe Wang, Ming Guo, Ao Jiang, Dong Guo, Wenjia Hu, Jiayi Yang, Zhidong Tang, Honglong Wu, Yongquan Lin, Meiyuan Zhang, Qi Zhang, Mang Shi, Yingle Liu, Yu Zhou, Ke Lan, Yu Chen
Genes significantly downregulated (p < 0.05) in bronchoalveolar lavage fluid (BALF) from SARS-CoV2 patients compared to healthy donors. Genes were taken from the BALF DEGs tab of Supplementary File 1 with value = "Down" in "Tag" column. Values are log2 fold change. Genes were entered as base Ensemble IDs.
Authors:
Yong Xiong, Yuan Liu, Liu Cao, Dehe Wang, Ming Guo, Ao Jiang, Dong Guo, Wenjia Hu, Jiayi Yang, Zhidong Tang, Honglong Wu, Yongquan Lin, Meiyuan Zhang, Qi Zhang, Mang Shi, Yingle Liu, Yu Zhou, Ke Lan, Yu Chen
Genes significantly upregulated (p < 0.05) in peripheral blood mononuclear cells (PBMC) specimens from SARS-CoV2 patients compared to healthy donors. Genes were taken from the PBMC DEGs tab of Supplementary File 1 with value = "Up" in "Tag" column. Values are log2 fold change. Genes were entered as base Ensemble IDs. The following gene identifiers were not in GeneWeaver at the time of loading: ENSG00000255306, ENSG00000235328, ENSG00000262202, ENSG00000279400, ENSG00000279227, ENSG00000186076, ENSG00000271122, ENSG00000287431, ENSG00000279605, ENSG00000235027, ENSG00000216285, ENSG00000247134, ENSG00000240859, ENSG00000251429, ENSG00000246731, ENSG00000250771, ENSG00000108958, ENSG00000264456, ENSG00000286194, ENSG00000276216, ENSG00000287979, ENSG00000259319, ENSG00000285646, ENSG00000272720, ENSG00000185839, ENSG00000274922, ENSG00000136315, ENSG00000230699, ENSG00000272825, ENSG00000270022.
Authors:
Yong Xiong, Yuan Liu, Liu Cao, Dehe Wang, Ming Guo, Ao Jiang, Dong Guo, Wenjia Hu, Jiayi Yang, Zhidong Tang, Honglong Wu, Yongquan Lin, Meiyuan Zhang, Qi Zhang, Mang Shi, Yingle Liu, Yu Zhou, Ke Lan, Yu Chen
Genes significantly downregulated (p < 0.05) in peripheral blood mononuclear cells (PBMC) specimens from SARS-CoV2 patients compared to healthy donors. Genes were taken from the PBMC DEGs tab of Supplementary File 1 with value = "Up" in "Tag" column. Values are log2 fold change. Genes were entered as base Ensemble IDs. The following gene identifiers were not in GeneWeaver at the time of loading: ENSG00000277739, ENSG00000236213, ENSG00000273824, ENSG00000285366, ENSG00000267523, ENSG00000260719, ENSG00000257176, ENSG00000261324, ENSG00000236449, ENSG00000279884, ENSG00000226380, ENSG00000276136, ENSG00000174171, ENSG00000260891, ENSG00000253736, ENSG00000253720, ENSG00000276853, ENSG00000279908, ENSG00000272256, ENSG00000273319, ENSG00000231858, ENSG00000286145, ENSG00000283674, ENSG00000284707, ENSG00000228655, ENSG00000251034, ENSG00000257802, ENSG00000278962, ENSG00000257277, ENSG00000233392, ENSG00000250696, ENSG00000287195, ENSG00000228140, ENSG00000231769, ENSG00000258875, ENSG00000273066, ENSG00000234156, ENSG00000273160, ENSG00000287218, ENSG00000273038, ENSG00000261208, ENSG00000287070, ENSG00000285847, ENSG00000234268, ENSG00000273284, ENSG00000287425, ENSG00000255545, ENSG00000264063, ENSG00000280614, ENSG00000281181, ENSG00000277437, ENSG00000280800, ENSG00000281383, ENSG00000268154, ENSG00000227598, ENSG00000285730.
Authors:
Yong Xiong, Yuan Liu, Liu Cao, Dehe Wang, Ming Guo, Ao Jiang, Dong Guo, Wenjia Hu, Jiayi Yang, Zhidong Tang, Honglong Wu, Yongquan Lin, Meiyuan Zhang, Qi Zhang, Mang Shi, Yingle Liu, Yu Zhou, Ke Lan, Yu Chen
Inflammatory cytokines significantly downregulated (p < 0.05) in bronchoalveolar lavage fluid (BALF) from SARS-CoV2 patients compared to healthy donors. Genes were taken from starred genes in Figure 4A and which have value = "Down" in "Tag" column of the BALF DEGs tab of Supplementary File 1. This tab is also the source of the values, which are log2 fold change and the gene IDs, which were entered as base Ensemble IDs.
Authors:
Yong Xiong, Yuan Liu, Liu Cao, Dehe Wang, Ming Guo, Ao Jiang, Dong Guo, Wenjia Hu, Jiayi Yang, Zhidong Tang, Honglong Wu, Yongquan Lin, Meiyuan Zhang, Qi Zhang, Mang Shi, Yingle Liu, Yu Zhou, Ke Lan, Yu Chen
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