common_sigAnnotData: Annotation information for published TB signatures.
In TBSignatureProfiler: Profile RA-Seq Data Using TB Pathway Signatures
Description
Usage
Format
Details
Source
Examples
Description
A data.frame of annotation information for published tuberculosis
signatures. This table differs from that of sigAnnotData as it
refers to signatures via the name given in scientific publications, and
via a consistent naming system otherwise.
Currently, this table includes two variables, disease and
tissue type.
Usage
1
Format
data.frame
Details
The disease variable indicates whether the signature was developed
to distinguish TB from LTBI ("Disease"), TB from some combination of other
diseases and possibly LTBI ("OD"), TB from Human Immunodeficiency Virus ("HIV"),
TB from pneumonia ("PNA"), or identify risk of progression to TB ("RISK"),
risk of TB treatment failure ("FAIL"), or classify treatment responses
(i.e., failures from cures, "RES").
The tissue type variable denotes whether the signature was developed
using samples of either whole blood/paxgene or peripheral blood mononuclear
cells (PBMCs). Due to the manipulation of cells inherently required to obtain
PBMCs, many scientists prefer to use only whole blood samples for analysis.
Source
Anderson_42: Anderson, Suzanne T., Myrsini Kaforou, Andrew J. Brent, Victoria J. Wright, Claire M. Banwell, George Chagaluka, Amelia C. Crampin, et al. 2014. "Diagnosis of Childhood Tuberculosis and Host RNA Expression in Africa." The New England Journal of Medicine 370 (18): 1712-23. 10.1056/NEJMoa1303657
Anderson_OD_51: Anderson, Suzanne T., Myrsini Kaforou, Andrew J. Brent, Victoria J. Wright, Claire M. Banwell, George Chagaluka, Amelia C. Crampin, et al. 2014. "Diagnosis of Childhood Tuberculosis and Host RNA Expression in Africa." The New England Journal of Medicine 370 (18): 1712-23. 10.1056/NEJMoa1303657
Berry_393: Berry, Matthew P. R., Christine M. Graham, Finlay W. McNab, Zhaohui Xu, Susannah A. A. Bloch, Tolu Oni, Katalin A. Wilkinson, et al. 2010. "An Interferon-Inducible Neutrophil-Driven Blood Transcriptional Signature in Human Tuberculosis." Nature 466 (7309): 973-77. 10.1038/nature09247
Berry_OD_86: Berry, Matthew P. R., Christine M. Graham, Finlay W. McNab, Zhaohui Xu, Susannah A. A. Bloch, Tolu Oni, Katalin A. Wilkinson, et al. 2010. "An Interferon-Inducible Neutrophil-Driven Blood Transcriptional Signature in Human Tuberculosis." Nature 466 (7309): 973-77. 10.1038/nature09247
Blankley_5: Blankley, Simon, Christine M. Graham, Joe Levin, Jacob Turner, Matthew P. R. Berry, Chloe I. Bloom, Zhaohui Xu, et al. 2016. "A 380-Gene Meta-Signature of Active Tuberculosis Compared with Healthy Controls." The European Respiratory Journal: Official Journal of the European Society for Clinical Respiratory Physiology 47 (6): 1873-76. 10.1183/13993003.02121-2015
Blankley_380: Blankley, Simon, Christine M. Graham, Joe Levin, Jacob Turner, Matthew P. R. Berry, Chloe I. Bloom, Zhaohui Xu, et al. 2016. "A 380-Gene Meta-Signature of Active Tuberculosis Compared with Healthy Controls." The European Respiratory Journal: Official Journal of the European Society for Clinical Respiratory Physiology 47 (6): 1873-76. 10.1183/13993003.02121-2015
Bloom_OD_144: Bloom, Chloe I., Christine M. Graham, Matthew P. R. Berry, Fotini Rozakeas, Paul S. Redford, Yuanyuan Wang, Zhaohui Xu, et al. 2013. "Transcriptional Blood Signatures Distinguish Pulmonary Tuberculosis, Pulmonary Sarcoidosis, Pneumonias and Lung Cancers." PloS One 8 (8): e70630. 10.1371/journal.pone.0070630
Esmail_82: Esmail, Hanif, Rachel P. Lai, Maia Lesosky, Katalin A. Wilkinson, Christine M. Graham, Stuart Horswell, Anna K. Coussens, Clifton E. Barry 3rd, Anne O'Garra, and Robert J. Wilkinson. 2018. "Complement Pathway Gene Activation and Rising Circulating Immune Complexes Characterize Early Disease in HIV-Associated Tuberculosis." Proceedings of the National Academy of Sciences of the United States of America 115 (5): E964-73. 10.1073/pnas.1711853115
Esmail_203: Esmail, Hanif, Rachel P. Lai, Maia Lesosky, Katalin A. Wilkinson, Christine M. Graham, Stuart Horswell, Anna K. Coussens, Clifton E. Barry 3rd, Anne O'Garra, and Robert J. Wilkinson. 2018. "Complement Pathway Gene Activation and Rising Circulating Immune Complexes Characterize Early Disease in HIV-Associated Tuberculosis." Proceedings of the National Academy of Sciences of the United States of America 115 (5): E964-73. 10.1073/pnas.1711853115
Esmail_893: Esmail, Hanif, Rachel P. Lai, Maia Lesosky, Katalin A. Wilkinson, Christine M. Graham, Stuart Horswell, Anna K. Coussens, Clifton E. Barry 3rd, Anne O'Garra, and Robert J. Wilkinson. 2018. "Complement Pathway Gene Activation and Rising Circulating Immune Complexes Characterize Early Disease in HIV-Associated Tuberculosis." Proceedings of the National Academy of Sciences of the United States of America 115 (5): E964-73. 10.1073/pnas.1711853115
Gliddon_OD_3: Gliddon, Harriet D., Kaforou, Myrsini, Alikian, Mary, Habgood-Coote, Dominic, Zhou, Chenxi, Oni, Tolu, Anderson, Suzanne T., Brent, Andrew J., Crampin, Amelia C., Eley, Brian, Kern, Florian, Langford, Paul R., Ottenhoff, Tom H. M., Hibberd, Martin L., French, Neil, Wright, Victoria J., Dockrell, Hazel M., Coin, Lachlan J., Wilkinson, Robert J., Levin, Michael. 2019 "Identification of reduced host transcriptomic signatures for tuberculosis and digital PCR-based validation and quantification" biorxiv.org: . 10.1101/583674
Gliddon_OD_4: Gliddon, Harriet D., Kaforou, Myrsini, Alikian, Mary, Habgood-Coote, Dominic, Zhou, Chenxi, Oni, Tolu, Anderson, Suzanne T., Brent, Andrew J., Crampin, Amelia C., Eley, Brian, Kern, Florian, Langford, Paul R., Ottenhoff, Tom H. M., Hibberd, Martin L., French, Neil, Wright, Victoria J., Dockrell, Hazel M., Coin, Lachlan J., Wilkinson, Robert J., Levin, Michael. 2019 "Identification of reduced host transcriptomic signatures for tuberculosis and digital PCR-based validation and quantification" biorxiv.org: . 10.1101/583674
Jacobsen_3: Jacobsen, Marc, Dirk Repsilber, Andrea Gutschmidt, Albert Neher, Knut Feldmann, Hans J. Mollenkopf, Andreas Ziegler, and Stefan H. E. Kaufmann. 2007. "Candidate Biomarkers for Discrimination between Infection and Disease Caused by Mycobacterium Tuberculosis." Journal of Molecular Medicine 85 (6): 613-21. 10.1007/s00109-007-0157-6
Kaforou_27: Kaforou, Myrsini, Victoria J. Wright, Tolu Oni, Neil French, Suzanne T. Anderson, Nonzwakazi Bangani, Claire M. Banwell, et al. 2013. "Detection of Tuberculosis in HIV-Infected and -Uninfected African Adults Using Whole Blood RNA Expression Signatures: A Case-Control Study." PLoS Medicine 10 (10): e1001538. 10.1371/journal.pmed.1001538
Kaforou_OD_44: Kaforou, Myrsini, Victoria J. Wright, Tolu Oni, Neil French, Suzanne T. Anderson, Nonzwakazi Bangani, Claire M. Banwell, et al. 2013. "Detection of Tuberculosis in HIV-Infected and -Uninfected African Adults Using Whole Blood RNA Expression Signatures: A Case-Control Study." PLoS Medicine 10 (10): e1001538. 10.1371/journal.pmed.1001538
Kaforou_OD_53: Kaforou, Myrsini, Victoria J. Wright, Tolu Oni, Neil French, Suzanne T. Anderson, Nonzwakazi Bangani, Claire M. Banwell, et al. 2013. "Detection of Tuberculosis in HIV-Infected and -Uninfected African Adults Using Whole Blood RNA Expression Signatures: A Case-Control Study." PLoS Medicine 10 (10): e1001538. 10.1371/journal.pmed.1001538
Lee_4: Lee, Shih-Wei, Lawrence Shih-Hsin Wu, Guan-Mau Huang, Kai-Yao Huang, Tzong-Yi Lee, and Julia Tzu-Ya Weng. 2016. "Gene Expression Profiling Identifies Candidate Biomarkers for Active and Latent Tuberculosis." BMC Bioinformatics 17 Suppl 1 (January): 3. 10.1186/s12859-015-0848-x
PREDICT29: Leong, S., Zhao, Y., Ribeiro-Rodrigues, R., Jones-L<c3><b3>pez, E. C., Acu<c3><b1>a-Villaordu<c3><b1>a, C., Rodrigues, P. M., Palaci, M., Alland, D., Dietze, R., Ellner, J. J., Johnson, W. E., Salgame, P., Cross-validation of existing signatures and derivation of a novel 29-gene transcriptomic signature predictive of progression to TB in a Brazilian cohort of household contacts of pulmonary TB. Tuberculosis (Edinb). 2020 Jan;120:101898. 10.1016/j.tube.2020.101898
DIAG4: Maertzdorf, Jeroen, Gayle McEwen, January Weiner 3rd, Song Tian, Eric Lader, Ulrich Schriek, Harriet Mayanja-Kizza, Martin Ota, John Kenneth, and Stefan He Kaufmann. 2016. "Concise Gene Signature for Point-of-Care Classification of Tuberculosis." EMBO Molecular Medicine 8 (2): 86-95. 10.15252/emmm.201505790
Maertzdorf_OD_100: Maertzdorf, Jeroen, January Weiner 3rd, Hans-Joachim Mollenkopf, TBornot TB Network, Torsten Bauer, Antje Prasse, Joachim M<c3><bc>ller-Quernheim, and Stefan H. E. Kaufmann. 2012. "Common Patterns and Disease-Related Signatures in Tuberculosis and Sarcoidosis." Proceedings of the National Academy of Sciences of the United States of America 109 (20): 7853-58. 10.1073/pnas.1121072109
Rajan_HIV_5: Rajan, Jayant V., Semitala, Fred C., Kamya, Moses R., Yoon, Christina., Mehta, Tejas., Cattamanchi, Adithya., Seielstad, Mark., Montalvo, Lani., Andama, Alfred., Katende, Jane., Asege, Lucy., Nakaye, Martha., Mwebe, Sandra. 2018 "A Novel, 5-Transcript, Whole-blood Gene-expression Signature for Tuberculosis Screening Among People Living With Human Immunodeficiency Virus" Clinical Infectious Diseases: 1-7. 10.1093/cid/ciy835
Roe_3: Roe, Jennifer, Venturini, Cristina, Gupta, Rishi K., Gurry, Celine, Chain, Benjamin M., Sun, Yuxin, Southern, Jo, Jackson, Charlotte, Lipman, Marc, C., Miller, Robert F., Martineau, Adrian R., Abubakar, Ibrahim, Noursadeghi, Mahdad. 2019 "T1 Blood transcriptomic stratification of short-term risk in contacts of tuberculosis": . 10.1093/cid/ciz252
Roe_OD_4: Roe, Jennifer K., Niclas Thomas, Eliza Gil, Katharine Best, Evdokia Tsaliki, Stephen Morris-Jones, Sian Stafford, et al. 2016. "Blood Transcriptomic Diagnosis of Pulmonary and Extrapulmonary Tuberculosis." JCI Insight 1 (16): e87238. 10.1172/jci.insight.87238
Sambarey_HIV_10: Sambarey, Awanti, Abhinandan Devaprasad, Abhilash Mohan, Asma Ahmed, Soumya Nayak, Soumya Swaminathan, George D'Souza, et al. 2017. "Unbiased Identification of Blood-Based Biomarkers for Pulmonary Tuberculosis by Modeling and Mining Molecular Interaction Networks." EBioMedicine 15 (February): 112-26. 10.1016/j.ebiom.2016.12.009
Singhania_OD_20: Singhania, Akul, Raman Verma, Christine M. Graham, Jo Lee, Trang Tran, Matthew Richardson, Patrick Lecine, et al. 2018. "A Modular Transcriptional Signature Identifies Phenotypic Heterogeneity of Human Tuberculosis Infection." Nature Communications 9 (1): 2308. 10.1038/s41467-018-04579-w
Sloot_HIV_2: Sloot, Rosa, Maarten F. Schim van der Loeff, Erik W. van Zwet, Mari<c3><ab>lle C. Haks, Sytze T. Keizer, Maarten Scholing, Tom H. M. Ottenhoff, Martien W. Borgdorff, and Simone A. Joosten. 2015. "Biomarkers Can Identify Pulmonary Tuberculosis in HIV-Infected Drug Users Months Prior to Clinical Diagnosis." EBioMedicine 2 (2): 172-79. 10.1016/j.ebiom.2014.12.001
Suliman_4: Suliman, Sara, Ethan Thompson, Jayne Sutherland, January Weiner Rd, Martin O. C. Ota, Smitha Shankar, Adam Penn-Nicholson, et al. 2018. "Four-Gene Pan-African Blood Signature Predicts Progression to Tuberculosis." American Journal of Respiratory and Critical Care Medicine, April. https://doi.org/10.1164/rccm.201711-2340OC. 10.1164/rccm.201711-2340OC
RISK4: Suliman, Sara, Ethan Thompson, Jayne Sutherland, January Weiner Rd, Martin O. C. Ota, Smitha Shankar, Adam Penn-Nicholson, et al. 2018. "Four-Gene Pan-African Blood Signature Predicts Progression to Tuberculosis." American Journal of Respiratory and Critical Care Medicine, April. https://doi.org/10.1164/rccm.201711-2340OC. 10.1164/rccm.201711-2340OC
DIAG3: Sweeney, Timothy E., Lindsay Braviak, Cristina M. Tato, and Purvesh Khatri. 2016. "Genome-Wide Expression for Diagnosis of Pulmonary Tuberculosis: A Multicohort Analysis." The Lancet. Respiratory Medicine 4 (3): 213-24. 10.1016/S2213-2600(16)00048-5
DISEASE: Thompson, Ethan G., Ying Du, Stephanus T. Malherbe, Smitha Shankar, Jackie Braun, Joe Valvo, Katharina Ronacher, et al. 2017. "Host Blood RNA Signatures Predict the Outcome of Tuberculosis Treatment." Tuberculosis 107 (December): 48-58. 10.1016/j.tube.2017.08.004
FAILURE: Thompson, Ethan G., Ying Du, Stephanus T. Malherbe, Smitha Shankar, Jackie Braun, Joe Valvo, Katharina Ronacher, et al. 2017. "Host Blood RNA Signatures Predict the Outcome of Tuberculosis Treatment." Tuberculosis 107 (December): 48-58. 10.1016/j.tube.2017.08.004
RESPONSE5: Thompson, Ethan G., Ying Du, Stephanus T. Malherbe, Smitha Shankar, Jackie Braun, Joe Valvo, Katharina Ronacher, et al. 2017. "Host Blood RNA Signatures Predict the Outcome of Tuberculosis Treatment." Tuberculosis 107 (December): 48-58. 10.1016/j.tube.2017.08.004
Walter_51: Walter, Nicholas D., Mikaela A. Miller, Joshua Vasquez, Marc Weiner, Adam Chapman, Melissa Engle, Michael Higgins, et al. 2016. "Blood Transcriptional Biomarkers for Active Tuberculosis among Patients in the United States: A Case-Control Study with Systematic Cross-Classifier Evaluation." Journal of Clinical Microbiology 54 (2): 274-82. 10.1128/JCM.01990-15
Walter_PNA_47: Walter, Nicholas D., Mikaela A. Miller, Joshua Vasquez, Marc Weiner, Adam Chapman, Melissa Engle, Michael Higgins, et al. 2016. "Blood Transcriptional Biomarkers for Active Tuberculosis among Patients in the United States: A Case-Control Study with Systematic Cross-Classifier Evaluation." Journal of Clinical Microbiology 54 (2): 274-82. 10.1128/JCM.01990-15
Walter_PNA_119: Walter, Nicholas D., Mikaela A. Miller, Joshua Vasquez, Marc Weiner, Adam Chapman, Melissa Engle, Michael Higgins, et al. 2016. "Blood Transcriptional Biomarkers for Active Tuberculosis among Patients in the United States: A Case-Control Study with Systematic Cross-Classifier Evaluation." Journal of Clinical Microbiology 54 (2): 274-82. 10.1128/JCM.01990-15
ACS_COR: Zak, Daniel E., Adam Penn-Nicholson, Thomas J. Scriba, Ethan Thompson, Sara Suliman, Lynn M. Amon, Hassan Mahomed, et al. 2016. "A Blood RNA Signature for Tuberculosis Disease Risk: A Prospective Cohort Study." The Lancet 387 (10035): 231222. 10.1016/S0140-6736(15)01316-1
Examples
1
data("common_sigAnnotData")
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Description Usage Format Details Source Examples
Description
A data.frame of annotation information for published tuberculosis
signatures. This table differs from that of sigAnnotData as it
refers to signatures via the name given in scientific publications, and
via a consistent naming system otherwise.
Currently, this table includes two variables, disease and
tissue type.
Usage
1 |
Format
data.frame
Details
The disease variable indicates whether the signature was developed
to distinguish TB from LTBI ("Disease"), TB from some combination of other
diseases and possibly LTBI ("OD"), TB from Human Immunodeficiency Virus ("HIV"),
TB from pneumonia ("PNA"), or identify risk of progression to TB ("RISK"),
risk of TB treatment failure ("FAIL"), or classify treatment responses
(i.e., failures from cures, "RES").
The tissue type variable denotes whether the signature was developed
using samples of either whole blood/paxgene or peripheral blood mononuclear
cells (PBMCs). Due to the manipulation of cells inherently required to obtain
PBMCs, many scientists prefer to use only whole blood samples for analysis.
Source
Anderson_42: Anderson, Suzanne T., Myrsini Kaforou, Andrew J. Brent, Victoria J. Wright, Claire M. Banwell, George Chagaluka, Amelia C. Crampin, et al. 2014. "Diagnosis of Childhood Tuberculosis and Host RNA Expression in Africa." The New England Journal of Medicine 370 (18): 1712-23. 10.1056/NEJMoa1303657
Anderson_OD_51: Anderson, Suzanne T., Myrsini Kaforou, Andrew J. Brent, Victoria J. Wright, Claire M. Banwell, George Chagaluka, Amelia C. Crampin, et al. 2014. "Diagnosis of Childhood Tuberculosis and Host RNA Expression in Africa." The New England Journal of Medicine 370 (18): 1712-23. 10.1056/NEJMoa1303657
Berry_393: Berry, Matthew P. R., Christine M. Graham, Finlay W. McNab, Zhaohui Xu, Susannah A. A. Bloch, Tolu Oni, Katalin A. Wilkinson, et al. 2010. "An Interferon-Inducible Neutrophil-Driven Blood Transcriptional Signature in Human Tuberculosis." Nature 466 (7309): 973-77. 10.1038/nature09247
Berry_OD_86: Berry, Matthew P. R., Christine M. Graham, Finlay W. McNab, Zhaohui Xu, Susannah A. A. Bloch, Tolu Oni, Katalin A. Wilkinson, et al. 2010. "An Interferon-Inducible Neutrophil-Driven Blood Transcriptional Signature in Human Tuberculosis." Nature 466 (7309): 973-77. 10.1038/nature09247
Blankley_5: Blankley, Simon, Christine M. Graham, Joe Levin, Jacob Turner, Matthew P. R. Berry, Chloe I. Bloom, Zhaohui Xu, et al. 2016. "A 380-Gene Meta-Signature of Active Tuberculosis Compared with Healthy Controls." The European Respiratory Journal: Official Journal of the European Society for Clinical Respiratory Physiology 47 (6): 1873-76. 10.1183/13993003.02121-2015
Blankley_380: Blankley, Simon, Christine M. Graham, Joe Levin, Jacob Turner, Matthew P. R. Berry, Chloe I. Bloom, Zhaohui Xu, et al. 2016. "A 380-Gene Meta-Signature of Active Tuberculosis Compared with Healthy Controls." The European Respiratory Journal: Official Journal of the European Society for Clinical Respiratory Physiology 47 (6): 1873-76. 10.1183/13993003.02121-2015
Bloom_OD_144: Bloom, Chloe I., Christine M. Graham, Matthew P. R. Berry, Fotini Rozakeas, Paul S. Redford, Yuanyuan Wang, Zhaohui Xu, et al. 2013. "Transcriptional Blood Signatures Distinguish Pulmonary Tuberculosis, Pulmonary Sarcoidosis, Pneumonias and Lung Cancers." PloS One 8 (8): e70630. 10.1371/journal.pone.0070630
Esmail_82: Esmail, Hanif, Rachel P. Lai, Maia Lesosky, Katalin A. Wilkinson, Christine M. Graham, Stuart Horswell, Anna K. Coussens, Clifton E. Barry 3rd, Anne O'Garra, and Robert J. Wilkinson. 2018. "Complement Pathway Gene Activation and Rising Circulating Immune Complexes Characterize Early Disease in HIV-Associated Tuberculosis." Proceedings of the National Academy of Sciences of the United States of America 115 (5): E964-73. 10.1073/pnas.1711853115
Esmail_203: Esmail, Hanif, Rachel P. Lai, Maia Lesosky, Katalin A. Wilkinson, Christine M. Graham, Stuart Horswell, Anna K. Coussens, Clifton E. Barry 3rd, Anne O'Garra, and Robert J. Wilkinson. 2018. "Complement Pathway Gene Activation and Rising Circulating Immune Complexes Characterize Early Disease in HIV-Associated Tuberculosis." Proceedings of the National Academy of Sciences of the United States of America 115 (5): E964-73. 10.1073/pnas.1711853115
Esmail_893: Esmail, Hanif, Rachel P. Lai, Maia Lesosky, Katalin A. Wilkinson, Christine M. Graham, Stuart Horswell, Anna K. Coussens, Clifton E. Barry 3rd, Anne O'Garra, and Robert J. Wilkinson. 2018. "Complement Pathway Gene Activation and Rising Circulating Immune Complexes Characterize Early Disease in HIV-Associated Tuberculosis." Proceedings of the National Academy of Sciences of the United States of America 115 (5): E964-73. 10.1073/pnas.1711853115
Gliddon_OD_3: Gliddon, Harriet D., Kaforou, Myrsini, Alikian, Mary, Habgood-Coote, Dominic, Zhou, Chenxi, Oni, Tolu, Anderson, Suzanne T., Brent, Andrew J., Crampin, Amelia C., Eley, Brian, Kern, Florian, Langford, Paul R., Ottenhoff, Tom H. M., Hibberd, Martin L., French, Neil, Wright, Victoria J., Dockrell, Hazel M., Coin, Lachlan J., Wilkinson, Robert J., Levin, Michael. 2019 "Identification of reduced host transcriptomic signatures for tuberculosis and digital PCR-based validation and quantification" biorxiv.org: . 10.1101/583674
Gliddon_OD_4: Gliddon, Harriet D., Kaforou, Myrsini, Alikian, Mary, Habgood-Coote, Dominic, Zhou, Chenxi, Oni, Tolu, Anderson, Suzanne T., Brent, Andrew J., Crampin, Amelia C., Eley, Brian, Kern, Florian, Langford, Paul R., Ottenhoff, Tom H. M., Hibberd, Martin L., French, Neil, Wright, Victoria J., Dockrell, Hazel M., Coin, Lachlan J., Wilkinson, Robert J., Levin, Michael. 2019 "Identification of reduced host transcriptomic signatures for tuberculosis and digital PCR-based validation and quantification" biorxiv.org: . 10.1101/583674
Jacobsen_3: Jacobsen, Marc, Dirk Repsilber, Andrea Gutschmidt, Albert Neher, Knut Feldmann, Hans J. Mollenkopf, Andreas Ziegler, and Stefan H. E. Kaufmann. 2007. "Candidate Biomarkers for Discrimination between Infection and Disease Caused by Mycobacterium Tuberculosis." Journal of Molecular Medicine 85 (6): 613-21. 10.1007/s00109-007-0157-6
Kaforou_27: Kaforou, Myrsini, Victoria J. Wright, Tolu Oni, Neil French, Suzanne T. Anderson, Nonzwakazi Bangani, Claire M. Banwell, et al. 2013. "Detection of Tuberculosis in HIV-Infected and -Uninfected African Adults Using Whole Blood RNA Expression Signatures: A Case-Control Study." PLoS Medicine 10 (10): e1001538. 10.1371/journal.pmed.1001538
Kaforou_OD_44: Kaforou, Myrsini, Victoria J. Wright, Tolu Oni, Neil French, Suzanne T. Anderson, Nonzwakazi Bangani, Claire M. Banwell, et al. 2013. "Detection of Tuberculosis in HIV-Infected and -Uninfected African Adults Using Whole Blood RNA Expression Signatures: A Case-Control Study." PLoS Medicine 10 (10): e1001538. 10.1371/journal.pmed.1001538
Kaforou_OD_53: Kaforou, Myrsini, Victoria J. Wright, Tolu Oni, Neil French, Suzanne T. Anderson, Nonzwakazi Bangani, Claire M. Banwell, et al. 2013. "Detection of Tuberculosis in HIV-Infected and -Uninfected African Adults Using Whole Blood RNA Expression Signatures: A Case-Control Study." PLoS Medicine 10 (10): e1001538. 10.1371/journal.pmed.1001538
Lee_4: Lee, Shih-Wei, Lawrence Shih-Hsin Wu, Guan-Mau Huang, Kai-Yao Huang, Tzong-Yi Lee, and Julia Tzu-Ya Weng. 2016. "Gene Expression Profiling Identifies Candidate Biomarkers for Active and Latent Tuberculosis." BMC Bioinformatics 17 Suppl 1 (January): 3. 10.1186/s12859-015-0848-x
PREDICT29: Leong, S., Zhao, Y., Ribeiro-Rodrigues, R., Jones-L<c3><b3>pez, E. C., Acu<c3><b1>a-Villaordu<c3><b1>a, C., Rodrigues, P. M., Palaci, M., Alland, D., Dietze, R., Ellner, J. J., Johnson, W. E., Salgame, P., Cross-validation of existing signatures and derivation of a novel 29-gene transcriptomic signature predictive of progression to TB in a Brazilian cohort of household contacts of pulmonary TB. Tuberculosis (Edinb). 2020 Jan;120:101898. 10.1016/j.tube.2020.101898
DIAG4: Maertzdorf, Jeroen, Gayle McEwen, January Weiner 3rd, Song Tian, Eric Lader, Ulrich Schriek, Harriet Mayanja-Kizza, Martin Ota, John Kenneth, and Stefan He Kaufmann. 2016. "Concise Gene Signature for Point-of-Care Classification of Tuberculosis." EMBO Molecular Medicine 8 (2): 86-95. 10.15252/emmm.201505790
Maertzdorf_OD_100: Maertzdorf, Jeroen, January Weiner 3rd, Hans-Joachim Mollenkopf, TBornot TB Network, Torsten Bauer, Antje Prasse, Joachim M<c3><bc>ller-Quernheim, and Stefan H. E. Kaufmann. 2012. "Common Patterns and Disease-Related Signatures in Tuberculosis and Sarcoidosis." Proceedings of the National Academy of Sciences of the United States of America 109 (20): 7853-58. 10.1073/pnas.1121072109
Rajan_HIV_5: Rajan, Jayant V., Semitala, Fred C., Kamya, Moses R., Yoon, Christina., Mehta, Tejas., Cattamanchi, Adithya., Seielstad, Mark., Montalvo, Lani., Andama, Alfred., Katende, Jane., Asege, Lucy., Nakaye, Martha., Mwebe, Sandra. 2018 "A Novel, 5-Transcript, Whole-blood Gene-expression Signature for Tuberculosis Screening Among People Living With Human Immunodeficiency Virus" Clinical Infectious Diseases: 1-7. 10.1093/cid/ciy835
Roe_3: Roe, Jennifer, Venturini, Cristina, Gupta, Rishi K., Gurry, Celine, Chain, Benjamin M., Sun, Yuxin, Southern, Jo, Jackson, Charlotte, Lipman, Marc, C., Miller, Robert F., Martineau, Adrian R., Abubakar, Ibrahim, Noursadeghi, Mahdad. 2019 "T1 Blood transcriptomic stratification of short-term risk in contacts of tuberculosis": . 10.1093/cid/ciz252
Roe_OD_4: Roe, Jennifer K., Niclas Thomas, Eliza Gil, Katharine Best, Evdokia Tsaliki, Stephen Morris-Jones, Sian Stafford, et al. 2016. "Blood Transcriptomic Diagnosis of Pulmonary and Extrapulmonary Tuberculosis." JCI Insight 1 (16): e87238. 10.1172/jci.insight.87238
Sambarey_HIV_10: Sambarey, Awanti, Abhinandan Devaprasad, Abhilash Mohan, Asma Ahmed, Soumya Nayak, Soumya Swaminathan, George D'Souza, et al. 2017. "Unbiased Identification of Blood-Based Biomarkers for Pulmonary Tuberculosis by Modeling and Mining Molecular Interaction Networks." EBioMedicine 15 (February): 112-26. 10.1016/j.ebiom.2016.12.009
Singhania_OD_20: Singhania, Akul, Raman Verma, Christine M. Graham, Jo Lee, Trang Tran, Matthew Richardson, Patrick Lecine, et al. 2018. "A Modular Transcriptional Signature Identifies Phenotypic Heterogeneity of Human Tuberculosis Infection." Nature Communications 9 (1): 2308. 10.1038/s41467-018-04579-w
Sloot_HIV_2: Sloot, Rosa, Maarten F. Schim van der Loeff, Erik W. van Zwet, Mari<c3><ab>lle C. Haks, Sytze T. Keizer, Maarten Scholing, Tom H. M. Ottenhoff, Martien W. Borgdorff, and Simone A. Joosten. 2015. "Biomarkers Can Identify Pulmonary Tuberculosis in HIV-Infected Drug Users Months Prior to Clinical Diagnosis." EBioMedicine 2 (2): 172-79. 10.1016/j.ebiom.2014.12.001
Suliman_4: Suliman, Sara, Ethan Thompson, Jayne Sutherland, January Weiner Rd, Martin O. C. Ota, Smitha Shankar, Adam Penn-Nicholson, et al. 2018. "Four-Gene Pan-African Blood Signature Predicts Progression to Tuberculosis." American Journal of Respiratory and Critical Care Medicine, April. https://doi.org/10.1164/rccm.201711-2340OC. 10.1164/rccm.201711-2340OC
RISK4: Suliman, Sara, Ethan Thompson, Jayne Sutherland, January Weiner Rd, Martin O. C. Ota, Smitha Shankar, Adam Penn-Nicholson, et al. 2018. "Four-Gene Pan-African Blood Signature Predicts Progression to Tuberculosis." American Journal of Respiratory and Critical Care Medicine, April. https://doi.org/10.1164/rccm.201711-2340OC. 10.1164/rccm.201711-2340OC
DIAG3: Sweeney, Timothy E., Lindsay Braviak, Cristina M. Tato, and Purvesh Khatri. 2016. "Genome-Wide Expression for Diagnosis of Pulmonary Tuberculosis: A Multicohort Analysis." The Lancet. Respiratory Medicine 4 (3): 213-24. 10.1016/S2213-2600(16)00048-5
DISEASE: Thompson, Ethan G., Ying Du, Stephanus T. Malherbe, Smitha Shankar, Jackie Braun, Joe Valvo, Katharina Ronacher, et al. 2017. "Host Blood RNA Signatures Predict the Outcome of Tuberculosis Treatment." Tuberculosis 107 (December): 48-58. 10.1016/j.tube.2017.08.004
FAILURE: Thompson, Ethan G., Ying Du, Stephanus T. Malherbe, Smitha Shankar, Jackie Braun, Joe Valvo, Katharina Ronacher, et al. 2017. "Host Blood RNA Signatures Predict the Outcome of Tuberculosis Treatment." Tuberculosis 107 (December): 48-58. 10.1016/j.tube.2017.08.004
RESPONSE5: Thompson, Ethan G., Ying Du, Stephanus T. Malherbe, Smitha Shankar, Jackie Braun, Joe Valvo, Katharina Ronacher, et al. 2017. "Host Blood RNA Signatures Predict the Outcome of Tuberculosis Treatment." Tuberculosis 107 (December): 48-58. 10.1016/j.tube.2017.08.004
Walter_51: Walter, Nicholas D., Mikaela A. Miller, Joshua Vasquez, Marc Weiner, Adam Chapman, Melissa Engle, Michael Higgins, et al. 2016. "Blood Transcriptional Biomarkers for Active Tuberculosis among Patients in the United States: A Case-Control Study with Systematic Cross-Classifier Evaluation." Journal of Clinical Microbiology 54 (2): 274-82. 10.1128/JCM.01990-15
Walter_PNA_47: Walter, Nicholas D., Mikaela A. Miller, Joshua Vasquez, Marc Weiner, Adam Chapman, Melissa Engle, Michael Higgins, et al. 2016. "Blood Transcriptional Biomarkers for Active Tuberculosis among Patients in the United States: A Case-Control Study with Systematic Cross-Classifier Evaluation." Journal of Clinical Microbiology 54 (2): 274-82. 10.1128/JCM.01990-15
Walter_PNA_119: Walter, Nicholas D., Mikaela A. Miller, Joshua Vasquez, Marc Weiner, Adam Chapman, Melissa Engle, Michael Higgins, et al. 2016. "Blood Transcriptional Biomarkers for Active Tuberculosis among Patients in the United States: A Case-Control Study with Systematic Cross-Classifier Evaluation." Journal of Clinical Microbiology 54 (2): 274-82. 10.1128/JCM.01990-15
ACS_COR: Zak, Daniel E., Adam Penn-Nicholson, Thomas J. Scriba, Ethan Thompson, Sara Suliman, Lynn M. Amon, Hassan Mahomed, et al. 2016. "A Blood RNA Signature for Tuberculosis Disease Risk: A Prospective Cohort Study." The Lancet 387 (10035): 231222. 10.1016/S0140-6736(15)01316-1
Examples
1 | data("common_sigAnnotData")
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