GEO DataSets

(Submitter supplied) Tuberculosis (TB) remains a leading cause of death from an infectious disease worldwide. This is partly due to a lack of tools to effectively screen and triage individuals with potential TB. Whole blood RNA signatures have been extensively studied as potential biomarkers for TB, but they have failed to meet the World Health Organization's (WHOs) optimal target product profiles (TPPs) for a non-sputum triage or diagnostic test. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

60 Samples

Download data: TSV

(Submitter supplied) Tuberculosis (TB) remains a leading cause of death from an infectious disease worldwide. This is partly due to a lack of tools to effectively screen and triage individuals with potential TB. Whole blood RNA signatures have been extensively studied as potential biomarkers for TB, but they have failed to meet the World Health Organization's (WHOs) optimal target product profiles (TPPs) for a non-sputum triage or diagnostic test. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

61 Samples

Download data: TSV

(Submitter supplied) Tuberculosis (TB) remains a leading cause of death from an infectious disease worldwide. This is partly due to a lack of tools to effectively screen and triage individuals with potential TB. Whole blood RNA signatures have been extensively studied as potential biomarkers for TB, but they have failed to meet the World Health Organization's (WHOs) optimal target product profiles (TPPs) for a non-sputum triage or diagnostic test. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

130 Samples

Download data: TSV

(Submitter supplied) Background: Tuberculosis (TB) among persons living with HIV (PLWH) poses diagnostic challenges. Although several transcriptional signatures have recently been identified as promising tool for TB diagnosis, data are limited in persons with advanced HIV. Methodology: Reads were aligned to the human transcriptome (GRCh38 version 100), comprising both mRNA and ncRNA, with Salmon v1.2.0. A Random Forest algorithm with “leave-one-out” cross-validation was applied in the variance stabilizing transformation gene expression. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

25 Samples

Download data: TXT

(Submitter supplied) The study aimed to define transcriptional signatures for detection of active TB (TB) compared to latent TB infection (LTBI) as well as to other diseases (OD) with similar clinical phenotypes in patients with and without HIV in two African adult populations. Transcriptional signatures were identified that distinguished active TB from LTBI, active TB from other diseases, and active TB from both LTBI and other diseases in HIV+/- patients.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

537 Samples

Download data: TXT

(Submitter supplied) Mycobacterium tuberculosis (Mtb) antigen-specific cellular response is promising for detectionof Mtb infection, but not efficient for diagnosis of TB. We firstly identified 16 TB disease-specific protein markers measured in the culture supernatant of Mtb-stimulated whole blood using a 640 human proteins array, the highest throughput antibody-based protein array available at the time when we did this study. more...

Organism:

Homo sapiens

Type:

Protein profiling by protein array

Platform:

GPL27898

521 Samples

Download data: TXT

(Submitter supplied) Mycobacterium tuberculosis (Mtb) antigen-specific cellular response is promising for detectionof Mtb infection, but not efficient for diagnosis of TB. We firstly identified 16 TB disease-specific protein markers measured in the culture supernatant of Mtb-stimulated whole blood using a 640 human proteins array, the highest throughput antibody-based protein array available at the time when we did this study. more...

Organism:

Homo sapiens

Type:

Protein profiling by protein array

Platform:

GPL26838

160 Samples

Download data: TXT

(Submitter supplied) More humans have died of tuberculosis (TB) than any other infectious disease and millions still die each year. Experts advocate for blood-based, protein biomarkers to help diagnosis TB, which is critical in high-burden countries. However, the protein biomarker pipeline is small. Here, we used the Diversity Outbred (DO) mouse population to address this gap, identifying five protein biomarker candidates. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL17791

37 Samples

Download data: CEL

(Submitter supplied) Knowing when a person was infected with Mycobacterium tuberculosis (M.tb) is critical as recent infection is the strongest clinical risk factor for progression to TB disease in immunocompetent individuals. However, time since M.tb infection is very difficult to determine in routine clinical practice. We determined whether gene expression patterns in blood RNA correlate with time since M.tb infection or exposure to develop a biomarker for recent exposure. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

26 Samples

Download data: TXT

(Submitter supplied) Genome wide DNA methylation profiling of PBMC from South African patients either infected with HIV only or coinfected with HIV and tuberculosis (TB). The Illumina Infinium 27k Human DNA methylation Beadchip was used to obtain DNA methylation profiles from PBMC samples. Samples included 19 HIV patients and 20 HIV/TB co-infected patients.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL8490

40 Samples

Download data: TXT

(Submitter supplied) Diagnosis of TB, especially in the presence of an HIV co-infection, can be challenging when using conventional diagnostic methods. In this study, we analyzed global gene expression data from PBMC of patients that were either mono-infected with HIV or co-infected with HIV and TB in order to identify a TB-specific gene signature.

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4786

Platform:

GPL10558

44 Samples

Download data: TXT

Analysis of PBMCs from HIV patients with and without M. tuberculosis (TB) co-infection. Co-infection with TB is a cause of death in HIV-infected individuals. Results provide insight into a molecular signature to distinguish HIV/TB co-infected patients from HIV mono-infected patients.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 infection sets

Platform:

GPL10558

Series:

GSE50834

44 Samples

Download data

(Submitter supplied) Background: Mycobacterium tuberculosis infection is a leading cause of infectious death worldwide. Gene-expression microarray studies profiling the blood transcriptional response of tuberculosis (TB) patients have been undertaken in order to better understand the host immune response as well as to identify potential biomarkers of disease. To date most of these studies have focused on pulmonary TB patients with gene-expression profiles of extra-pulmonary TB patients yet to be compared to those of patients with pulmonary TB or sarcoidosis. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

202 Samples

Download data: TXT

(Submitter supplied) Tuberculosis (TB) is the major cause of death in HIV-infected individuals. However, diagnosis of TB in HIV remains challenging. The aim of this study was to determine the performance of published gene signatures in distinguishing active TB in advanced HIV. We concluded that gene expression of FcGR1A and BATF2, and plasma protein levels of IFNγ and CXCL10 can singly classify active TB in HIV-infected with advanced HIV.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

33 Samples

Download data: XLSX

(Submitter supplied) We report a study about differentially expressed small non-coding RNAs in the blood of humans harboring a latent (LTBI) or active tuberculosis (TB) infection in comparison with exposed controls (ExC) and treated LTBI (LTBItt). All non-TB subjects enrolled in this study were recent close contacts (rCt) of a newly diagnosed contagious TB cases enrolled in Rio de Janeiro, Brazil. The detailed methodology is described below. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16791

49 Samples

Download data: TXT

(Submitter supplied) Tuberculosis (TB), caused by infection with Mycobacterium tuberculosis (M. tuberculosis), is a major cause of morbidity and mortality worldwide and efforts to control TB are hampered by difficulties with diagnosis, prevention and treatment. Most people infected with M. tuberculosis remain asymptomatic, termed latent TB, with a 10% lifetime risk of developing active TB disease, but current tests cannot identify which individuals will develop disease. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6947

274 Samples

Download data: TXT

(Submitter supplied) This series regroups different datasets (training set, test set, validation set, longitudinal set, separated cell set) to identify and characterise a specific transcriptional signature for patients with active TB, distinct from patients with latent TB and healthy controls. The training set dataset was used to identify a whole blood transcriptional signature for active TB patients in London, across a range of ethnicity. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6947

498 Samples

Download data: TXT

(Submitter supplied) This dataset aims to validate and confirm the signature identified in the training set. The aim of the experiment was to define transcriptional signatures in whole blood of TB patients (before drug treatment) and healthy controls to distinguish the signature of Latent and Active TB patients from each other and from healthy controls. This will help in diagnosis of active tuberculosis which normally relies on culture of the bacilli, which can take up to 6 wks, and sometimes the bacilli cannot be obtained from sputum thus requiring invasive techniques obtaining bronchoalveolar lavage (BAL). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6947

54 Samples

Download data: TXT

(Submitter supplied) This dataset aims to dissect the whole blood transcriptional signature by determining if elements of the whole blood signature are still present in purified cell subpopulations. We aimed to characterise the transcriptional response during TB and identify if cell subsets drove changes in whole blood cellular composition. The aim of the experiment was to define transcriptional signatures in neutrophils, monocytes, CD4+ and CD8+ cells from blood of active TB patients and healthy controls to distinguish the signature of active TB patients from each other and from healthy controls. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6947

44 Samples

Download data: TXT

(Submitter supplied) The aim of this study was to compare the transcriptional response to TB in regions of different incidence / prevalence.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6947

51 Samples

Download data: TXT