Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptional Responses of M. tuberculosis to inhibitors of metabolism

ABSTRACT: Transcriptional profiling of M.tuberculosis was performed using 430 whole-genome microarrays to measure the effects of 75 different drugs, drug combinations or different growth conditions at various times relative to a sample of logarithmically growing MTb. Analysis of this data set revealed 150 underlying clusters of coordinately regulated genes as described in Boshoff et al., 2004. Keywords = Gene clusters Keywords = Mechanism of action Keywords = tuberculosis Keywords = antimycobacterial drugs Keywords = natural product Keywords = respiration

ORGANISM(S): Mycobacterium tuberculosis H37Rv

SUBMITTER: Timothy Myers

PROVIDER: E-GEOD-1642 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

The transcriptional responses of Mycobacterium tuberculosis to inhibitors of metabolism: novel insights into drug mechanisms of action.

Boshoff Helena I M HI Myers Timothy G TG Copp Brent R BR McNeil Michael R MR Wilson Michael A MA Barry Clifton E CE

The Journal of biological chemistry 20040709 38

The differential transcriptional response of Mycobacterium tuberculosis to drugs and growth-inhibitory conditions was monitored to generate a data set of 430 microarray profiles. Unbiased grouping of these profiles independently clustered agents of known mechanism of action accurately and was successful at predicting the mechanism of action of several unknown agents. These predictions were validated biochemically for two agents of previously uncategorized mechanism, pyridoacridones and phenothia ...[more]

PMID: 15247240

Similar Datasets

Transcriptional Responses of M. tuberculosis to inhibitors of metabolism

Project description:Transcriptional profiling of M.tuberculosis was performed using 430 whole-genome microarrays to measure the effects of 75 different drugs, drug combinations or different growth conditions at various times relative to a sample of logarithmically growing MTb. Analysis of this data set revealed 150 underlying clusters of coordinately regulated genes as described in Boshoff et al., 2004. Keywords = Gene clusters Keywords = Mechanism of action Keywords = tuberculosis Keywords = antimycobacterial drugs Keywords = natural product Keywords = respiration Keywords: other

2004-09-01 | GSE1642 | GEO

Hybrid wine yeast strains

Project description:This experiment is the analysis of the transcriptomes of several hybrid yeast strains obtained by crossing natural (from wine) isolates of S. cerevisiae and S. uvarum. All isolations have been done from hybrid strains growing in exponential phase in YPD. Keywords: Strain comparison Transcriptomic analysis of three independent replicates of each yeast strain growing in exponential phase. Each replicate has been hybridized on a different macroarray (F19-F22-F24) as indicated in the sample files. A single DNA (S. cerevisiae 3002 wine strain) genomic hybridization, from the same labeling reaction, was done on the same macroarrays for normalization.

2010-06-25 | E-GEOD-9888 | biostudies-arrayexpress

Dermatophytes CGH based on a Trichophyton rubrum cDNA microarray

Project description:A cDNA microarray was constructed from the expressed sequence tags (ESTs) of different developmental stages, and comparative genome hybridization based on microarray procedures were carried out. Dermatophyte species are classified into three genera: Epidermophyton, Microsporum, and Trichophyton. To determine the relationship between these three groups comparative genome hybridization were used in our experiment. Trichophyton rubrum genmic DNA was reference DNA and labelled by Cy3 while the other dermatophytes genomic DNA were test DNA and labelled by CY5. Test and reference DNA were co-hybridized with the T. rubrum cDNA microarray and the numbers of genes shared between each species and T. rubrum were determined. Keywords: Comparative Genomic Hybridization We used a Trichophyton rubrum cDNA microarray prepared in our lab through comparative genome hybridization of genomic DNA of 21 dermatophyte strains (belonging to 20 species) to elucidate the taxonomy and evolution profiles of 20 dermatophyte species. The numbers of genes shared between each species and T. rubrum were determined. Each strain DNA hybridized for 3 times. The slides were separated into three groups base on different datasets.

2010-05-03 | E-GEOD-7909 | biostudies-arrayexpress

Molecular networking coupled to high-resolution mass spectrometry fragmentation reveals a multitude of urinary antihypertensive drug metabolites

Project description:Mass spectrometry is the current technique of choice in studying drug metabolism. High-resolution mass spectrometry (HR-MS) in combination with fragment analysis (MS/MS) has the potential to contribute to rapid advances in this field. However, the data emerging from such fragmentation spectra pose challenges to downstream analysis, given their complexity and size. Here we apply a molecular networking approach to seek drugs and their metabolites, in fragmentation spectra from urine derived from a cohort of 26 patients on antihypertensive therapy. In total, 165 separate drug metabolites were found and structurally annotated (17 by spectral matching and 122 by classification based on a clustered fragmentation pattern). The clusters could be traced to 13 drugs including the known antihypertensives verapamil, losartan and amlopidine. The molecular networking approach also generated networks of endogenous metabolites, including carnitine derivatives, and conjugates containing glutamine, glutamate and trigonelline. The approach offers unprecedented capability in the untargeted identification of drugs and their metabolites at the population level and has great potential to contribute to understanding stratified responses to drugs where differences in drug metabolism may determine treatment outcome. Keywords: Antihypertensive drugs, Drug metabolism, Fragmentation, High-resolution mass spectrometry, Metabolomics, Urine.

2016-05-23 | MTBLS307 | MetaboLights

Secreted transcription factor controls Mycobacterium tuberculosis virulence

Project description:This SuperSeries is composed of the following subset Series: GSE11696: Gene expression profile of M.tuberculosis espR (Rv3849) mutant GSE12379: Gene expression profile of M.tuberculosis espR (Rv3849) mutant complemented with an N-terminal Flag espR gene GSE12380: Gene expression profile of M.tuberculosis espR (Rv3849) mutants containing N- or C-terminal mutations in the espR gene GSE12381: Comparative analysis of the gene expression profiles of M.tuberculosis espR (Rv3849) transposon and knockout mutants Refer to individual Series

2010-05-25 | E-GEOD-12382 | biostudies-arrayexpress

The IRF3 dependent response of macrophages to M. tuberculosis infection

Project description:Transcriptional profiling of macrophages (wild-type and IRF3-/- ) infected with various M.tuberculosis strains (wild-type and ESX-1 mutant) Comparison of the global gene expression of wild-type BMDM macrophages and IRF3-/- macrophages infected with either wild-type M.tuberculosis or ESX-1 mutant M.tuberculosis, with two biological replicates per group

2012-03-31 | E-GEOD-36686 | biostudies-arrayexpress

Transcriptional profiles of lung macrophage subsets in Mycobacterium Tuberculosis infection

Project description:We investigated transcriptional responses of different lung macrophage lineages during M.tuberculosis infection by RNAseq. Our data revealed that different lineages of macrophages respond differentially to M.Tuberculosis infection.

2018-02-21 | GSE108844 | GEO

Genomic predictors of response to doxorubicin versus docetaxel in breast cancer

Project description:Low topo2a expression and ER-negative status were predictors of response to doxorubicin, while small tumor size and ER-negative status predicted response to docetaxel. Docetaxel was superior to doxorubicin in triple-negative/basal-like tumors, while no significant differences between these drugs were seen in the remaining intrinsic subtypes Keywords: reference x sample reference x sample

2011-05-27 | E-GEOD-21997 | biostudies-arrayexpress

Genome-wide Definition of the SigF Regulon in Mycobacterium tuberculosis (ChIP-chip)

Project description:The genome wide ChIP-on-chip analysis to identify the DNA binding sites for the M.tuberculosis sigma factor Rv3286c (SigF) SigF binding sites were determined by microarray analysis of anti-sigF immunoprecipitated DNA from H37Rv(ΔrsbW/sigF)::pmySigF compared to H37Rv(ΔrsbW/sigF)::pMY769 (both cultured with pristinamycin for 3 days). 4 biological replicates were performed.

2012-01-20 | E-GEOD-34919 | biostudies-arrayexpress

Genome-wide Definition of the SigF Regulon in Mycobacterium tuberculosis (Expression)

Project description:The genome wide transcriptome analysis to identify the M.tuberculosis sigma factor Rv3286c (SigF) dependent transcripts as well as Pristimaycin induced transcripts Pristinamycin induced transcripts were identified by comparing the cDNA extracted from H37Rv::pMY769 with and without pristinamycin (3 biological replicates). SigF controlled transcripts were identified by comparing the cDNA extracted from H37Rv::pMYsigF with and without pristinamycin (4 biological replicates).

2012-01-20 | E-GEOD-34922 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data