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Protocols

TBDB specifications

Information


Unique identifier OMICS_03220
Name TBDB
Alternative name TuBerculosis DataBase
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained No

Taxon


  • Bacteria
    • Mycobacterium tuberculosis

Maintainer


This tool is not available anymore.

Publications for TuBerculosis DataBase

TBDB citations

 (24)
library_books

Neomorphosis and heterochrony of skull shape in dog domestication

2017
Sci Rep
PMCID: 5647425
PMID: 29044203
DOI: 10.1038/s41598-017-12582-2

[…] housed in the Zoologisches Institut und Museum der Universität Zürich, Switzerland (ZMUZH) and three CT-scanned specimens were contributed from the Tierpark Bern, Dählhölzli & Bärenpark, Switzerland (TBDB). No specimen was killed for this study and no live specimens were used.The three-dimensional coordinates of 34 landmarks on the left and the right side of the skull (Fig. , Table ) were captured […]

library_books

Efficient inference for sparse latent variable models of transcriptional regulation

2017
Bioinformatics
PMCID: 5860323
PMID: 28961802
DOI: 10.1093/bioinformatics/btx508

[…] ing time-series covering hypoxia. We obtained pre-processed ChIP-seq data for 113 MTB TFs (through personal communication with James Galagan, the same data are now publicly available at http://genome.tbdb.org/annotation/genome/tbdb/Resources.html). This constituted a prior topology matrix with 113 columns representing TFs and 3863 rows representing genes with at least one TF connection and for whi […]

library_books

Integration of Metabolomics and Transcriptomics Reveals a Complex Diet of Mycobacterium tuberculosis during Early Macrophage Infection

2017
mSystems
PMCID: 5566787
PMID: 28845460
DOI: 10.1128/mSystems.00057-17

[…] ate (FDR) by the Benjamini-Hochberg procedure. For functional group and pathway enrichment, metabolite classes were defined as in the HMDB database. Pathway descriptions were downloaded from KEGG and TBDB databases. Metabolites passing the threshold of |log2 fold change| > log2 1.5, FDR < 0.05, and FDR(change to control) < 0.05 and transcripts passing the threshold of |log2 fold change| > log2 1.5 […]

call_split

Characterisation of iunH gene knockout strain from Mycobacterium tuberculosis

2017
PMCID: 5319374
PMID: 28225907
DOI: 10.1590/0074-02760160462
call_split See protocol

[…] l Lab) column. Samples were analysed in technical triplicates. Mass spectra were acquired in a top 8 data-dependent manner with dynamic exclusion applied, and were searched against a non-redundant M. tuberculosis database for candidate peptides with the software Comet () in the platform PatternLab for Proteomics (). The validity of the peptide spectra matches was assessed using the module Search E […]

library_books

Evaluation of Rv0220, Rv2958c, Rv2994 and Rv3347c of Mycobacterium tuberculosis for serodiagnosis of tuberculosis

2017
PMCID: 5404193
PMID: 28217905
DOI: 10.1111/1751-7915.12697

[…] ansmembrane proteins or secreted proteins of M. tuberculosis.To exploit the ideal diagnostic antigens, we analysed all annotated genes in the M. tuberculosis genome using the web tools (http://genome.tbdb.org/) and the M. tuberculosis H37Rv database (tuberculist.epfl.ch). Those genes that are virulence‐related and essential for growth, metabolism and cell wall synthesis were selected, and then the […]

library_books

Mycobacterium tuberculosis Lineage 4 comprises globally distributed and geographically restricted sublineages

2016
Nat Genet
PMCID: 5238942
PMID: 27798628
DOI: 10.1038/ng.3704

[…] ed in each of the 10 sublineages were assessed for predicted functional consequence with the „Sorting Intolerant From Tolerant“ (SIFT) in the software SIFT4G (v2.1) and the pre-compiled Mycobacterium tuberculosis database „GCA_000195955.2.22“. Conservation levels of SNPs in the pre-compiled database had been obtained by comparing Mycobacterium tuberculosis H37Rv proteins to all proteins in the Uni […]

Citations

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TBDB institution(s)
Department of Biochemistry, Stanford University, CA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Genetics, Stanford University, CA, USA; Department of Biomedical Engineering, Boston University, Boston, MA, USA; National Emerging Infectious Diseases Lab, Boston University, Boston MA, USA; Department of Microbiology & Immunology, Stanford University, CA, USA

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