Data Center

Welcome to MTB Portal Data Center. This section provides quick access to data files hosted at the portal. Each panel provides overview of the corresponding data files. You can access to more data by clicking on "more" button or to the panel header.

MTB Signed TRN

MTB Signed Transcriptional Regulatory Network
The following file is a supplementary material for Peterson et al.(submitted)

The compiled signed transcriptional regulatory network contains TF-gene interactions with both physical (detected with ChIP-seq experiments; Minch et al. 2015) and functional evidence (detected with TFOE transcriptional profiling; Rustad et al. 2014). Activation and repression are indicated with 1 and -1.

Download Excel Worksheet

 

OTB supplement: Systems analysis of TB progression in RhCMV/MTB vaccinated NHP. Whole blood multi-omics profiling of MTB-challenged Rhesus macaques after vaccination with RhCMV and/or BCG.

Currently, data files in this section are private and download link will be available after login.

Title Body Release Date Sample Type
RhCMV-TB Metabolomics Data

Whole blood metabolomics profiling of MTB-challenged Rhesus macaques after vaccination with RhCMV and/or BCG. 

Each row is a metabolite and each column is a monkey at the defined time point

2018 Metabolomics
RhCMV-TB Proteomics Data

Whole blood proteomics profiling of MTB-challenged Rhesus macaques after vaccination with RhCMV and/or BCG

2018 Protein
RhCMV-TB Transcriptomic Data

Whole blood transcriptomes of MTB-challenged Rhesus macaques after vaccination with RhCMV and/or BCG

Log2 standardized counts (using edgeR) are reported. Each row is a gene and each column is a monkey at the defined time point.

2018 RNA
RhCMV-TB Meta Data

Whole blood omics profiling of MTB-challenged Rhesus macaques after vaccination with RhCMV and/or BCG

Meta-data information is listed. Columns are the monkey ID, which trial the monkey is from, the disease score after challenge, and the vaccination group.

2018 Meta-data

Quantitative Proteomics Data

Publication: 
Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network.

To investigate the MTB transcriptional landscape in a systematic manner, we developed a high-throughput approach to identify the genes controlled by nearly all predicted MTB TFs. We individually cloned and conditionally overexpressed 206 MTB TFs to induce the regulatory signature of each one. Using this approach we identified the sets of genes affected by TF overexpression (TFOE) and assembled them into an easily searchable map of transcriptional regulation in MTB.

Accessing large datasets like the TFOE expression data can be difficult when the data spreads over thousands of genes and hundreds of regulators. To address the difficulties usually associated with accessing large data sets, we have designed a simple Excel spreadsheet for querying TFOE data to find regulators of specific genes or sets of genes. (Rustad et al. Genome Biol. 2014)

Last update: 29/02/2015
BioProject: PRJNA254351

Expression data from transcription factor over expression experiments. TFOE are matched to the ChIP-seq experiment done simultaneously.

Title Gene BioProject GEO Series Platform Accession Sample Method Sample Type References Release Date Repository Contact
TFOE_5242_3334_C
Mercuric resistance operon regulatory protein
PRJNA254351 GSE59086 GPL14824 GSM1426987 Tiling Array RNA 25232098 4-Jul-14 GEO
TFOE_6629_3334_B
Mercuric resistance operon regulatory protein
PRJNA254351 GSE59086 GPL14824 GSM1426988 Tiling Array RNA 25232098 4-Jul-14 GEO
TFOE_9642_3334
Mercuric resistance operon regulatory protein
PRJNA254351 GSE59086 GPL14824 GSM1426989 Tiling Array RNA 25232098 4-Jul-14 GEO
TFOE_5343_3295
Transcriptional regulator, TetR family
PRJNA254351 GSE59086 GPL14824 GSM1426977 Tiling Array RNA 25232098 4-Jul-14 GEO
TFOE_3866_3295
Transcriptional regulator, TetR family
PRJNA254351 GSE59086 GPL14824 GSM1426976 Tiling Array RNA 25232098 4-Jul-14 GEO
TFOE_3822_3260c
Sporulation regulatory protein WhiB
PRJNA254351 GSE59086 GPL14824 GSM1426966 Tiling Array RNA 25232098 4-Jul-14 GEO
TFOE_7368_3260c
Sporulation regulatory protein WhiB
PRJNA254351 GSE59086 GPL14824 GSM1426967 Tiling Array RNA 25232098 4-Jul-14 GEO
TFOE_1382_3286c
RNA polymerase sigma factor SigB
PRJNA254351 GSE59086 GPL14824 GSM1426968 Tiling Array RNA 25232098 4-Jul-14 GEO
TFOE_6181_3286c
RNA polymerase sigma factor SigB
PRJNA254351 GSE59086 GPL14824 GSM1426969 Tiling Array RNA 25232098 4-Jul-14 GEO
TFOE_9544_3286c
RNA polymerase sigma factor SigB
PRJNA254351 GSE59086 GPL14824 GSM1426970 Tiling Array RNA 25232098 4-Jul-14 GEO