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_7750_3597c
Histone protein Lsr2
PRJNA254351 GSE59086 GPL14824 GSM1427019 Tiling Array RNA 25232098 4-Jul-14 GEO
TFOE_3847_3676
cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases
PRJNA254351 GSE59086 GPL14824 GSM1427020 Tiling Array RNA 25232098 4-Jul-14 GEO
TFOE_4445_3676
cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases
PRJNA254351 GSE59086 GPL14824 GSM1427021 Tiling Array RNA 25232098 4-Jul-14 GEO
TFOE_6346_3676
cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases
PRJNA254351 GSE59086 GPL14824 GSM1427022 Tiling Array RNA 25232098 4-Jul-14 GEO
TFOE_9192_3681c
WhiB-type transcription regulator
PRJNA254351 GSE59086 GPL14824 GSM1427024 Tiling Array RNA 25232098 4-Jul-14 GEO
TFOE_9798_3681c
WhiB-type transcription regulator
PRJNA254351 GSE59086 GPL14824 GSM1427025 Tiling Array RNA 25232098 4-Jul-14 GEO
TFOE_1864_3830c
Beta-carotene ketolase (EC 1.14.-.-)
PRJNA254351 GSE59086 GPL14824 GSM1427038 Tiling Array RNA 25232098 4-Jul-14 GEO
TFOE_8264_3830c
Beta-carotene ketolase (EC 1.14.-.-)
PRJNA254351 GSE59086 GPL14824 GSM1427039 Tiling Array RNA 25232098 4-Jul-14 GEO
TFOE_9939_3830c
Beta-carotene ketolase (EC 1.14.-.-)
PRJNA254351 GSE59086 GPL14824 GSM1427040 Tiling Array RNA 25232098 4-Jul-14 GEO
TFOE_3194_3855
Transcriptional repressor EthR, TetR family
PRJNA254351 GSE59086 GPL14824 GSM1427054 Tiling Array RNA 25232098 4-Jul-14 GEO