Reverse Engineering Directed Gene Regulatory Networks from Transcriptomics and Proteomics Data of Biomining Bacterial Communities

The main objective of the ERANET proposal Systems Biology Applications - ERASysAPP (app = application = translational systems biology) is to promote multidimensional and complementary European systems biology projects, programmes and research initiatives on a number of selected research topics. Inter alia, ERASysAPP will initiate, execute and monitor a number of joint transnational calls on systems biology research projects with a particular focus on applications - or in other words so called ...

Biomining is a biotechnological process carried out in many parts of the world that exploits acid loving microorganisms to extract metals from sulphide minerals. One industrial biomining method is called ‘heap bioleaching’ where typically copper containing minerals are piled into very large heaps, acid and microorganisms are added to the top and the soluble metal is collected at the heap base.

The role of the different types of microbes in the process is to speed up metal solubilisation by oxidising ...

Proteomics and transcriptomics data tables, sample IDs and description, source code

Data derived from RNAseq

Data derived from protein samples

Scripts for running network simulations

TPM counts for protein coding genes, alongside functional annotations

LFQ intensities derived from proteomics measurements

Source code for running simulations

Information for RNA and protein samples and cultures they were derived from.