Proteomic-Genomic Nexus (AP11)

Overview

With the large amount of genomics and proteomics data currently available there was, until this project, a lack of tools to integrate data from these two fields. This project aims to provide a ‘nexus’ for integrating genomics and transcriptomics data generated from next-generation sequencing with proteomics data generated from protein mass spectrometry.

Aims

This project aims to provide a ‘nexus’ for integrating genomics and transcriptomics data generated from next-generation sequencing with proteomics data generated from protein mass spectrometry.

We developed a set of tools which allow users to:

  • co-visualise genomics, transcriptomics and proteomics data  using the Integrated Genomics Viewer (IGV)
  • validate the existence of genes and mRNAs using peptides identified from mass spectrometry experiments
  • validate alternatively spliced mRNA isoforms

Key Deliverables:

1. A deployed, tested and documented software system that:

  • allows genomics and transcriptomics data from next-generation sequencing to be integrated with that from proteomics;
  • allows the integrated data to assist in the confirmation of open reading frames and/or splice isoforms in a directed or naive way; and
  • enables a significant demonstration of value in the transformation of this previously disparate information.

2. Operational automated feeds of RIF-CS collection descriptions, with related party and activity descriptions, as well as service descriptions where relevant, to Research Data Australia (RDA).

Benefits

Integration of 'omics data is involved and complex, but this approach asks some specific questions which are answerable with an integrated data analysis approach (e.g. is my assembly of high quality? have I found the genes? which isotigs are actually protein coding?).

It is likely to spawn other research questions which involve a cross-comparison of proteomic and genomic or transcriptomic data. It will certainly encourage the use of two or more 'omic analysis types; this has been difficult until now as few if any tools co-analyse these data in any comprehensive and time-efficient way.

The project outcomes are of immediate applicability to:

  •  users of the Ramaciotti Centre for Gene Function Analysis or the Bioanalytical Mass Spectrometry Facility who wish to co-analyse next-gen sequencing data with proteomic data
  •  the framework dataset project of Bioplatforms Australia, especially for wine yeast, soil-dwelling microbes and wheat pathogenomics projects.

This project will result in ‘omics data of different types (e.g. agricultural and medical) and from multiple sources being integrated to produce an analysis resource that will help elucidate biological and molecular function to ultimately help in advancing diagnosis and treatment of diseases and increasing crop yields and quality.

This project is supported by the Australian National Data Service (ANDS). ANDS is supported by the Australian Government through the National Collaborative Research Infrastructure Strategy Program and the Education Investment Fund (EIF) Super Science Initiative.