Data-mining pipelines for unbiased interpretation of large-scale microarray datasets in environmental research using non-model species
Lead Research Organisation:
University of Liverpool
Department Name: Sch of Biological Sciences
Abstract
New genetic techniques have led to a massively increased volume of data across the biological sciences, including on the biology of organisms within the natural environment. Typically the level of activity of thousands of genes is studied in multiple replicates in multiple experiments. The problem is to turn this huge volume of data into biological understanding. For organisms that are relevant to understanding the natural environment, this problem is compounded by the fact that they are not as well resourced as the typical models like a fruitfly or a lab mouse, where a detailed understanding of the function of thousands of genes is generated by well-resourced research communities. If we want to study the genetics of organisms in the natural environment, we need to try to summarise the sheer volume of data in a biologically meaningful way, and we need to relate our organisms of environmental interest to their better-studied, model organism relatives. Within the last few years, the tools to do these two things have become available and we are in a position to wrap these tools into a 'pipeline' that will allow us to analyse rapidly the large amounts of data that have been generated by three NERC-funded projects. Combining the data analyses from these separate projects is an efficient use of resources that will lead to additional peer-reviewed papers from these projects. The methods that we develop will also help other researchers within the NERC community.
Organisations
Publications
Bittner D
(2011)
Identification of candidate genes and physiological pathways involved in gonad deformation in whitefish (Coregonus spp.) from Lake Thun, Switzerland.
in International journal of environmental research and public health
Forootan SS
(2016)
Transcriptome sequencing of human breast cancer reveals aberrant intronic transcription in amplicons and dysregulation of alternative splicing with major therapeutic implications.
in International journal of oncology
Li W
(2009)
Application of ESTs in microarray analysis.
in Methods in molecular biology (Clifton, N.J.)
Li W
(2009)
ExprAlign--the identification of ESTs in non-model species by alignment of cDNA microarray expression profiles.
in BMC genomics
Liu X
(2017)
Transcriptomic signatures differentiate survival from fatal outcomes in humans infected with Ebola virus
in Genome Biology
Mennigen JA
(2008)
Effects of fluoxetine on the reproductive axis of female goldfish (Carassius auratus).
in Physiological genomics
Mráz J
(2010)
Sesamin as a potential modulator of fatty acid composition in common carp (Cyprinus carpio) Sesamin, a modulator of lipids in carp?
in Aquaculture Research
Olohan L
(2008)
Detection of anoxia-responsive genes in cultured cells of the rainbow trout Oncorhynchus mykiss (Walbaum), using an optimized, genome-wide oligoarray
in Journal of Fish Biology
Pascoal S
(2013)
Transcriptomics and in vivo tests reveal novel mechanisms underlying endocrine disruption in an ecological sentinel, Nucella lapillus.
in Molecular ecology
Popesku JT
(2008)
The goldfish (Carassius auratus) as a model for neuroendocrine signaling.
in Molecular and cellular endocrinology
Reilly SC
(2008)
Novel candidate genes identified in the brain during nociception in common carp (Cyprinus carpio) and rainbow trout (Oncorhynchus mykiss).
in Neuroscience letters
Sawle AD
(2010)
An information-rich alternative, chemicals testing strategy using a high definition toxicogenomics and zebrafish (Danio rerio) embryos.
in Toxicological sciences : an official journal of the Society of Toxicology
Sneddon LU
(2011)
Molecular correlates of social dominance: a novel role for ependymin in aggression.
in PloS one
Stensløkken KO
(2014)
Life without oxygen: gene regulatory responses of the crucian carp (Carassius carassius) heart subjected to chronic anoxia.
in PloS one
Williams D
(2008)
Genomic resources and microarrays for the common carp Cyprinus carpio L.
in Journal of Fish Biology
Description | This grant allowed us to develop bioinformatic tools and resources for the NERC community. These have been applied to a number of grants from NERC and BBSRC, as indicated in the publications. The pipelines have been incorporated into the NERC core-funded activities of the Liverpool CGR within the NERC NBAF node. |
Exploitation Route | Further development of packages using newer statistical approaches. |
Sectors | Agriculture, Food and Drink,Environment |
Description | This grant provided bioinformatic tools and resources which have been applied in a large number of projects. |
First Year Of Impact | 2009 |
Sector | Environment,Pharmaceuticals and Medical Biotechnology |
Impact Types | Societal |
Title | Development of a new machine learning classification technique |
Description | This technique was developed by statistician Yongxiang Fang. It uses a ratio technique based on selecting gene pairs that can most clearly discriminate in a two class prediction model, avoiding problems caused by systematic bias in new datasets being applied to the training pre-existing model. The predictive power of this technique was consistently better than the more conventional techniques of random forests and SVMs. |
Type Of Material | Technology assay or reagent |
Year Produced | 2017 |
Provided To Others? | Yes |
Impact | A method was developed to identify the optimal combination of gene pairs with the successful application to a typical two-class problem, namely predicting the outcome (survival or fatality) in Ebola patients. |
Description | Major international conference (Prague) - plenary presentation |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | To present the annual 'Bidder Lecture' of the Society for Experimental Biology, which is the premier European academic society for comparative and environmental biology. |
Year(s) Of Engagement Activity | 2015 |
Description | Research Visit to the Chinese Academy of Fisheries Science |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Industry/Business |
Results and Impact | Attended two centres in the Chinese Academy of Fisheries Science, in Harbin and Beijing. In both I gave research seminars and engaged in collaborative research discussions. The outcome was a series of research proposals and interactions around the issue of protecting carp aquaculture from losses caused by koi herpes virus. |
Year(s) Of Engagement Activity | 2016 |