Bahlo Lab

Gene co-expression matrix for candidate genes for Childhood Apraxia of Speech (CAS).
This matrix shows pairwise Spearman Correlations between genes, based on samples from the BrainSpan Atlas of the Developing Human Brain.

Pairs of genes which are positively correlated (ie co-expressed) are shown in blue; pairs of genes that are negatively correlated are shown in red.

Gene co-expression of candidate genes with known speech disorder genes increases burden of evidence for these genes and is performed using methods previously developed by the Bahlo lab (Oliver et al, PLOS ONE, 2014, Freytag et al, BMC Bioinformatics, 2015, Freytag et al, Genome Medicine, 2017).

Detecting repeat expansions
The statistical methods we have developed can identify samples with repeat expansions using short read sequencing data.

Samples likely to be affected by the repeat expansion disorder have an increased number of repeated bases and appear shifted to the right which can be seen for the coloured samples in the figure above.

This image displays more than 800 metabolites and their connections to each other as measured in a group of 50 MacTel patients. Connections are displayed as blue lines (positive connection) or red lines (negative connection).

We performed a stratified factorial analysis to explore and create potential clusters of metabolites (designated by different colours) which show evidence of an increased risk of developing MacTel disease. Metabolites that appear to be closer in this network should belong to the same cluster. The size of each dot indicates the relevance of each metabolite on the disease risk. Glycine and Serine identified in our genetic study as being very important in MacTel appear in this network as the two largest points of the blue cluster, confirming the importance of their role on the disease.

Relatedness network for pairs of P. falciparum isolates that are related over the chloroquine resistance transporter gene, Pfcrt.
Each node represents a unique P. falciparum isolate, and a line is drawn between two isolates if they were inferred either partially or completely IBD over the gene Pfcrt. Isolates with a single infection, i.e. multiplicity of infection (MOI), of 1 are represented by circles while isolates with multiple infections (MOI > 1) are represented by squares.

Here we see that many isolates from both Southeast Asia and Africa are IBD over Pfcrt, which is consistent with literature that suggests a haplotype conferring resistance to the antimalarial drug chloroquine has spread between Southeast Asia and Africa.