London Calling 2018 poster

This poster was presented at London Calling (Oxford Nanopore Technology's annual meeting) in May 2018

Phylogenetic analysis of LipM and LplA.

<p>Maximum likelihood phylogenetic tree including 131 LipM and LplA sequences from archaea, LplA sequences from major eukaryotic species (<i>S. cerevisiae, D. melanogaster</i>, <i>M. musculus</i> and <i>H. sapiens</i>) and LplA and LipM sequences from eubacteria representing Actinobacteria (<i>S. coelicolor),</i> Bacteroidetes (<i>B. thetaiotaomicron</i>), Firmicutes (<i>B. subtilis</i> and <i>S. aureus</i>) and Proteobacteria (<i>E. coli</i> and <i>B. pseudomallei).</i> Putative cases of horizontal gene transfer are indicated (asterisk) and major phylogenetic clades are highlighted: archaeal LplA (Clade I - orange; Clade II - green), LipM (red), and eukaryotic and eubacterial LplA (blue). The full phylogenetic tree including species names and bootstrap values is provided <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087063#pone.0087063.s002" target="_blank">Figure S2</a>.</p

Phylogenetic analysis of the biotin-lipoate A/B protein ligase family.

<p>Neighbor-joining phylogenetic tree of the cofactor transferase domain (Pfam03099) that includes 11,826 biotin and lipoate-ligase proteins and octanoyl-carrier proteins from eukaryotes, eubacteria and archaea. Annotation of the five broad protein domain clades as LipM (red), LplA (orange), LipL (blue), LipB (green) and biotin protein-ligase (black) clades was based upon the presence of biochemically characterized proteins within each protein set. In total, 295 archaeal sequences were included in this analysis with 161 residing in the biotin-ligase clade (54.5%) and the remainder residing in the LipM, LplA or LipB clades.</p

Genomic co-retention of <i>LipB</i> and <i>LipM</i> lipoylation genes with OADHC <i>E2</i>.

<p>(A) The presence of the <i>LipB</i> and OADHC <i>E2</i> genes in sequenced Thermoproteales genomes is indicated (species lacking both are highlighted in grey). <i>Pyrobaculum sp 1860</i> and <i>Pyrobaculum oguniense</i> have yet to be incorporated into the <i>Pyrobaculum</i> phylogeny and have been placed arbitrarily in the <i>Pyrobaculum</i> genus. (B) The presence of <i>LipM</i> and OADHC <i>E2</i> in sequenced Halobacteriales genomes is indicated (species lacking both are highlighted in grey). Phylogenetic relationships are based on Brochier-Armanet <i>et al. </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087063#pone.0087063-BrochierArmanet1" target="_blank">[53]</a>; branch lengths are not drawn to scale.</p

Comparative genomic analysis of lipoylation pathways in archaea.

<p>The genomic presence of lipoylation enzymes <i>LplA-N</i>, LipM or <i>LipB</i> and their substrate OADHC <i>E2</i> is indicated. Archaeal orders lacking lipoylation pathways are highlighted (grey shading). The broad metabolic environment of each archaeal order and the number of species analyzed are also indicated. Phylogenetic relationships are based on Brochier-Armanet <i>et al. </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087063#pone.0087063-BrochierArmanet1" target="_blank">[53]</a>; branch lengths are not drawn to scale.</p

Genes differentially expressed in short survival versus long survival patients, considered according to cancer type and cancer class.

Volcano plots showing significantly downregulated (the thresholds are FDR -0.5) genes in green and red, respectively. Here short survival patients are compared with long survival patients, so in all three panels genes found to be upregulated are genes that are upregulated in short survival patients, and genes found downregulated are genes that are downregulated in short survival patients. Grey indicates genes that are not significantly downregulated or upregulated. Log of fold change (LogFC) is on the x-axis and significance level (-log10P) is on the y-axis. Panel A shows differentially expressed genes when all of the patients are considered (n = 515). Panel B shows differentially expressed genes when only patients with solid cancers are considered (n = 293), and panel C shows differentially expressed genes when only patients with blood cancers are considered (n = 222). In all panels, the significantly downregulated and upregulated genes are labelled with their Hugo Gene Nomenclature Committee (HGNC) gene symbols. The three genes (SSX1, MAGEC2 and ULBP2) that are found to be significantly differentially expressed in all three analyses are shown in bold.</p

Patients statistics.

(DOCX)</p