Journal: BMC Genomics

Article Title: Sulfur, sterol and trehalose metabolism in the deep-sea hydrocarbon seep tubeworm Lamellibrachia luymesi

doi: 10.1186/s12864-023-09267-8

Figure Lengend Snippet: Partial sequence alignment of L. luymesi ATHs and human PGGHG. HsPGGHG, Homo sapiens PGGHG (NCBI accession no. NP_079368.3); Ll ATH1/2, L. luymesi acid trehalase 1/2. Identical amino acids are marked by an asterisk and shaded in grey. More than 50% of the conserved residues are shaded in blue. The amino acids in red indicate that three carboxyl residues (corresponding to Asp301, Glu430 and Glu574 of human PGGHG) are essential for catalytic activity

Article Snippet: The transcript comp47803_c0 (ATH1) with enzymes from other worms further formed a branch, while the unigene comp47931_c1 (ATH2) was assigned another independent branch (Fig. ).

Techniques: Sequencing, Activity Assay

Journal: PLoS Computational Biology

Article Title: Computational Predictions Provide Insights into the Biology of TAL Effector Target Sites

doi: 10.1371/journal.pcbi.1002962

Figure Lengend Snippet: We consider as performance measures the number of predicted targets consistent with up-regulation in gene expression microarrays for different rank cutoffs and thresholds of 1 and 0.5 on the log-fold changes (left panel), and the precision-recall (PR) curve (right panel) using a threshold of 1 on the log-fold changes.

Article Snippet: The expression levels of A. thaliana genes are measured by Affymetrix Ath1 microarrays (imaGenes GmbH, Berlin, Germany), RMA normalized, and fold changes are determined for each of the 3 transgenic lines compared to 3 non-transgenic lines independently.

Techniques: Expressing

Journal: PLoS ONE

Article Title: GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Gene Expression Differences

doi: 10.1371/journal.pone.0025279

Figure Lengend Snippet: ( A ) Comparison of estimated log 2 -fold changes from analysis of microarrays (x-axis) and RNA-Seq using GENE-counter running NBPSeq (y-axis). Only induced genes measurable by both platforms are presented. Differentially induced genes are colored to highlight genes uniquely identified using microarrays (open red down triangles) or RNA-Seq (open blue up triangles) and found common between the two methods (purple crosses). ( B ) Three-way Venn comparing differentially expressed genes identified from GENE-counter's assessment of RNA-Seq data and analysis of microarrays. Only genes measurable using both methods were included in the comparison.

Article Snippet: The mRNA labeling, hybridization, and scanning of Affymetrix ATH1 microarrays were done by the CGRB core facility at OSU.

Techniques: Comparison, RNA Sequencing