Predicted Drosophila Interactome Resource and web tool for functional interpretation of differentially expressed genes

Abstract

Drosophila melanogaster is a well-established model organism that is widely used in genetic studies. This species enjoys the availability of a wide range of research tools, well-annotated reference databases and highly similar gene circuitry to other insects. To facilitate molecular mechanism studies in Drosophila, we present the Predicted Drosophila Interactome Resource (PDIR), a database of high-quality predicted functional gene interactions. These interactions were inferred from evidence in 10 public databases providing information for functional gene interactions from diverse perspectives. The current version of PDIR includes 102 835 putative functional associations with balanced sensitivity and specificity, which are expected to cover 22.56% of all Drosophila protein interactions. This set of functional interactions is a good reference for hypothesis formulation in molecular mechanism studies. At the same time, these interactions also serve as a high-quality reference interactome for gene set linkage analysis (GSLA), which is a web tool for the interpretation of the potential functional impacts of a set of changed genes observed in transcriptomics analyses. In a case study, we show that the PDIR/GSLA system was able to produce a more comprehensive and concise interpretation of the collective functional impact of multiple simultaneously changed genes compared with the widely used gene set annotation tools, including PANTHER and David. PDIR and its associated GSLA service can be accessed at http://drosophila.biomedtzc.cn.

Heterogeneity in the Response of Different Subtypes of Drosophila melanogaster Midgut Cells to Viral Infections

“…A high quality predicted interactome of D. melanogaster was downloaded from http://drosophila.biomedtzc.cn v2018_01 (last accessed 15 November 2021) [37]. Gene interaction networks were analyzed as undirected graphs with the igraph R package v1.2.5 [38].…”

Expanding Interactome Analyses beyond Model Eukaryotes

“…Several studies have been dedicated to understanding the interactome of this important species [13,188,198,307,[338][339][340][341][342][343][344][345][346][347][348][349][350][351][352][353][354][355]. The Drosophila Interactions Database (DroID) [355,356] and the Predicted Drosophila Interactome Resource (PDIR) are integrated database containing both experimental and predicted interactions [354].…”

“…Several studies have been dedicated to understanding the interactome of this important species [13,188,198,307,[338][339][340][341][342][343][344][345][346][347][348][349][350][351][352][353][354][355]. The Drosophila Interactions Database (DroID) [355,356] and the Predicted Drosophila Interactome Resource (PDIR) are integrated database containing both experimental and predicted interactions [354]. Interactome analyses have been applied to the disease vectors Glossina morsitans morsitans (tsetse flies) [290,291], Aedes aegypti [357][358][359] and Anopheles gambiae [13,188] (mosquitos), and the pests Acyrthosiphon pisum (aphid) and Tribolium castaneum (flour beetle) [13].…”

Four Immune-Related Long Non-coding RNAs for Prognosis Prediction in Patients With Hepatocellular Carcinoma

“…GO and KEGG analysis indicated that the four immune-related LncRNAs might be connected with several biological characteristics including acetylation, inflammatory response, protein binding, stimulatory C-type lectin receptor signaling pathway, cytoplasm, regulation of gene expression, epigenetics, mutagenesis site, isopeptide bond, cytosol, and erythrocyte differentiation through the DAVID web annotation tool ( Figures 5B,C ; Shao et al, 2018 ; Yuan et al, 2018 ). The analysis could help us to understand the potential molecular mechanisms of the four LncRNAs in the occurrence and development of HCC ( Ding et al, 2020 ).…”