Genome-wide interologous interactome map (TeaGPIN) ofCamellia sinensis

Abstract

Tea, prepared from the young leaves of Camellia sinensis, is a non-alcoholic beverage globally consumed due to its antioxidant properties, strong taste and aroma. Although, the genomic data of this medicinally and commercially important plant is available, studies related to its sub-cellular interactomic maps are less explored. In this work, we propose a genome-wide interologous protein-protein interaction (PPI) network of tea, termed as TeaGPIN, consisting of 12,033 nodes and 216,107 interactions, developed using draft genome of tea and known PPIs exhaustively collected from 49 template plants. TeaGPIN interactions are prioritized using domain-domain interactions along with the interolog information. A high-confidence TeaGPIN consisting of 5,983 nodes and 58,867 edges is reported and its interactions are further evaluated using protein co-localization similarities. Based on three network centralities (degree, betweenness and eigenvector), 1,302 key proteins are reported in tea to have p-value < 0.01 by comparing the TeaGPIN with 10,000 realizations of Erdős-Rényi and Barabási-Albert based corresponding random network models. Functional content of TeaGPIN is assessed using KEGG and GO annotations and its modular architecture is explored. Network based characterization is carried-out on the transcription factors, and proteins involved flavonoid biosynthesis and photosynthesis pathways to find novel candidates involved in various regulatory processes. We believe the proposed TeaGPIN will impart useful insights in understanding various mechanisms related to growth and development as well as defence against biotic and abiotic perturbations.

Characterizing circadian connectome ofO. tenuiflorumusing an integrated network theoretic framework

“…So, in this section, we used PPI information form TulsiPIN and Gene Ontology (GO) and KEGG Orthology (KO) annotation information of interacting proteins to infer the validity of candidate CC associated proteins. It has been shown earlier that similar proteins may perform similar molecular functions, localize in same cellular milieu and may be involved in similar biological processes [58, 55]. Thus candidate proteins having similar functional annotations as that of CC proteins may be novel CC associated proteins.…”

“…Linkage test is based on the premise that interacting proteins are more likely to share common functions [58, 55]. So, in this section, we used PPI information form TulsiPIN and Gene Ontology (GO) and KEGG Orthology (KO) annotation information of interacting proteins to infer the validity of candidate CC associated proteins.…”

Identification of pterygium-related conjunctival epithelium microRNA and mRNA expression profiles by high-throughput screening analysis

“…The protein-protein interactions between DEmRNAs were extracted based on the Pathway Commons database (http://www.pathwaycommons.org/). (Singh et al 2021) Only directional interactions were kept. Three attributes of each gene in the PPI network were assessed to determine whether the gene is important in the network with R igraph package.…”

Expanding Interactome Analyses beyond Model Eukaryotes

“…Protein physiochemical properties, such as charge, hydrophobicity and structure, can be used in combination with domain and sequence to infer interaction [85][86][87]. The domain-domain interaction (DDI) method is often used in conjunction with interolog mapping [61,[88][89][90][91][92]. The 3D structure of a protein forms an active site essential for its function.…”

“…A turnip (Brassica rapa) interolog network has been inferred from A. thalina data [258] and a predicted interactome was produced for coffee, Coffea canephora, using orthology to model organisms including A. thalaina [259]. Predicted networks have also been built for the tea plant Camellia sinensis [92,260], cassava Manihot esculenta [261,262], orange Citrus sinensis [263], thai basil, Ocimum tenuiflorum [264], the poplar tree Populus trichocarpa, and the moss Physcomitrella patens [187].…”