ABSTRACT
Our lab has developed a new visualization tool, anexVis, for transcriptome analysis of glycosaminoglycan-related genes. This tool allows one to analyze a large number of genes that are related to biosynthetic and catabolic pathways of all glycosaminoglycans, such as heparan sulfate, chondroitin sulfate, keratan sulfate, and hyaluronic acid, in parallel across various human tissues/organs. Such visual analyses have not been accessible to the broad research community despite the accumulation of a large amount of RNA-seq data. We use publicly available data provided by the GTEx project with NIH permission to generate this new framework. Herein, we describe the use of anexVis in understanding the relationship among all biosynthetic and catabolic enzymes, core protein proteoglycans, and various transporters and understanding factors that control organ-specific GAG biosynthesis and catabolism in humans at the transcriptome level. This visualization tool may also assist us in understanding the impact of lysosomal diseases and rare glycan-related diseases on specific organs in humans.
Subject(s)
Transcriptome , Chondroitin Sulfates , Gene Expression Profiling , Glycosaminoglycans , Heparitin Sulfate , Humans , ProteoglycansABSTRACT
Microproteins are a novel and expanding group of small proteins encoded by less than 100-150 codons that are translated from small open reading frames (smORFs). It has been shown that smORFs and their corresponding microproteins make up a sizable fraction of the genome and proteome, but very little information on microproteins' structural features exists in the literature. In this paper, we present the results of analyzing the predicted structures of 44 microproteins. The results show that this set of microproteins have a different amino acid composition profiles, similar structural characteristics and fewer small-molecule ligand binding sites than regular proteins.Communicated by Ramaswamy H. Sarma.
