IntroductionThe Pig Atlas is a collaboration between BGI and the Human Protein Atlas focusing on transcriptomics based characterization of pig tissues. The pig is highly relevant as a large animal model for pharmacological and biomedical research. Here, we present a resource of the genome-wide expression of protein-coding genes across all major tissues and organs in pig. Aspects such as tissue specific expression, UMAP based holistic classification of the transcriptome and human disease genes are discussed in individual chapters with illustrations and clickable links for further exploration. The aim of this resource is to support the biomedical use of pigs and to increase our basic understanding of the pig biology. The pig genome was sequenced in 2012 by the Swine Genome Sequencing Consortium (SGSC) (Groenen MA et al. (2012) ) and a microarray based atlas was created the same year (Freeman TC et al. (2012)). The Pig Atlas will complement these efforts with detailed maps of RNA expression in pig tissues and facilitate easy comparison to human gene expression profiles. The pig brain has been explored in detail and previously published (Sjöstedt E et al. (2020)) as part of a collaboration between BGI and the Human Protein Atlas. The pig brain expression profiles are incorporated in the HPA Brain Atlas together with mouse brain expression data. The Pig Atlas is a stand-alone atlas based on expression of pig genes, that includes integrated human orthologue expression data from the HPA Tissue Atlas. The data presented in version 1 of the Pig RNA Atlas is described in Karlsson M et al. (2022). BackgroundHuman Protein AtlasThe Human Protein Atlas is a Swedish-based program initiated in 2003 with the aim to map all the human proteins in cells, tissues and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome. The Human Protein Atlas consists of six separate parts, each focusing on a particular aspect of the genome-wide analysis of the human proteins; the Tissue Atlas showing the distribution of the proteins across all major tissues and organs in the human body, the Cell Atlas showing the subcellular localization of proteins in single cells, the Pathology Atlas showing the impact of protein levels for survival of patients with cancer, the Blood Atlas, the Brain Atlas and the Metabolic Atlas. The Human Protein Atlas program has already contributed to several thousands of publications in the field of human biology and disease and it is selected by the organization ELIXIR (www.elixir-europe.org) as a European core resource due to its fundamental importance for a wider life science community. The Human Protein Atlas consortium is mainly funded by the Knut and Alice Wallenberg Foundation. The Human Protein Atlas project involves the joint efforts of the Royal Institute of Technology in Stockholm, Uppsala University, Uppsala Akademiska University Hospital, and more recently also Science for Life Laboratory based in both Uppsala and Stockholm. Formal collaborations are with groups in India, South Korea, Japan, China, Germany, France, Switzerland, USA, Canada, Denmark, Finland, The Netherlands, Spain, and Italy. The first version of the Human Protein Atlas website was launched in 2005 and consisted of protein expression data based on approximately 700 antibodies. Since then, each new release has included more data and new functionalities and features to the website. Uhlén M et al., Tissue-based map of the human proteome. Science (2015) BGI GroupFounded in 1999, BGI is one of the world's leading life science and genomics organizations. BGI’s mission is to use genomics to benefit mankind and to be a leader in the era of life sciences. BGI follows a genomics development model of “research, production and application”. With businesses in more than 100 countries and regions around the world, BGI has established cooperation and partnerships with thousands of different organizations across multi-disciplinary research areas including medical health, resource conservation and judicial services. At the same time, BGI provides equipment, technical support and solutions for the needs of national economies and people's livelihoods, such as precision medicine and precision health. BGI is committed to applying its genetic and technological achievements to real world settings in order to realize the dream of trans-omics for a better life. BGI has been involved in several ground breaking projects, besides the first pig genome sequencing mentioned above, also the first rice genome, the Yanhuang project and the 1000 genome project. Yu J et al., A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science. (2002) |