The human protein atlas—Integrated omics for single cell mapping of the human proteome

Abstract

Studying the spatial distribution of proteins provides the basis for understanding the biology, molecular repertoire, and architecture of every human cell. The Human Protein Atlas (HPA) has grown into one of the world's largest biological databases, and in the most recent version, a major update of the structure of the database was performed. The data has now been organized into 10 different comprehensive sections, each summarizing different aspects of the human proteome and the protein‐coding genes. In particular, large datasets with information on the single cell type level have been integrated, refining the tissue and cell type specificity and detailing the expression in cell states with an increased resolution. The multi‐modal data constitute an important resource for both basic and translational science, and hold promise for integration with novel emerging technologies at the protein and RNA level.

BioNexusSentinel: a visual tool for bioregulatory network and cytohistological RNA-seq genetic expression profiling within the context of multicellular simulation research using ChatGPT-augmented software engineering

“…MIR21 produced a description but no gene matches in the database. Indeed, the HPA was built on protein coding data ( Digre and Lindskog 2023 ), and various Ensemble gene identifier searches with R were negative. This limitation can be investigated further.…”

“…rna_celline.tsv dataset from the HPA could be considered for cancer phenotypes, and there was also neurological expression data with localization. The HPA also possesses 10 million high-resolution stained cytohistological images ( Digre and Lindskog 2023 ). The ‘secretome’ is another area of interest in the omics, and could be one source of omics data in terms of incorporating disease biomarkers.…”

A high-resolution spatial map of cilia-associated proteins based on characterization of the human fallopian tube-specific proteome

“…However, since the analysis was performed on whole-cell excised material, the subcellular localization is lost. Detailed spatial analysis with conventional methods such as IHC provide important complements to the DVP analysis, generating a high-resolution map of individual proteins 52 .…”

Identification of novel biomarkers based on lipid metabolism-related molecular subtypes for moderately severe and severe acute pancreatitis

“…Meanwhile, using the Human Protein Atlas (HPA: https://www.proteinatlas.org/ ), immunofluorescence was used to demonstrate cellular localization. The latest version of the HPA database has integrated large datasets with single-cell type level information, and the single-cell type data is integrated into the gene search results page, making it possible for visitors to access all the information from a gene-specific perspective [ 31 ]. Therefore, we also examined the single-cell type atlases of the model genes in the pancreatic tissues using the HPA platform.…”