Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics*

By Linn Fagerberg, B. Hallström, P. Oksvold, C. Kampf, D. Djureinovic, J. Odeberg, Masato Habuka, Simin Tahmasebpoor, Angelika Danielsson, K. Edlund and 24 more. 2013

2,436 citations recorded by the source corpus.

Global classification of the human proteins with regards to spatial expression patterns across organs and tissues is important for studies of human biology and disease. Here, we used a quantitative transcriptomics analysis (RNA-Seq) to classify the tissue-specific expression of genes across a representative set of all major human organs and tissues and combined this analysis with antibody-based profiling of the same tissues. To present the data, we launch a new version of the Human Protein Atlas that integrates RNA and protein expression data corresponding to ∼80% of the human protein-coding genes with access to the primary data for both the RNA and the protein analysis on an individual gene level. We present a classification of all human protein-coding genes with regards to tissue-specificity and spatial expression pattern. The integrative human expression map can be used as a starting point to explore the molecular constituents of the human body.

Subfields: Molecular Biology

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Citations in the corpus

The human protein atlas: A spatial map of the human proteome (2018, background): “Since then, each new release has included both more data and new website functionalities, and major milestones consist of a gene-centric database with information on all human genes predicted by Ensembl(8) and addition of transcriptomics data based on high-throughput mRNA sequencing.(9) Both in-hous”
WikiPathways: capturing the full diversity of pathway knowledge (2015, methodology): “The goal of this feature is to combine the pathway knowledge from WikiPathways with baseline expression data for 27 different tissues from Expression Atlas (11,12) to study the activity of biological pathways in a specific tissue.”
Database resources of the National Center for Biotechnology Information (2017, background): “Expression profiles are both useful complements to already characterized gene functions and also potential means of initially characterizing the function of novel genes (4,5).”
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation (2015, methodology): “Curation of human genes utilizes analyzed RNA-Seq reads from the Illumina BodyMap 2 (BioProject: PRJEB2445) and Human Protein Atlas projects (BioProject: PRJEB4337) (16).”
A benchmark of gene expression tissue-specificity metrics (2015, methodology): “(Fagerberg et al. 2013) downloaded from their Supplementary Materials, 22 mouse tissues (GSE36025) from the ENCODE project (The ENCODE Project Consortium 2011; Lin et al.”
Mapping genomic loci implicates genes and synaptic biology in schizophrenia (2022, background): “Sets representing genes that are intolerant to loss-of function mutations 40 (LoF-intolerant) and brain-expressed genes 41 are also shown.”
Multidimensional proteomics for cell biology (2015, methodology): “…by the search tool for the retrieval of interacting genes/proteins (STRING) database 120 ( , and tissue-specific protein expression patterns in humans (see Supplementary information S2 (figure)), as determined both by mass spectrometry-based proteomics 7,8 and antibody-based detection 121,122 .”
Tissue-based map of the human proteome (2015, methodology): “Recently, we performed a transcriptomics study of 27 different tissues using this approach (15), followed by subsequent in-depth studies of the global proteome in a number of these tissues and organs, such as liver (16), testis (17), and the gastrointestinal (GI) tract (18).”