A deep proteome and transcriptome abundance atlas of 29 healthy human tissues
Abstract Genome‐, transcriptome‐ and proteome‐wide measurements provide insights into how biological systems are regulated. However, fundamental aspects relating to which human proteins exist, where they are expressed and in which quantities are not fully understood. Therefore, we generated a quanti...
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| Format: | Article |
| Language: | English |
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Springer Nature
2019-02-01
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| Series: | Molecular Systems Biology |
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| Online Access: | https://doi.org/10.15252/msb.20188503 |
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| author | Dongxue Wang Basak Eraslan Thomas Wieland Björn Hallström Thomas Hopf Daniel Paul Zolg Jana Zecha Anna Asplund Li‐hua Li Chen Meng Martin Frejno Tobias Schmidt Karsten Schnatbaum Mathias Wilhelm Frederik Ponten Mathias Uhlen Julien Gagneur Hannes Hahne Bernhard Kuster |
| author_facet | Dongxue Wang Basak Eraslan Thomas Wieland Björn Hallström Thomas Hopf Daniel Paul Zolg Jana Zecha Anna Asplund Li‐hua Li Chen Meng Martin Frejno Tobias Schmidt Karsten Schnatbaum Mathias Wilhelm Frederik Ponten Mathias Uhlen Julien Gagneur Hannes Hahne Bernhard Kuster |
| author_sort | Dongxue Wang |
| collection | DOAJ |
| description | Abstract Genome‐, transcriptome‐ and proteome‐wide measurements provide insights into how biological systems are regulated. However, fundamental aspects relating to which human proteins exist, where they are expressed and in which quantities are not fully understood. Therefore, we generated a quantitative proteome and transcriptome abundance atlas of 29 paired healthy human tissues from the Human Protein Atlas project representing human genes by 18,072 transcripts and 13,640 proteins including 37 without prior protein‐level evidence. The analysis revealed that hundreds of proteins, particularly in testis, could not be detected even for highly expressed mRNAs, that few proteins show tissue‐specific expression, that strong differences between mRNA and protein quantities within and across tissues exist and that protein expression is often more stable across tissues than that of transcripts. Only 238 of 9,848 amino acid variants found by exome sequencing could be confidently detected at the protein level showing that proteogenomics remains challenging, needs better computational methods and requires rigorous validation. Many uses of this resource can be envisaged including the study of gene/protein expression regulation and biomarker specificity evaluation. |
| format | Article |
| id | doaj-art-e262c700c4e842809774970b2244374d |
| institution | Kabale University |
| issn | 1744-4292 |
| language | English |
| publishDate | 2019-02-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj-art-e262c700c4e842809774970b2244374d2025-08-20T03:42:04ZengSpringer NatureMolecular Systems Biology1744-42922019-02-0115211610.15252/msb.20188503A deep proteome and transcriptome abundance atlas of 29 healthy human tissuesDongxue Wang0Basak Eraslan1Thomas Wieland2Björn Hallström3Thomas Hopf4Daniel Paul Zolg5Jana Zecha6Anna Asplund7Li‐hua Li8Chen Meng9Martin Frejno10Tobias Schmidt11Karsten Schnatbaum12Mathias Wilhelm13Frederik Ponten14Mathias Uhlen15Julien Gagneur16Hannes Hahne17Bernhard Kuster18Chair of Proteomics and Bioanalytics, Technische Universität MünchenComputational Biology, Department of Informatics, Technical University of MunichOmicScouts GmbHScience for Life Laboratory, KTH ‐ Royal Institute of TechnologyOmicScouts GmbHChair of Proteomics and Bioanalytics, Technische Universität MünchenChair of Proteomics and Bioanalytics, Technische Universität MünchenScience for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala UniversityChair of Proteomics and Bioanalytics, Technische Universität MünchenChair of Proteomics and Bioanalytics, Technische Universität MünchenChair of Proteomics and Bioanalytics, Technische Universität MünchenChair of Proteomics and Bioanalytics, Technische Universität MünchenJPT Peptide Technologies GmbHChair of Proteomics and Bioanalytics, Technische Universität MünchenScience for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala UniversityScience for Life Laboratory, KTH ‐ Royal Institute of TechnologyComputational Biology, Department of Informatics, Technical University of MunichOmicScouts GmbHChair of Proteomics and Bioanalytics, Technische Universität MünchenAbstract Genome‐, transcriptome‐ and proteome‐wide measurements provide insights into how biological systems are regulated. However, fundamental aspects relating to which human proteins exist, where they are expressed and in which quantities are not fully understood. Therefore, we generated a quantitative proteome and transcriptome abundance atlas of 29 paired healthy human tissues from the Human Protein Atlas project representing human genes by 18,072 transcripts and 13,640 proteins including 37 without prior protein‐level evidence. The analysis revealed that hundreds of proteins, particularly in testis, could not be detected even for highly expressed mRNAs, that few proteins show tissue‐specific expression, that strong differences between mRNA and protein quantities within and across tissues exist and that protein expression is often more stable across tissues than that of transcripts. Only 238 of 9,848 amino acid variants found by exome sequencing could be confidently detected at the protein level showing that proteogenomics remains challenging, needs better computational methods and requires rigorous validation. Many uses of this resource can be envisaged including the study of gene/protein expression regulation and biomarker specificity evaluation.https://doi.org/10.15252/msb.20188503human proteomehuman transcriptomeproteogenomicsquantitative mass spectrometryRNA‐Seq |
| spellingShingle | Dongxue Wang Basak Eraslan Thomas Wieland Björn Hallström Thomas Hopf Daniel Paul Zolg Jana Zecha Anna Asplund Li‐hua Li Chen Meng Martin Frejno Tobias Schmidt Karsten Schnatbaum Mathias Wilhelm Frederik Ponten Mathias Uhlen Julien Gagneur Hannes Hahne Bernhard Kuster A deep proteome and transcriptome abundance atlas of 29 healthy human tissues Molecular Systems Biology human proteome human transcriptome proteogenomics quantitative mass spectrometry RNA‐Seq |
| title | A deep proteome and transcriptome abundance atlas of 29 healthy human tissues |
| title_full | A deep proteome and transcriptome abundance atlas of 29 healthy human tissues |
| title_fullStr | A deep proteome and transcriptome abundance atlas of 29 healthy human tissues |
| title_full_unstemmed | A deep proteome and transcriptome abundance atlas of 29 healthy human tissues |
| title_short | A deep proteome and transcriptome abundance atlas of 29 healthy human tissues |
| title_sort | deep proteome and transcriptome abundance atlas of 29 healthy human tissues |
| topic | human proteome human transcriptome proteogenomics quantitative mass spectrometry RNA‐Seq |
| url | https://doi.org/10.15252/msb.20188503 |
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