Biases in the experimental annotations of protein function and their effect on our understanding of protein function space.
The ongoing functional annotation of proteins relies upon the work of curators to capture experimental findings from scientific literature and apply them to protein sequence and structure data. However, with the increasing use of high-throughput experimental assays, a small number of experimental st...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2013-01-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23737737/pdf/?tool=EBI |
| _version_ | 1818459302519635968 |
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| author | Alexandra M Schnoes David C Ream Alexander W Thorman Patricia C Babbitt Iddo Friedberg |
| author_facet | Alexandra M Schnoes David C Ream Alexander W Thorman Patricia C Babbitt Iddo Friedberg |
| author_sort | Alexandra M Schnoes |
| collection | DOAJ |
| description | The ongoing functional annotation of proteins relies upon the work of curators to capture experimental findings from scientific literature and apply them to protein sequence and structure data. However, with the increasing use of high-throughput experimental assays, a small number of experimental studies dominate the functional protein annotations collected in databases. Here, we investigate just how prevalent is the "few articles - many proteins" phenomenon. We examine the experimentally validated annotation of proteins provided by several groups in the GO Consortium, and show that the distribution of proteins per published study is exponential, with 0.14% of articles providing the source of annotations for 25% of the proteins in the UniProt-GOA compilation. Since each of the dominant articles describes the use of an assay that can find only one function or a small group of functions, this leads to substantial biases in what we know about the function of many proteins. Mass-spectrometry, microscopy and RNAi experiments dominate high throughput experiments. Consequently, the functional information derived from these experiments is mostly of the subcellular location of proteins, and of the participation of proteins in embryonic developmental pathways. For some organisms, the information provided by different studies overlap by a large amount. We also show that the information provided by high throughput experiments is less specific than those provided by low throughput experiments. Given the experimental techniques available, certain biases in protein function annotation due to high-throughput experiments are unavoidable. Knowing that these biases exist and understanding their characteristics and extent is important for database curators, developers of function annotation programs, and anyone who uses protein function annotation data to plan experiments. |
| first_indexed | 2024-12-14T23:12:12Z |
| format | Article |
| id | doaj.art-ff733fce51854fb0809c9273fe4365c4 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-12-14T23:12:12Z |
| publishDate | 2013-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-ff733fce51854fb0809c9273fe4365c42022-12-21T22:44:11ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582013-01-0195e100306310.1371/journal.pcbi.1003063Biases in the experimental annotations of protein function and their effect on our understanding of protein function space.Alexandra M SchnoesDavid C ReamAlexander W ThormanPatricia C BabbittIddo FriedbergThe ongoing functional annotation of proteins relies upon the work of curators to capture experimental findings from scientific literature and apply them to protein sequence and structure data. However, with the increasing use of high-throughput experimental assays, a small number of experimental studies dominate the functional protein annotations collected in databases. Here, we investigate just how prevalent is the "few articles - many proteins" phenomenon. We examine the experimentally validated annotation of proteins provided by several groups in the GO Consortium, and show that the distribution of proteins per published study is exponential, with 0.14% of articles providing the source of annotations for 25% of the proteins in the UniProt-GOA compilation. Since each of the dominant articles describes the use of an assay that can find only one function or a small group of functions, this leads to substantial biases in what we know about the function of many proteins. Mass-spectrometry, microscopy and RNAi experiments dominate high throughput experiments. Consequently, the functional information derived from these experiments is mostly of the subcellular location of proteins, and of the participation of proteins in embryonic developmental pathways. For some organisms, the information provided by different studies overlap by a large amount. We also show that the information provided by high throughput experiments is less specific than those provided by low throughput experiments. Given the experimental techniques available, certain biases in protein function annotation due to high-throughput experiments are unavoidable. Knowing that these biases exist and understanding their characteristics and extent is important for database curators, developers of function annotation programs, and anyone who uses protein function annotation data to plan experiments.https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23737737/pdf/?tool=EBI |
| spellingShingle | Alexandra M Schnoes David C Ream Alexander W Thorman Patricia C Babbitt Iddo Friedberg Biases in the experimental annotations of protein function and their effect on our understanding of protein function space. PLoS Computational Biology |
| title | Biases in the experimental annotations of protein function and their effect on our understanding of protein function space. |
| title_full | Biases in the experimental annotations of protein function and their effect on our understanding of protein function space. |
| title_fullStr | Biases in the experimental annotations of protein function and their effect on our understanding of protein function space. |
| title_full_unstemmed | Biases in the experimental annotations of protein function and their effect on our understanding of protein function space. |
| title_short | Biases in the experimental annotations of protein function and their effect on our understanding of protein function space. |
| title_sort | biases in the experimental annotations of protein function and their effect on our understanding of protein function space |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23737737/pdf/?tool=EBI |
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