| Chapter title |
Gene Ontology: Pitfalls, Biases, and Remedies
|
|---|---|
| Chapter number | 14 |
| Book title |
The Gene Ontology Handbook
|
| Published in |
Methods in molecular biology, January 2017
|
| DOI | 10.1007/978-1-4939-3743-1_14 |
| Pubmed ID | |
| Book ISBNs |
978-1-4939-3741-7, 978-1-4939-3743-1
|
| Authors |
Pascale Gaudet, Christophe Dessimoz |
| Editors |
Christophe Dessimoz, Nives Škunca |
| Abstract |
The Gene Ontology (GO) is a formidable resource, but there are several considerations about it that are essential to understand the data and interpret it correctly. The GO is sufficiently simple that it can be used without deep understanding of its structure or how it is developed, which is both a strength and a weakness. In this chapter, we discuss some common misinterpretations of the ontology and the annotations. A better understanding of the pitfalls and the biases in the GO should help users make the most of this very rich resource. We also review some of the misconceptions and misleading assumptions commonly made about GO, including the effect of data incompleteness, the importance of annotation qualifiers, and the transitivity or lack thereof associated with different ontology relations. We also discuss several biases that can confound aggregate analyses such as gene enrichment analyses. For each of these pitfalls and biases, we suggest remedies and best practices. |
X Demographics
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 4 | 16% |
| Switzerland | 3 | 12% |
| Germany | 2 | 8% |
| Taiwan | 1 | 4% |
| Norway | 1 | 4% |
| United Kingdom | 1 | 4% |
| Canada | 1 | 4% |
| France | 1 | 4% |
| Unknown | 11 | 44% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 13 | 52% |
| Scientists | 12 | 48% |
Mendeley readers
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Netherlands | 1 | <1% |
| Sweden | 1 | <1% |
| Czechia | 1 | <1% |
| United Kingdom | 1 | <1% |
| Mexico | 1 | <1% |
| Nigeria | 1 | <1% |
| Russia | 1 | <1% |
| United States | 1 | <1% |
| Unknown | 118 | 94% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 32 | 25% |
| Researcher | 20 | 16% |
| Student > Master | 14 | 11% |
| Student > Doctoral Student | 8 | 6% |
| Student > Bachelor | 8 | 6% |
| Other | 19 | 15% |
| Unknown | 25 | 20% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 36 | 29% |
| Biochemistry, Genetics and Molecular Biology | 30 | 24% |
| Computer Science | 12 | 10% |
| Immunology and Microbiology | 6 | 5% |
| Medicine and Dentistry | 4 | 3% |
| Other | 11 | 9% |
| Unknown | 27 | 21% |