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The Gene Ontology Handbook

Overview of attention for book
Cover of 'The Gene Ontology Handbook'

Table of Contents

  1. Altmetric Badge
    Book Overview
  2. Altmetric Badge
    Chapter 1 Primer on Ontologies
  3. Altmetric Badge
    Chapter 2 The Gene Ontology and the Meaning of Biological Function
  4. Altmetric Badge
    Chapter 3 Primer on the Gene Ontology
  5. Altmetric Badge
    Chapter 4 Best Practices in Manual Annotation with the Gene Ontology
  6. Altmetric Badge
    Chapter 5 Computational Methods for Annotation Transfers from Sequence
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    Chapter 6 Text Mining to Support Gene Ontology Curation and Vice Versa
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    Chapter 7 How Does the Scientific Community Contribute to Gene Ontology?
  9. Altmetric Badge
    Chapter 8 Evaluating Computational Gene Ontology Annotations
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    Chapter 9 Evaluating Functional Annotations of Enzymes Using the Gene Ontology
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    Chapter 10 Community-Wide Evaluation of Computational Function Prediction
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    Chapter 11 Get GO! Retrieving GO Data Using AmiGO, QuickGO, API, Files, and Tools
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    Chapter 12 Semantic Similarity in the Gene Ontology
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    Chapter 13 Gene-Category Analysis
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    Chapter 14 Gene Ontology: Pitfalls, Biases, and Remedies
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    Chapter 15 Visualizing GO Annotations
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    Chapter 16 A Gene Ontology Tutorial in Python
  18. Altmetric Badge
    Chapter 17 Annotation Extensions
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    Chapter 18 The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations
  20. Altmetric Badge
    Chapter 19 Complementary Sources of Protein Functional Information: The Far Side of GO
  21. Altmetric Badge
    Chapter 20 Integrating Bio-ontologies and Controlled Clinical Terminologies: From Base Pairs to Bedside Phenotypes
  22. Altmetric Badge
    Chapter 21 The Vision and Challenges of the Gene Ontology
Attention for Chapter 13: Gene-Category Analysis
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Chapter title
Gene-Category Analysis
Chapter number 13
Book title
The Gene Ontology Handbook
Published in
Methods in molecular biology, January 2017
DOI 10.1007/978-1-4939-3743-1_13
Pubmed ID
Book ISBNs
978-1-4939-3741-7, 978-1-4939-3743-1
Authors

Sebastian Bauer

Editors

Christophe Dessimoz, Nives Škunca

Abstract

Gene-category analysis is one important knowledge integration approach in biomedical sciences that combines knowledge bases such as Gene Ontology with lists of genes or their products, which are often the result of high-throughput experiments, gained from either wet-lab or synthetic experiments. In this chapter, we will motivate this class of analyses and describe an often used variant that is based on Fisher's exact test. We show that this approach has some problems in the context of Gene Ontology of which users should be aware. We then describe some more recent algorithms that try to address some of the shortcomings of the standard approach.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 8 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Mexico 1 13%
Unknown 7 88%

Demographic breakdown

Readers by professional status Count As %
Student > Doctoral Student 3 38%
Researcher 2 25%
Student > Ph. D. Student 1 13%
Professor > Associate Professor 1 13%
Unknown 1 13%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 2 25%
Agricultural and Biological Sciences 2 25%
Mathematics 1 13%
Social Sciences 1 13%
Neuroscience 1 13%
Other 0 0%
Unknown 1 13%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 5. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 28 November 2016.
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#6,068,873
of 22,899,952 outputs
Outputs from Methods in molecular biology
#1,798
of 13,134 outputs
Outputs of similar age
#113,401
of 420,444 outputs
Outputs of similar age from Methods in molecular biology
#206
of 1,074 outputs
Altmetric has tracked 22,899,952 research outputs across all sources so far. This one has received more attention than most of these and is in the 73rd percentile.
So far Altmetric has tracked 13,134 research outputs from this source. They receive a mean Attention Score of 3.4. This one has done well, scoring higher than 86% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 420,444 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 72% of its contemporaries.
We're also able to compare this research output to 1,074 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 80% of its contemporaries.