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Avoiding the pitfalls of gene set enrichment analysis with SetRank

Overview of attention for article published in BMC Bioinformatics, March 2017
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About this Attention Score

  • Above-average Attention Score compared to outputs of the same age (64th percentile)
  • Good Attention Score compared to outputs of the same age and source (67th percentile)

Mentioned by

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2 X users
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1 patent

Citations

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99 Dimensions

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313 Mendeley
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Title
Avoiding the pitfalls of gene set enrichment analysis with SetRank
Published in
BMC Bioinformatics, March 2017
DOI 10.1186/s12859-017-1571-6
Pubmed ID
Authors

Cedric Simillion, Robin Liechti, Heidi E.L. Lischer, Vassilios Ioannidis, Rémy Bruggmann

Abstract

The purpose of gene set enrichment analysis (GSEA) is to find general trends in the huge lists of genes or proteins generated by many functional genomics techniques and bioinformatics analyses. Here we present SetRank, an advanced GSEA algorithm which is able to eliminate many false positive hits. The key principle of the algorithm is that it discards gene sets that have initially been flagged as significant, if their significance is only due to the overlap with another gene set. The algorithm is explained in detail and its performance is compared to that of other methods using objective benchmarking criteria. Furthermore, we explore how sample source bias can affect the results of a GSEA analysis. The benchmarking results show that SetRank is a highly specific tool for GSEA. Furthermore, we show that the reliability of results can be improved by taking sample source bias into account. SetRank is available as an R package and through an online web interface.

X Demographics

X Demographics

The data shown below were collected from the profiles of 2 X users who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 313 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 1 <1%
Unknown 312 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 72 23%
Researcher 67 21%
Student > Master 44 14%
Student > Bachelor 30 10%
Student > Doctoral Student 15 5%
Other 31 10%
Unknown 54 17%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 89 28%
Agricultural and Biological Sciences 77 25%
Medicine and Dentistry 16 5%
Engineering 14 4%
Computer Science 11 4%
Other 38 12%
Unknown 68 22%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 4. 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 17 December 2020.
All research outputs
#6,472,271
of 22,958,253 outputs
Outputs from BMC Bioinformatics
#2,490
of 7,307 outputs
Outputs of similar age
#105,855
of 310,371 outputs
Outputs of similar age from BMC Bioinformatics
#41
of 135 outputs
Altmetric has tracked 22,958,253 research outputs across all sources so far. This one has received more attention than most of these and is in the 70th percentile.
So far Altmetric has tracked 7,307 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 5.4. This one has gotten more attention than average, scoring higher than 64% 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 310,371 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 64% of its contemporaries.
We're also able to compare this research output to 135 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 67% of its contemporaries.