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Pathway-based dissection of the genomic heterogeneity of cancer hallmarks’ acquisition with SLAPenrich

Overview of attention for article published in Scientific Reports, April 2018
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  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (88th percentile)
  • High Attention Score compared to outputs of the same age and source (87th percentile)

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1 news outlet
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19 X users
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1 Facebook page

Citations

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24 Dimensions

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61 Mendeley
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2 CiteULike
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Title
Pathway-based dissection of the genomic heterogeneity of cancer hallmarks’ acquisition with SLAPenrich
Published in
Scientific Reports, April 2018
DOI 10.1038/s41598-018-25076-6
Pubmed ID
Authors

Francesco Iorio, Luz Garcia-Alonso, Jonathan S. Brammeld, Iňigo Martincorena, David R. Wille, Ultan McDermott, Julio Saez-Rodriguez

Abstract

Cancer hallmarks are evolutionary traits required by a tumour to develop. While extensively characterised, the way these traits are achieved through the accumulation of somatic mutations in key biological pathways is not fully understood. To shed light on this subject, we characterised the landscape of pathway alterations associated with somatic mutations observed in 4,415 patients across ten cancer types, using 374 orthogonal pathway gene-sets mapped onto canonical cancer hallmarks. Towards this end, we developed SLAPenrich: a computational method based on population-level statistics, freely available as an open source R package. Assembling the identified pathway alterations into sets of hallmark signatures allowed us to connect somatic mutations to clinically interpretable cancer mechanisms. Further, we explored the heterogeneity of these signatures, in terms of ratio of altered pathways associated with each individual hallmark, assuming that this is reflective of the extent of selective advantage provided to the cancer type under consideration. Our analysis revealed the predominance of certain hallmarks in specific cancer types, thus suggesting different evolutionary trajectories across cancer lineages. Finally, although many pathway alteration enrichments are guided by somatic mutations in frequently altered high-confidence cancer genes, excluding these driver mutations preserves the hallmark heterogeneity signatures, thus the detected hallmarks' predominance across cancer types. As a consequence, we propose the hallmark signatures as a ground truth to characterise tails of infrequent genomic alterations and identify potential novel cancer driver genes and networks.

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X Demographics

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 61 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
France 1 2%
Unknown 60 98%

Demographic breakdown

Readers by professional status Count As %
Researcher 15 25%
Student > Ph. D. Student 13 21%
Student > Bachelor 5 8%
Student > Master 5 8%
Other 3 5%
Other 5 8%
Unknown 15 25%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 20 33%
Agricultural and Biological Sciences 7 11%
Computer Science 5 8%
Medicine and Dentistry 3 5%
Psychology 2 3%
Other 8 13%
Unknown 16 26%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 20. 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 11 February 2021.
All research outputs
#1,795,519
of 24,980,180 outputs
Outputs from Scientific Reports
#16,589
of 136,935 outputs
Outputs of similar age
#37,636
of 331,516 outputs
Outputs of similar age from Scientific Reports
#426
of 3,367 outputs
Altmetric has tracked 24,980,180 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 92nd percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 136,935 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 18.7. This one has done well, scoring higher than 87% 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 331,516 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 88% of its contemporaries.
We're also able to compare this research output to 3,367 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 87% of its contemporaries.