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Case-oriented pathways analysis in pancreatic adenocarcinoma using data from a sleeping beauty transposon mutagenesis screen

Overview of attention for article published in BMC Medical Genomics, April 2016
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Title
Case-oriented pathways analysis in pancreatic adenocarcinoma using data from a sleeping beauty transposon mutagenesis screen
Published in
BMC Medical Genomics, April 2016
DOI 10.1186/s12920-016-0176-7
Pubmed ID
Authors

Yen-Yi Ho, Timothy K. Starr, Rebecca S. LaRue, David A. Largaespada

Abstract

Mutation studies of pancreatic ductal adenocarcinoma (PDA) have revealed complicated heterogeneous genomic landscapes of the disease. These studies cataloged a number of genes mutated at high frequencies, but also report a very large number of genes mutated in lower percentages of tumors. Taking advantage of a well-established forward genetic screening technique, with the Sleeping Beauty (SB) transposon, several studies produced PDA and discovered a number of common insertion sites (CIS) and associated genes that are recurrently mutated at high frequencies. As with human mutation studies, a very large number of genes were found to be altered by transposon insertion at low frequencies. These low frequency CIS associated genes may be very valuable to consider for their roles in cancer, since collectively they might emerge from a core group of genetic pathways. In this paper, we determined whether the genetic mutations in SB-accelerated PDA occur within a collated group of biological processes defined as gene sets. The approach considered both genes mutated in high and lower frequencies. We implemented a case-oriented, gene set enrichment analysis (CO-GSEA) on SB altered genes in PDA. Compared to traditional GSEA, CO-GSEA enables us to consider individual characteristics of mutation profiles of each PDA tumor. We identified genetic pathways with higher numbers of genetic mutations than expected by chance. We also present the correlations between these significant enriched genetic pathways, and their associations with CIS genes. These data suggest that certain pathway alterations cooperate in PDA development.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 11 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 11 100%

Demographic breakdown

Readers by professional status Count As %
Other 4 36%
Student > Bachelor 3 27%
Student > Ph. D. Student 3 27%
Unspecified 1 9%
Readers by discipline Count As %
Agricultural and Biological Sciences 3 27%
Medicine and Dentistry 2 18%
Computer Science 2 18%
Biochemistry, Genetics and Molecular Biology 2 18%
Unspecified 1 9%
Other 1 9%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. 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 04 April 2016.
All research outputs
#5,670,486
of 7,492,829 outputs
Outputs from BMC Medical Genomics
#324
of 410 outputs
Outputs of similar age
#191,302
of 272,154 outputs
Outputs of similar age from BMC Medical Genomics
#12
of 15 outputs
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