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Mendeley readers
Attention Score in Context
| Title |
Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes
|
|---|---|
| Published in |
BMC Genomics, July 2018
|
| DOI | 10.1186/s12864-018-4903-7 |
| Pubmed ID | |
| Authors |
Zhuyi Xue, René L. Warren, Ewan A. Gibb, Daniel MacMillan, Johnathan Wong, Readman Chiu, S. Austin Hammond, Chen Yang, Ka Ming Nip, Catherine A. Ennis, Abigail Hahn, Sheila Reynolds, Inanc Birol |
| Abstract |
Alternative polyadenylation (APA) results in messenger RNA molecules with different 3' untranslated regions (3' UTRs), affecting the molecules' stability, localization, and translation. APA is pervasive and implicated in cancer. Earlier reports on APA focused on 3' UTR length modifications and commonly characterized APA events as 3' UTR shortening or lengthening. However, such characterization oversimplifies the processing of 3' ends of transcripts and fails to adequately describe the various scenarios we observe. We built a cloud-based targeted de novo transcript assembly and analysis pipeline that incorporates our previously developed cleavage site prediction tool, KLEAT. We applied this pipeline to elucidate the APA profiles of 114 genes in 9939 tumor and 729 tissue normal samples from The Cancer Genome Atlas (TCGA). The full set of 10,668 RNA-Seq samples from 33 cancer types has not been utilized by previous APA studies. By comparing the frequencies of predicted cleavage sites between normal and tumor sample groups, we identified 77 events (i.e. gene-cancer type pairs) of tumor-specific APA regulation in 13 cancer types; for 15 genes, such regulation is recurrent across multiple cancers. Our results also support a previous report showing the 3' UTR shortening of FGF2 in multiple cancers. However, over half of the events we identified display complex changes to 3' UTR length that resist simple classification like shortening or lengthening. Recurrent tumor-specific regulation of APA is widespread in cancer. However, the regulation pattern that we observed in TCGA RNA-seq data cannot be described as straightforward 3' UTR shortening or lengthening. Continued investigation into this complex, nuanced regulatory landscape will provide further insight into its role in tumor formation and development. |
X Demographics
The data shown below were collected from the profile of 1 X user who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 1 | 100% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 1 | 100% |
Mendeley readers
The data shown below were compiled from readership statistics for 52 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 52 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 13 | 25% |
| Researcher | 8 | 15% |
| Student > Master | 4 | 8% |
| Student > Bachelor | 4 | 8% |
| Student > Doctoral Student | 2 | 4% |
| Other | 7 | 13% |
| Unknown | 14 | 27% |
| Readers by discipline | Count | As % |
|---|---|---|
| Biochemistry, Genetics and Molecular Biology | 16 | 31% |
| Agricultural and Biological Sciences | 13 | 25% |
| Medicine and Dentistry | 4 | 8% |
| Computer Science | 2 | 4% |
| Nursing and Health Professions | 1 | 2% |
| Other | 3 | 6% |
| Unknown | 13 | 25% |
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 14 July 2018.
All research outputs
#18,643,992
of 23,096,849 outputs
Outputs from BMC Genomics
#8,229
of 10,705 outputs
Outputs of similar age
#252,403
of 327,048 outputs
Outputs of similar age from BMC Genomics
#140
of 203 outputs
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So far Altmetric has tracked 10,705 research outputs from this source. They receive a mean Attention Score of 4.7. This one is in the 12th percentile – i.e., 12% of its peers scored the same or lower than it.
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