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Computational prediction of CRISPR cassettes in gut metagenome samples from Chinese type-2 diabetic patients and healthy controls

Overview of attention for article published in BMC Systems Biology, January 2016
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  • Above-average Attention Score compared to outputs of the same age (53rd percentile)
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2 tweeters

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61 Mendeley
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Title
Computational prediction of CRISPR cassettes in gut metagenome samples from Chinese type-2 diabetic patients and healthy controls
Published in
BMC Systems Biology, January 2016
DOI 10.1186/s12918-015-0248-x
Pubmed ID
Authors

Tatiana C. Mangericao, Zhanhao Peng, Xuegong Zhang

Abstract

CRISPR has been becoming a hot topic as a powerful technique for genome editing for human and other higher organisms. The original CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats coupled with CRISPR-associated proteins) is an important adaptive defence system for prokaryotes that provides resistance against invading elements such as viruses and plasmids. A CRISPR cassette contains short nucleotide sequences called spacers. These unique regions retain a history of the interactions between prokaryotes and their invaders in individual strains and ecosystems. One important ecosystem in the human body is the human gut, a rich habitat populated by a great diversity of microorganisms. Gut microbiomes are important for human physiology and health. Metagenome sequencing has been widely applied for studying the gut microbiomes. Most efforts in metagenome study has been focused on profiling taxa compositions and gene catalogues and identifying their associations with human health. Less attention has been paid to the analysis of the ecosystems of microbiomes themselves especially their CRISPR composition. We conducted a preliminary analysis of CRISPR sequences in a human gut metagenomic data set of Chinese individuals of type-2 diabetes patients and healthy controls. Applying an available CRISPR-identification algorithm, PILER-CR, we identified 3169 CRISPR cassettes in the data, from which we constructed a set of 1302 unique repeat sequences and 36,709 spacers. A more extensive analysis was made for the CRISPR repeats: these repeats were submitted to a more comprehensive clustering and classification using the web server tool CRISPRmap. All repeats were compared with known CRISPRs in the database CRISPRdb. A total of 784 repeats had matches in the database, and the remaining 518 repeats from our set are potentially novel ones. The computational analysis of CRISPR composition based contigs of metagenome sequencing data is feasible. It provides an efficient approach for finding potential novel CRISPR arrays and for analysing the ecosystem and history of human microbiomes.

Twitter Demographics

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

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 %
Brazil 2 3%
Unknown 59 97%

Demographic breakdown

Readers by professional status Count As %
Researcher 14 23%
Student > Master 12 20%
Student > Ph. D. Student 6 10%
Student > Bachelor 4 7%
Professor 3 5%
Other 11 18%
Unknown 11 18%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 14 23%
Agricultural and Biological Sciences 13 21%
Medicine and Dentistry 5 8%
Immunology and Microbiology 5 8%
Nursing and Health Professions 2 3%
Other 9 15%
Unknown 13 21%

Attention Score in Context

This research output has an Altmetric Attention Score of 2. 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 29 January 2016.
All research outputs
#3,088,356
of 7,060,796 outputs
Outputs from BMC Systems Biology
#336
of 793 outputs
Outputs of similar age
#138,365
of 319,810 outputs
Outputs of similar age from BMC Systems Biology
#16
of 32 outputs
Altmetric has tracked 7,060,796 research outputs across all sources so far. This one has received more attention than most of these and is in the 54th percentile.
So far Altmetric has tracked 793 research outputs from this source. They receive a mean Attention Score of 3.2. This one has gotten more attention than average, scoring higher than 52% 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 319,810 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 53% of its contemporaries.
We're also able to compare this research output to 32 others from the same source and published within six weeks on either side of this one. This one is in the 46th percentile – i.e., 46% of its contemporaries scored the same or lower than it.