37 research outputs found

    Additional file 2: of Prediction of sensitivity to gefitinib/erlotinib for EGFR mutations in NSCLC based on structural interaction fingerprints and multilinear principal component analysis

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    The list of extracted 20 features for EGFR mutant-gefitinib and -erlotinib complexes. The first column is the mutation name. The last column is the response level to gefitinib or erlotinib. The first row is the index of features. (XLSX 27 kb

    MIPE: A metagenome-based community structure explorer and SSU primer evaluation tool

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    <div><p>An understanding of microbial community structure is an important issue in the field of molecular ecology. The traditional molecular method involves amplification of small subunit ribosomal RNA (SSU rRNA) genes by polymerase chain reaction (PCR). However, PCR-based amplicon approaches are affected by primer bias and chimeras. With the development of high-throughput sequencing technology, unbiased SSU rRNA gene sequences can be mined from shotgun sequencing-based metagenomic or metatranscriptomic datasets to obtain a reflection of the microbial community structure in specific types of environment and to evaluate SSU primers. However, the use of short reads obtained through next-generation sequencing for primer evaluation has not been well resolved. The software MIPE (MIcrobiota metagenome Primer Explorer) was developed to adapt numerous short reads from metagenomes and metatranscriptomes. Using metagenomic or metatranscriptomic datasets as input, MIPE extracts and aligns rRNA to reveal detailed information on microbial composition and evaluate SSU rRNA primers. A mock dataset, a real Metagenomics Rapid Annotation using Subsystem Technology (MG-RAST) test dataset, two PrimerProspector test datasets and a real metatranscriptomic dataset were used to validate MIPE. The software calls Mothur (v1.33.3) and the SILVA database (v119) for the alignment and classification of rRNA genes from a metagenome or metatranscriptome. MIPE can effectively extract shotgun rRNA reads from a metagenome or metatranscriptome and is capable of classifying these sequences and exhibiting sensitivity to different SSU rRNA PCR primers. Therefore, MIPE can be used to guide primer design for specific environmental samples.</p></div

    Frequency of <i>OR</i>s greater than 1 by educational attainment at the county level in the United States and the nine divisions.

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    <p>CI: confident interval;</p><p>Percentage was derived by the number of geographic units for each education level divided by the total number of counties at each geographic division.</p

    Clusters for benzene pollution exposure by education at county level.

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    <p>(A): Educational attainment (0–4); (B): Educational attainment (5–8); (C): Educational attainment (9–12). Division 1 is New England; Division 2 is Mid-Atlantic; Division 3 is East North Central; Division 4 is West North Central; Division 5 is South Atlantic; Division 6 is East South Central; Division 7 is West South Central; Division 8 is Mountain; Division 9 is Pacific.</p

    Annual exposure concentrations of total benzene at the census tract level in the United States.

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    <p>Annual exposure concentrations of census tracts have been utilized to calculate county level mean exposure concentration values, which was used as a ‘relative exposure level’ metric to evaluate benzene pollution exposure inequities. Division 1 is New England; Division 2 is Mid-Atlantic; Division 3 is East North Central; Division 4 is West North Central; Division 5 is South Atlantic; Division 6 is East South Central; Division 7 is West South Central; Division 8 is Mountain; Division 9 is Pacific.</p

    Clusters for benzene pollution exposure by race at county level.

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    <p>(A): Black; (B): American Indian; (C): Asian; (D): Other races. Division 1 is New England; Division 2 is Mid-Atlantic; Division 3 is East North Central; Division 4 is West North Central; Division 5 is South Atlantic; Division 6 is East South Central; Division 7 is West South Central; Division 8 is Mountain; Division 9 is Pacific.</p
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