Improving Infinium MethylationEPIC data processing: re-annotation of enhancers and long noncoding RNA genes and benchmarking of normalization methods

Bizet, Martin; Defrance, Matthieu; Calonne, Emilie; Bontempi, Gianluca; Sotiriou, Christos; Fuks, François; Jeschke, Jana

doi:10.1080/15592294.2022.2135201

Cited by 4 publications

(1 citation statement)

References 77 publications

(80 reference statements)

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“…Moreover, different algorithms are adopted for data standardization of positive and negative indicators because of their different meanings. The specific methods are as follows [56]:…”

Section: Measurements Of Rural Restructuringmentioning

confidence: 99%

The Correlation Effects and Mechanisms of Rural Restructuring and Transformation: A Case Study of the Jianghan Plain in China

2022

Sustainability

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The rural decline accompanying industrialization and urbanization is a lingering puzzle in human society, while promoting rural restructuring and transformation is considered the primary task of contemporary rural development. It is the historical mission of rural geography research in the new era to scientifically understand the characteristics of contemporary rural development and accurately explain the patterns of rural reconstructing and transformation. In this paper, the Jianghan Plain in China is selected for the case study. Characteristic indexes are selected based on the “structure–function” correlation to interpret rural restructuring. Measurement benchmarks are unified through functional value marketization to interpret rural transformation. Multiple statistical analysis is adopted to identify the action paths and decipher the correlation mechanisms. The case study yields the following findings. (1) The rural restructuring on Jianghan Plain has spatial and temporal differences. Rural restructuring has roughly gone through the social restructuring-led, economic restructuring-led, and spatial restructuring-led evolution stages, showing spatially divergent patterns with high rural comprehensive restructuring index (RRC) areas concentrated around the main traffic arteries and linear low RRC areas along the Yangtze River banks. (2) Rural restructuring and transformation on Jianghan Plain show significant correlation effects. During the study period, the rural transformation magnitude (RTM) continues to increase and shows a spatial map similar to that of rural restructuring, with economic-spatial restructuring-led and economic-social restructuring-led as the main modes of rural transformation. (3) The correlation mechanism of rural restructuring and transformation on Jianghan Plain has characteristics typical of less-developed agricultural areas. The economic restructuring led by agricultural land changes and the social restructuring led by rural population outward migration remain the main paths of rural transformation, and the agricultural function still plays an important role in some rural areas. The quantitative measurement of rural region functions in this study need further optimization, and the refinement and accuracy of regional function accounting needs further exploration. The research results are expected to provide a scientific basis for stimulating rural development and promoting sustainable rural development in contemporary developing countries.

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“…Moreover, different algorithms are adopted for data standardization of positive and negative indicators because of their different meanings. The specific methods are as follows [56]:…”

Section: Measurements Of Rural Restructuringmentioning

confidence: 99%

The Correlation Effects and Mechanisms of Rural Restructuring and Transformation: A Case Study of the Jianghan Plain in China

2022

Sustainability

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Comprehensive evaluation of the implementation of episignatures for diagnosis of neurodevelopmental disorders (NDDs)

Giuili,

Grolaux,

Macedo

et al. 2023

Hum. Genet.

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Episignatures are popular tools for the diagnosis of rare neurodevelopmental disorders. They are commonly based on a set of differentially methylated CpGs used in combination with a support vector machine model. DNA methylation (DNAm) data often include missing values due to changes in data generation technology and batch effects. While many normalization methods exist for DNAm data, their impact on episignature performance have never been assessed. In addition, technologies to quantify DNAm evolve quickly and this may lead to poor transposition of existing episignatures generated on deprecated array versions to new ones. Indeed, probe removal between array versions, technologies or during preprocessing leads to missing values. Thus, the effect of missing data on episignature performance must also be carefully evaluated and addressed through imputation or an innovative approach to episignatures design. In this paper, we used data from patients suffering from Kabuki and Sotos syndrome to evaluate the influence of normalization methods, classification models and missing data on the prediction performances of two existing episignatures. We compare how six popular normalization methods for methylarray data affect episignature classification performances in Kabuki and Sotos syndromes and provide best practice suggestions when building new episignatures. In this setting, we show that Illumina, Noob or Funnorm normalization methods achieved higher classification performances on the testing sets compared to Quantile, Raw and Swan normalization methods. We further show that penalized logistic regression and support vector machines perform best in the classification of Kabuki and Sotos syndrome patients. Then, we describe a new paradigm to build episignatures based on the detection of differentially methylated regions (DMRs) and evaluate their performance compared to classical differentially methylated cytosines (DMCs)-based episignatures in the presence of missing data. We show that the performance of classical DMC-based episignatures suffers from the presence of missing data more than the DMR-based approach. We present a comprehensive evaluation of how the normalization of DNA methylation data affects episignature performance, using three popular classification models. We further evaluate how missing data affect those models’ predictions. Finally, we propose a novel methodology to develop episignatures based on differentially methylated regions identification and show how this method slightly outperforms classical episignatures in the presence of missing data.

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Classroom Evaluation and Impact in Sino-Foreign Cooperative Education Through the Integration of WOA and Multimodal Information Fusion

Wang

2023

2023 7th Asian Conference on Artificial Intelligence Technology (ACAIT)

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Improving Infinium MethylationEPIC data processing: re-annotation of enhancers and long noncoding RNA genes and benchmarking of normalization methods

Cited by 4 publications

References 77 publications

The Correlation Effects and Mechanisms of Rural Restructuring and Transformation: A Case Study of the Jianghan Plain in China

The Correlation Effects and Mechanisms of Rural Restructuring and Transformation: A Case Study of the Jianghan Plain in China

Comprehensive evaluation of the implementation of episignatures for diagnosis of neurodevelopmental disorders (NDDs)

Classroom Evaluation and Impact in Sino-Foreign Cooperative Education Through the Integration of WOA and Multimodal Information Fusion

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