Principal component analysis

Abdi, Hervé; Williams, Lynne J.

doi:10.1002/wics.101

Cited by 8,242 publications

(4,608 citation statements)

References 43 publications

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“…Spectral and topographic variables, namely, NDVI [22], PCA [23], MSAVI [24], and DEM [25], were integrated with texture features such as homogeneity (HOM), second moment (M2), dissimilarity (DIS), entropy (ENT), and contrast (CON), for the object-based classification. Few studies have noted that the addition of DEM, NDVI, PCA, and MSAVI could help improve image classification results in terms of feature discrimination and accuracy of featured classes (e.g., [26,27]).…”

Section: Data and Methodsologymentioning

confidence: 99%

Geographic Layers as Landscape Drivers for the Marco Polo Argali Habitat in the Southeastern Pamir Mountains of Tajikistan

Salas

Valdez

Boykin

2015

IJGI

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Abstract:We described in this report the essential geographic layers used as landscape drivers for the Marco Polo Argali habitat in the eastern Tajik Pamirs. Using remote sensing techniques and geographic information systems (GIS), individual layers were generated in order to acquire more information on argali patterns and habitat suitability and to make the dataset available online. We introduced an improved object-based image analysis in our mapping of the vegetation cover by utilizing spectral, topographic, and texture variables. We exhausted every Landsat image band and texture feature combination to select the best pairing of band-texture components. For vegetation class alone, the producer's accuracy was 90.8% and the user's accuracy was 91.6%.

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Section: Data and Methodsologymentioning

confidence: 99%

Geographic Layers as Landscape Drivers for the Marco Polo Argali Habitat in the Southeastern Pamir Mountains of Tajikistan

Salas

Valdez

Boykin

2015

IJGI

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“…10, 14-18 PC loadings are commonly used to identify features within the data set which best explain the variance in the data. 44 The spectrumlike PC loadings characterise the main spectral features with the highest significance in the data (e.g. peaks in a SERS spectrum) 45 as well as they correlate the corresponding PC score to the original data.…”

Section: Experimental Design Based On the Pulse-depletion Technique Tmentioning

confidence: 99%

Characterization and Visualization of Vesicles in the Endo-Lysosomal Pathway with Surface-Enhanced Raman Spectroscopy and Chemometrics

et al. 2015

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Surface-enhanced Raman spectroscopy (SERS) is an ultra-sensitive vibrational fingerprinting technique widely used in analytical and biosensing applications. For intracellular sensing, typically gold nanoparticles (AuNPs) are employed as transducers to enhance the otherwise weak Raman spectroscopy signals. Thus the signature patterns of the molecular nanoenvironment around intracellular unlabelled AuNPs can be monitored in a reporter-free manner by SERS. The challenge of selectively identifying molecular changes resulting from cellular processes in large and multidimensional data sets and the lack of simple tools for extracting this information has resulted in limited characterization of fundamental cellular processes by SERS. Here, this shortcoming in analysis of SERS data sets is tackled by developing a suitable methodology of reference-based PCA-LDA (principal component analysis-linear discriminant analysis). This method is validated and exemplarily used to extract spectral features characteristic of the endocytic compartment inside cells. The voluntary uptake through vesicular endocytosis is widely used for the internalisation of AuNPs into cells but the characterization of the individual stages of this pathway has not been carried out. Herein, we use reporter-free SERS to identify the stages of endocytosis of AuNPs in cells, visualize them and map the molecular changes via the adaptation and advantageous use of chemometric methods in combination with tailored sample preparation. Thus our study demonstrates the capabilities of reporter-free SERS for intracellular analysis and its ability to provide a way of characterizing intracellular composition. The developed analytical approach is generic and enables the application of reporter-free SERS to identify unknown components in different biological matrices and materials.3 During the last decade, nanoparticle-based surface-enhanced Raman spectroscopy (SERS) has been extensively employed to study biological systems such as cells and tissues. [1][2][3] There are primarily two approaches: The SERS reporter approach and the label-free (reporter-free) SERS approach. In the former, a molecule is functionalized as a self-assembled monolayer on the nanoparticle and the SERS detection of its characteristic spectrum serves to visualize the location of the nanoparticle(s) inside the cell or tissue. 1, 2 This SERS reporter approach has been used in a variety of applications including detection of pathologic cells and tissues such as in cancer 4-6 or cancer markers in biofluids such as blood. 7,8 The reporters can also serve as pH sensors by an appropriate choice of the functionalized molecule with an exchangeable H + . 9 On the other hand, reporter-free SERS samples the direct environment in the vicinity of the nanoparticles and makes the spectral features contributed by the multiple molecular components available for the identification and understanding of the molecular changes around them. The nanoparticle probes can be tailored, such as by sparse functionalizatio...

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“…It is because b-values have severe heteroscedasticity for highly methylated or unmethylated CpG sites. 25 For identification of patterns in DNA methylation, unsupervised analysis including unsupervised hierarchical clustering 26 and Principal Component Analysis (PCA) 27 were performed. For heatmaps, the Euclidian distance between the 2 groups of samples (EAs and AAs) was calculated by the average linkage.…”

Section: Locus-by-locus Analysis To Identify Differential Methylationmentioning

confidence: 99%

Racial differences in genome-wide methylation profiling and gene expression in breast tissues from healthy women

et al. 2015

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Breast cancer is more common in European Americans (EAs) than in African Americans (AAs) but mortality from breast cancer is higher among AAs. While there are racial differences in DNA methylation and gene expression in breast tumors, little is known whether such racial differences exist in breast tissues of healthy women. Genome-wide DNA methylation and gene expression profiling was performed in histologically normal breast tissues of healthy women. Linear regression models were used to identify differentially-methylated CpG sites (CpGs) between EAs (n D 61) and AAs (n D 22). Correlations for methylation and expression were assessed. Biological functions of the differentially-methylated genes were assigned using the Ingenuity Pathway Analysis. Among 485 differentially-methylated CpGs by race, 203 were hypermethylated in EAs, and 282 were hypermethylated in AAs. Promoter-related differentially-methylated CpGs were more frequently hypermethylated in EAs (52%) than AAs (27%) while gene body and intergenic CpGs were more frequently hypermethylated in AAs. The differentially-methylated CpGs were enriched for cancer-associated genes with roles in cell death and survival, cellular development, and cell-to-cell signaling. In a separate analysis for correlation in EAs and AAs, different patterns of correlation were found between EAs and AAs. The correlated genes showed different biological networks between EAs and AAs; networks were connected by Ubiquitin C. To our knowledge, this is the first comprehensive genome-wide study to identify differences in methylation and gene expression between EAs and AAs in breast tissues from healthy women. These findings may provide further insights regarding the contribution of epigenetic differences to racial disparities in breast cancer.

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Principal component analysis

Cited by 8,242 publications

References 43 publications

Geographic Layers as Landscape Drivers for the Marco Polo Argali Habitat in the Southeastern Pamir Mountains of Tajikistan

Geographic Layers as Landscape Drivers for the Marco Polo Argali Habitat in the Southeastern Pamir Mountains of Tajikistan

Characterization and Visualization of Vesicles in the Endo-Lysosomal Pathway with Surface-Enhanced Raman Spectroscopy and Chemometrics

Racial differences in genome-wide methylation profiling and gene expression in breast tissues from healthy women

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