Principal component analysis

Lever, Jake; Krzywinski, Martin; Altman, Naomi

doi:10.1038/nmeth.4346

Cited by 1,058 publications

(652 citation statements)

References 4 publications

Supporting

Mentioning

635

Contrasting

Unclassified

Order By: Relevance

“…PCA can reduce multidimensional data in efforts to interpret the results by discovering clusters and important patterns (36). The heatmap and associated dendrogram show the expected clustering of replicates.…”

Section: Resultsmentioning

confidence: 99%

Streamlined Tandem Mass Tag (SL-TMT) Protocol: An Efficient Strategy for Quantitative (Phospho)proteome Profiling Using Tandem Mass Tag-Synchronous Precursor Selection-MS3

et al. 2018

View full text Add to dashboard Cite

Mass spectrometry (MS)-based isobaric labeling has developed rapidly into a powerful strategy for high throughput protein quantification. Sample multiplexing and exceptional sensitivity allow for the quantification of tens of thousands of peptides and by inference thousands of proteins from multiple samples in a single mass spectrometry experiment. Accurate quantification demands a consistent and robust sample preparation strategy. Here, we present a detailed workflow for SPS-MS3-based quantitative abundance profiling of Tandem Mass Tag (TMT)-labeled proteins and phosphopeptides, which we have termed the Streamlined (SL)-TMT protocol. We describe a universally-applicable strategy that requires minimal individual sample processing and permits the seamless addition of a phosphopeptide enrichment step (“mini-phos”) with little deviation from the deep proteome analysis. To showcase our workflow, we profile the proteome of wild-type S. cerevisiae yeast grown with either glucose or pyruvate as the carbon source. Here, we have established a streamlined TMT protocol that enables deep proteome and medium-scale phosphoproteome analysis.

show abstract

Section: Resultsmentioning

confidence: 99%

Streamlined Tandem Mass Tag (SL-TMT) Protocol: An Efficient Strategy for Quantitative (Phospho)proteome Profiling Using Tandem Mass Tag-Synchronous Precursor Selection-MS3

et al. 2018

View full text Add to dashboard Cite

show abstract

“…Given a dataset of n observations of m variables x 1 , …, x m or, equivalently, an n × m matrix X . PCA reduces X by geometrically projecting it onto lower dimensions called principal components (PCs), with the goal of finding the best summary of X using a limited number k of PCs (Ringnér, ; Lever et al, ). X can be written as a random function of X(t,s) as:

X ((), t, s) = \sum_{i = 1}^{n} {EOF}_{i} ((), t) . {PC}_{i} ((), s)

\approx \sum_{i = 1}^{k} {EOF}_{i} ((), t) . {PC}_{i} ((), s), k ≪ n,

where all k vectors EOF i are orthogonal to each other and

{PC}_{i}^{T} \times {PC}_{i}

equals the i th eigenvalue.…”

Section: Methodsmentioning

confidence: 99%

Space–time variability of drought over Vietnam

Phan-Van

Khiem

et al. 2019

Intl Journal of Climatology

View full text Add to dashboard Cite

Drought may have severe societal, economic, and environmental consequences. However, the space–time characteristics of drought over Vietnam remain poorly understood. In this study, we investigate the spatio‐temporal variability of drought using the Palmer Drought Severity Index (PDSI) over mainland Vietnam for the 1980–2014 period. Through data analysis at 131 stations, we identified the main characteristics, historical trends, and dominant variability of drought across seven climatic sub‐regions in Vietnam. The results show regional patterns of drought duration, inter‐arrival time, frequency, and severity, but no consistent trend of drought variation during the study period. Based on the supply and demand concepts of water balance, PDSI captures well the large frequency and severity of drought in some sub‐regions that are related to soil moisture deficit associated with high temperature and low rainfall during summer. Moreover, drought over Vietnam was predominantly controlled by climate seasonality. The linkages between drought in Vietnam and large‐scale drivers are quite different among areas, suggesting a possibility of early prediction for drought at some sub‐regions using ENSO.

show abstract

“…The combined spectral data set of all the samples was used. The spectral pattern variations are expressed in terms of percentage variance and ranking done . The results are represented on a set of orthogonal axes referred as principal components (PCs).…”

Section: Methodsmentioning

confidence: 99%

Application of Raman spectroscopy in comparative study of antiobesity influence of oxytocin and freeze‐dried extracts of Uvariodendron anisatum Verdeck (Annonaceae) in Sprague Dawley rats

Birech

Mwangi

Sehmi

et al. 2019

J Raman Spectroscopy

View full text Add to dashboard Cite

Obesity is a condition affecting a substantial number of people in the world. Obese people have increased risks of developing chronic metabolic diseases such as type II diabetes, hypertension, and cancer, among others. Predicting potential development together with rapid diagnosis of the condition followed by early interventions is therefore necessary. This work investigated, first, utility of Raman spectroscopy in performing comparative antiobesity influence studies of oxytocin and a freeze‐dried extract of a local herbal plant exhibiting oxytocin‐like properties called Uvariodendron anisatum Verdeck (Annonaceae) (UAV) on diet induced obesity in Sprague Dawley rat models. Second, we looked for obesity biomarker Raman spectral bands. The blood extracted from the rats were applied onto conductive silver paste smeared glass slides and excited using a 785‐nm laser. Raman spectra of blood from oxytocin‐ and UAV‐treated rats displayed similar profiles with low doses of UAV (100 mg/kg of body weight) being more similar to oxytocin than high doses (200 mg/kg of body weight) as revealed by cosine similarity value of 0.997. Their profiles were also different from blood of obese and nonobese (normal controls) animals. A prominent peak in spectra of treated rats centred at 401 cm−1 can be oxytocin's biomarker band in blood. Comparison of average intensity trend of fructose bands at around 638 and 812 cm−1 between prepared fructose solution and blood of treated rats revealed elevated levels of fructose in blood of rats intraperitoneally injected oxytocin and UAV extracts. The result implied upregulation of fructose in oxytocin‐ and UAV‐treated animals. Principal component analysis confirmed that Raman spectral profiles from blood of obese rats were different from those of nonobese rats with bands ascribed to fructose (638, 812, and 1,217 cm−1) and branched chain amino acids (BCAAs; 478, 1,318, and 1,443 cm−1), being utilized in the segregation of the spectral data sets. It also showed that spectra from oxytocin‐treated and UAV‐treated rat's blood were similar implying identical influence of the drugs on the animals. The study showed potential of Raman spectroscopy as tool for quick obesity (or metabolic syndrome) screening with intensity of Raman bands associated with fructose and BCAAs as biomarkers. Besides, the same bands may be used in comparative efficacy studies of antiobesity drugs. The results reported here are rare in literature.

show abstract

Principal component analysis

Cited by 1,058 publications

References 4 publications

Streamlined Tandem Mass Tag (SL-TMT) Protocol: An Efficient Strategy for Quantitative (Phospho)proteome Profiling Using Tandem Mass Tag-Synchronous Precursor Selection-MS3

Streamlined Tandem Mass Tag (SL-TMT) Protocol: An Efficient Strategy for Quantitative (Phospho)proteome Profiling Using Tandem Mass Tag-Synchronous Precursor Selection-MS3

Space–time variability of drought over Vietnam

Application of Raman spectroscopy in comparative study of antiobesity influence of oxytocin and freeze‐dried extracts of Uvariodendron anisatum Verdeck (Annonaceae) in Sprague Dawley rats

Contact Info

Product

Resources

About