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Umetrics squares discriminant analysis pls da
The scores plot at 6 h (A) and 24 h (B) from the <t>SIMCA</t> <t>PLS</t> training set modeling using the 41 metabolites. VIP plots display the contribution of each metabolite to the modeling at 6 h (C) and 24 h (D). Each dot in the score plots represents one animal labeled as dose compound followed by high dose (H), time point (1 for 6 h and 2 for 24 h) and animal number, for example APAPH14 is animal #4 in the APAP high dose group at 6 h; while APAPH27 is animal #7 in the APAP high dose group at 24 h.
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1) Product Images from "Identification of a metabolic biomarker panel in rats for prediction of acute and idiosyncratic hepatotoxicity"

Article Title: Identification of a metabolic biomarker panel in rats for prediction of acute and idiosyncratic hepatotoxicity

Journal: Computational and Structural Biotechnology Journal

doi: 10.1016/j.csbj.2014.08.001

The scores plot at 6 h (A) and 24 h (B) from the SIMCA PLS training set modeling using the 41 metabolites. VIP plots display the contribution of each metabolite to the modeling at 6 h (C) and 24 h (D). Each dot in the score plots represents one animal labeled as dose compound followed by high dose (H), time point (1 for 6 h and 2 for 24 h) and animal number, for example APAPH14 is animal #4 in the APAP high dose group at 6 h; while APAPH27 is animal #7 in the APAP high dose group at 24 h.
Figure Legend Snippet: The scores plot at 6 h (A) and 24 h (B) from the SIMCA PLS training set modeling using the 41 metabolites. VIP plots display the contribution of each metabolite to the modeling at 6 h (C) and 24 h (D). Each dot in the score plots represents one animal labeled as dose compound followed by high dose (H), time point (1 for 6 h and 2 for 24 h) and animal number, for example APAPH14 is animal #4 in the APAP high dose group at 6 h; while APAPH27 is animal #7 in the APAP high dose group at 24 h.

Techniques Used: Labeling

The scores plot from the Simca PLS training set modeling using 6 metabolites at 6 h (A), 7 metabolites at 24 h (B), and 20 metabolites at both 6 h (C) and 24 h (D). The metabolites were chosen based on the VIP value from the Simca PLS modeling ( Fig. 1 C D). Animal labeling is the same as Fig. 1 .
Figure Legend Snippet: The scores plot from the Simca PLS training set modeling using 6 metabolites at 6 h (A), 7 metabolites at 24 h (B), and 20 metabolites at both 6 h (C) and 24 h (D). The metabolites were chosen based on the VIP value from the Simca PLS modeling ( Fig. 1 C D). Animal labeling is the same as Fig. 1 .

Techniques Used: Labeling

2) Product Images from "Exploring potential biomarkers for lung adenocarcinoma using LC-MS/MS metabolomics"

Article Title: Exploring potential biomarkers for lung adenocarcinoma using LC-MS/MS metabolomics

Journal: The Journal of International Medical Research

doi: 10.1177/0300060519897215

PCA, PLS-DA, and OPLS-DA score maps from the negative ion mode. PCA, principle component analysis; PLS-DA, partial least squares discriminant analysis; OPLS-DA, orthogonal partial least squares discriminant analysis.
Figure Legend Snippet: PCA, PLS-DA, and OPLS-DA score maps from the negative ion mode. PCA, principle component analysis; PLS-DA, partial least squares discriminant analysis; OPLS-DA, orthogonal partial least squares discriminant analysis.

Techniques Used:

PCA, PLS-DA, and OPLS-DA score maps from the positive ion mode. PCA, principle component analysis; PLS-DA, partial least squares discriminant analysis; OPLS-DA, orthogonal partial least squares discriminant analysis.
Figure Legend Snippet: PCA, PLS-DA, and OPLS-DA score maps from the positive ion mode. PCA, principle component analysis; PLS-DA, partial least squares discriminant analysis; OPLS-DA, orthogonal partial least squares discriminant analysis.

Techniques Used:

3) Product Images from "Metabonomic Profiling of Serum and Urine by 1H NMR-Based Spectroscopy Discriminates Patients with Chronic Obstructive Pulmonary Disease and Healthy Individuals"

Article Title: Metabonomic Profiling of Serum and Urine by 1H NMR-Based Spectroscopy Discriminates Patients with Chronic Obstructive Pulmonary Disease and Healthy Individuals

Journal: PLoS ONE

doi: 10.1371/journal.pone.0065675

Multivariate data analysis of 1 H NMR spectra obtained from COPD patients and healthy controls. Scores scatter plots generated from applying (A) PCA, (C) PLS-DA and (E) OPLS-DA to the 1 H NMR spectra of serum. The corresponding scores plots derived from 1 H NMR spectra of urine are shown in (B), (D) and (F), respectively.
Figure Legend Snippet: Multivariate data analysis of 1 H NMR spectra obtained from COPD patients and healthy controls. Scores scatter plots generated from applying (A) PCA, (C) PLS-DA and (E) OPLS-DA to the 1 H NMR spectra of serum. The corresponding scores plots derived from 1 H NMR spectra of urine are shown in (B), (D) and (F), respectively.

Techniques Used: Nuclear Magnetic Resonance, Generated, Derivative Assay

4) Product Images from "Impact of the Pd2Spm (Spermine) Complex on the Metabolism of Triple-Negative Breast Cancer Tumors of a Xenograft Mouse Model"

Article Title: Impact of the Pd2Spm (Spermine) Complex on the Metabolism of Triple-Negative Breast Cancer Tumors of a Xenograft Mouse Model

Journal: International Journal of Molecular Sciences

doi: 10.3390/ijms221910775

Score scatter plots of PCA (left) and PLS-DA (middle) models obtained for 1 H NMR spectra of aqueous extracts of tumors from MDA-MB-231 CDX mouse model, obtained for each pairwise analysis: ( a ) cDDP vs. Controls; ( b ) Pd 2 Spm vs. Controls; and ( c ) Pd 2 Spm vs. cDDP. LV1 loadings plots (right) from the correspondent PLS-DA model are colored according to variable importance to projection (VIP) and exhibit the assignment of main peaks (*: cut-off spectral region corresponding to the water resonance). Abbreviations: DMA, dimethylamine; GA, guanidine acetate; HX, hypoxanthine; PE, phosphoethanolamine; UTP, uridine triphosphate. Other abbreviations are defined in the caption of Figure 1 .
Figure Legend Snippet: Score scatter plots of PCA (left) and PLS-DA (middle) models obtained for 1 H NMR spectra of aqueous extracts of tumors from MDA-MB-231 CDX mouse model, obtained for each pairwise analysis: ( a ) cDDP vs. Controls; ( b ) Pd 2 Spm vs. Controls; and ( c ) Pd 2 Spm vs. cDDP. LV1 loadings plots (right) from the correspondent PLS-DA model are colored according to variable importance to projection (VIP) and exhibit the assignment of main peaks (*: cut-off spectral region corresponding to the water resonance). Abbreviations: DMA, dimethylamine; GA, guanidine acetate; HX, hypoxanthine; PE, phosphoethanolamine; UTP, uridine triphosphate. Other abbreviations are defined in the caption of Figure 1 .

Techniques Used: Nuclear Magnetic Resonance, Multiple Displacement Amplification

5) Product Images from "Deciphering the correlations between aging and constipation by metabolomics and network pharmacology"

Article Title: Deciphering the correlations between aging and constipation by metabolomics and network pharmacology

Journal: Aging (Albany NY)

doi: 10.18632/aging.202340

Multivariate data analysis of 1 H NMR fecal extract spectra among the negative control group (NC), the aging model group (AG) and the constipation model group (CG). ( A ) PCA scores plot of fecal specimens based on NC (blue dots), AG (red boxes) and CG (green triangles). ( B ) Statistical validation of the corresponding PLS-DA model by permutation analysis (permutation No.: 200). R 2 is the explained variance, and Q 2 is the predictive ability of the model. ( C ) The corresponding S-plot and VIP value of fecal specimens in aging and constipation, as well as SUS-plot plots showing the discriminations between aging and constipation. PCA, principal component analysis; PLS-DA, partial least squares discriminant analysis; SUS-plot, shared-and-unique-structures plot.
Figure Legend Snippet: Multivariate data analysis of 1 H NMR fecal extract spectra among the negative control group (NC), the aging model group (AG) and the constipation model group (CG). ( A ) PCA scores plot of fecal specimens based on NC (blue dots), AG (red boxes) and CG (green triangles). ( B ) Statistical validation of the corresponding PLS-DA model by permutation analysis (permutation No.: 200). R 2 is the explained variance, and Q 2 is the predictive ability of the model. ( C ) The corresponding S-plot and VIP value of fecal specimens in aging and constipation, as well as SUS-plot plots showing the discriminations between aging and constipation. PCA, principal component analysis; PLS-DA, partial least squares discriminant analysis; SUS-plot, shared-and-unique-structures plot.

Techniques Used: Nuclear Magnetic Resonance, Negative Control

6) Product Images from "Cell metabolomics to study the function mechanism of Cyperus rotundus L. on triple-negative breast cancer cells"

Article Title: Cell metabolomics to study the function mechanism of Cyperus rotundus L. on triple-negative breast cancer cells

Journal: BMC Complementary Medicine and Therapies

doi: 10.1186/s12906-020-02981-w

The result of multivariate statistical analysis in positive mode. PCA score plot of MDA-MB-231 cells and MDA-MB-468 cells were showed in a and b . The green circle represents the control group respectively named 231–0 or 468–0; the blue box represents the middle dose group such as 231–200 or 468–400; the red triangle means the high dose group name 231–400 or 468–600. The EECR treatment groups were obviously distinct with the control groups through the PCA analysis ( a , b ). The PLS-DA was performed between the high dose group and the control group resulted in R2X = 0.389, R2Y = 0.991, Q2 = 0.959 in MDA-MB-231 cells ( c ), and R2X = 0.443, R2Y = 0.996, Q2 = 0.972 in MDA-MB-468 cells ( d ). The permutation plot tests the Statistical validation of the PLS-DA model ( n = 200) showing the values of R 2 (green circle) and Q 2 (blue box) ( e , f )
Figure Legend Snippet: The result of multivariate statistical analysis in positive mode. PCA score plot of MDA-MB-231 cells and MDA-MB-468 cells were showed in a and b . The green circle represents the control group respectively named 231–0 or 468–0; the blue box represents the middle dose group such as 231–200 or 468–400; the red triangle means the high dose group name 231–400 or 468–600. The EECR treatment groups were obviously distinct with the control groups through the PCA analysis ( a , b ). The PLS-DA was performed between the high dose group and the control group resulted in R2X = 0.389, R2Y = 0.991, Q2 = 0.959 in MDA-MB-231 cells ( c ), and R2X = 0.443, R2Y = 0.996, Q2 = 0.972 in MDA-MB-468 cells ( d ). The permutation plot tests the Statistical validation of the PLS-DA model ( n = 200) showing the values of R 2 (green circle) and Q 2 (blue box) ( e , f )

Techniques Used: Multiple Displacement Amplification

7) Product Images from "Jasmonate-Elicited Stress Induces Metabolic Change in the Leaves of Leucaena leucocephala"

Article Title: Jasmonate-Elicited Stress Induces Metabolic Change in the Leaves of Leucaena leucocephala

Journal: Molecules : A Journal of Synthetic Chemistry and Natural Product Chemistry

doi: 10.3390/molecules23020188

Partial least squares discriminant analysis (PLS-DA) of metabolites in L . leucocephala leaf extracts under JA-Ile elicitation. ( A ) The summary of fit of PLS-DA model of JA-Ile and control. The cumulative R2Y and Q2 were 0.897 and 0.776 respectively, when two components were calculated; ( B ) PLS-DA score plot discriminated L. leucocephala extracts from JA-Ile (triangle) and control treatment (CK, box) more clearly than PCA score plot; ( C ) PLS-DA loading plot. The notations of 1-21 were corresponding to different metabolites as listed in Table 1 . JA-Ile caused an accumulation of lactic acid ( 6 ), β -glucose ( 10 ), alanine ( 12 ), threonine ( 13 ), steroids ( 18 ), 3,4-dihydroxypyridine ( 19 ) and an unidentified compound 20 .
Figure Legend Snippet: Partial least squares discriminant analysis (PLS-DA) of metabolites in L . leucocephala leaf extracts under JA-Ile elicitation. ( A ) The summary of fit of PLS-DA model of JA-Ile and control. The cumulative R2Y and Q2 were 0.897 and 0.776 respectively, when two components were calculated; ( B ) PLS-DA score plot discriminated L. leucocephala extracts from JA-Ile (triangle) and control treatment (CK, box) more clearly than PCA score plot; ( C ) PLS-DA loading plot. The notations of 1-21 were corresponding to different metabolites as listed in Table 1 . JA-Ile caused an accumulation of lactic acid ( 6 ), β -glucose ( 10 ), alanine ( 12 ), threonine ( 13 ), steroids ( 18 ), 3,4-dihydroxypyridine ( 19 ) and an unidentified compound 20 .

Techniques Used:

8) Product Images from "Metabolomic Analysis Reveals That the Mechanism of Astaxanthin Improves the Osteogenic Differentiation Potential in Bone Marrow Mesenchymal Stem Cells"

Article Title: Metabolomic Analysis Reveals That the Mechanism of Astaxanthin Improves the Osteogenic Differentiation Potential in Bone Marrow Mesenchymal Stem Cells

Journal: Oxidative Medicine and Cellular Longevity

doi: 10.1155/2020/3427430

PCA, PLS-DA, and OPLSDA of AST1, AST10, and control group cells. (a–c) Positive ion mode: AST1 vs. control; (a1–c1) negative ion mode: AST1 vs. control; (d–f) positive ion mode: AST10 vs. control; (d1–f1) negative ion mode: AST10 vs. control; (g–i) positive ion mode: AST10 vs. AST1; (g1–i1) negative ion mode: AST10 vs. AST1. ★ represents control samples, ● represents AST-1 μ g/ml samples, and ■ represents AST-10 μ g/ml samples.
Figure Legend Snippet: PCA, PLS-DA, and OPLSDA of AST1, AST10, and control group cells. (a–c) Positive ion mode: AST1 vs. control; (a1–c1) negative ion mode: AST1 vs. control; (d–f) positive ion mode: AST10 vs. control; (d1–f1) negative ion mode: AST10 vs. control; (g–i) positive ion mode: AST10 vs. AST1; (g1–i1) negative ion mode: AST10 vs. AST1. ★ represents control samples, ● represents AST-1 μ g/ml samples, and ■ represents AST-10 μ g/ml samples.

Techniques Used: AST Assay

9) Product Images from "Exploration of Stereoselectivity in Embryo-Larvae (Danio rerio) Induced by Chiral PCB149 at the Bioconcentration and Gene Expression Levels"

Article Title: Exploration of Stereoselectivity in Embryo-Larvae (Danio rerio) Induced by Chiral PCB149 at the Bioconcentration and Gene Expression Levels

Journal: PLoS ONE

doi: 10.1371/journal.pone.0155263

VIP-plot via PLS-DA on the expression level of indicated genes. A: differential genes through comparison of racemic and (+)- PCB149; B: differential genes through comparison of (-)- and (+)- PCB149.
Figure Legend Snippet: VIP-plot via PLS-DA on the expression level of indicated genes. A: differential genes through comparison of racemic and (+)- PCB149; B: differential genes through comparison of (-)- and (+)- PCB149.

Techniques Used: Expressing

10) Product Images from "Serum Metabolomic Profiling Reveals the Amelioration Effect of Methotrexate on Imiquimod-Induced Psoriasis in Mouse"

Article Title: Serum Metabolomic Profiling Reveals the Amelioration Effect of Methotrexate on Imiquimod-Induced Psoriasis in Mouse

Journal: Frontiers in Pharmacology

doi: 10.3389/fphar.2020.558629

Score plots of multivariate statistical analysis on serum samples ( n = 7 in the control and MTX groups and n = 6 in the IMQ group). (A) PCA score plot of control group, IMQ group, and MTX group (R 2 X = 0.812 and Q 2 = 0.371). (B) PLS-DA score plots of control group, IMQ group, and MTX group (R 2 X = 0.823, R 2 Y = 0.947, and Q 2 = 0.723). (C,D) OPLS-DA score plots of serum samples: (C) control group vs. IMQ group (R 2 X = 0.97, R 2 Y = 0.993, and Q 2 = 0.719). (D) IMQ group vs. MTX group (R 2 X = 0.826, R2Y = 0.995, and Q 2 = 0.862). t[1], the first principal component, represents the first largest variance of the data projection, and t[2], the second principal component, represents the second largest variance of the data projection.
Figure Legend Snippet: Score plots of multivariate statistical analysis on serum samples ( n = 7 in the control and MTX groups and n = 6 in the IMQ group). (A) PCA score plot of control group, IMQ group, and MTX group (R 2 X = 0.812 and Q 2 = 0.371). (B) PLS-DA score plots of control group, IMQ group, and MTX group (R 2 X = 0.823, R 2 Y = 0.947, and Q 2 = 0.723). (C,D) OPLS-DA score plots of serum samples: (C) control group vs. IMQ group (R 2 X = 0.97, R 2 Y = 0.993, and Q 2 = 0.719). (D) IMQ group vs. MTX group (R 2 X = 0.826, R2Y = 0.995, and Q 2 = 0.862). t[1], the first principal component, represents the first largest variance of the data projection, and t[2], the second principal component, represents the second largest variance of the data projection.

Techniques Used:

11) Product Images from "Parallel Metabolomic Profiling of Cerebrospinal Fluid and Serum for Identifying Biomarkers of Injury Severity after Acute Human Spinal Cord Injury"

Article Title: Parallel Metabolomic Profiling of Cerebrospinal Fluid and Serum for Identifying Biomarkers of Injury Severity after Acute Human Spinal Cord Injury

Journal: Scientific Reports

doi: 10.1038/srep38718

PCA score plots for ( A ) serum and ( B ) CSF. Green box: non-injured control; black: t 1 ; red: t 2 ; blue: t 3 ; diamond: AIS A; circle: AIS B; star: AIS C; orange triangle: quality control. PLS-DA score plots for ( C ) serum and ( D ) CSF. Black: t 1 ; red: t 2 ; blue: t 3 . The PLS-DA model was cross-validated using twenty permutation tests.
Figure Legend Snippet: PCA score plots for ( A ) serum and ( B ) CSF. Green box: non-injured control; black: t 1 ; red: t 2 ; blue: t 3 ; diamond: AIS A; circle: AIS B; star: AIS C; orange triangle: quality control. PLS-DA score plots for ( C ) serum and ( D ) CSF. Black: t 1 ; red: t 2 ; blue: t 3 . The PLS-DA model was cross-validated using twenty permutation tests.

Techniques Used:

12) Product Images from "Understanding of metals dysregulation in patients with systolic and diastolic dysfunction in ischemic heart disease"

Article Title: Understanding of metals dysregulation in patients with systolic and diastolic dysfunction in ischemic heart disease

Journal: Scientific Reports

doi: 10.1038/s41598-020-70733-4

Scores scatter plots ( A ) PCA, ( B ) 3D PLS-DA, ( C ) 3D OPLS-DA and ( D ) OPLS-DA loadings plot of serum with Grade 0–1 (green), Grade 1A (blue) and Grade 2 (red) of diastolic dysfunctions.
Figure Legend Snippet: Scores scatter plots ( A ) PCA, ( B ) 3D PLS-DA, ( C ) 3D OPLS-DA and ( D ) OPLS-DA loadings plot of serum with Grade 0–1 (green), Grade 1A (blue) and Grade 2 (red) of diastolic dysfunctions.

Techniques Used:

Scores scatter plots ( A ) PCA, ( B ) 3D PLS-DA, ( C ) 3D OPLS-DA and ( D ) OPLS-DA loadings plot of serum with E/eʹ
Figure Legend Snippet: Scores scatter plots ( A ) PCA, ( B ) 3D PLS-DA, ( C ) 3D OPLS-DA and ( D ) OPLS-DA loadings plot of serum with E/eʹ

Techniques Used:

Scores scatter plots ( A ) PCA, ( B ) 3D PLS-DA, ( C ) 3D OPLS-DA and ( D ) OPLS-DA loadings plot colored as a function of VIP of serum (SR) from healthy (green) and ischemic heart disease (IHD) (blue).
Figure Legend Snippet: Scores scatter plots ( A ) PCA, ( B ) 3D PLS-DA, ( C ) 3D OPLS-DA and ( D ) OPLS-DA loadings plot colored as a function of VIP of serum (SR) from healthy (green) and ischemic heart disease (IHD) (blue).

Techniques Used:

Scores scatter plots ( A ) PCA, ( B ) 3D PLS-DA, ( C ) 3D OPLS-DA and ( D ) OPLS-DA loadings plot of serum with preserved EF > 45% (green) and reduced EF
Figure Legend Snippet: Scores scatter plots ( A ) PCA, ( B ) 3D PLS-DA, ( C ) 3D OPLS-DA and ( D ) OPLS-DA loadings plot of serum with preserved EF > 45% (green) and reduced EF

Techniques Used:

13) Product Images from "Structural, Functional, and Metabolic Alterations in Human Cerebrovascular Endothelial Cells during Toxoplasma gondii Infection and Amelioration by Verapamil In Vitro"

Article Title: Structural, Functional, and Metabolic Alterations in Human Cerebrovascular Endothelial Cells during Toxoplasma gondii Infection and Amelioration by Verapamil In Vitro

Journal: Microorganisms

doi: 10.3390/microorganisms8091386

Metabolomic profiling revealed distinct changes in metabolites between T. gondii -infected and control cells. ( A ) PCA score plots of metabolites of infected and uninfected BMECs at 6, 24, and 48 hpi. Infected cells were slightly separated from uninfected cells along PC1 ( R 2 X = 0.262, 0.309, and 0.272 for 6, 24, and 48 hpi, respectively). Each point in the plot represents one replicate 1 H NMR spectra. Gray and red circles denote control and infected samples, respectively. ( B ) PLS-DA score plots (top row) and cross-validation plots (bottom row) of the metabolites. Infected BMECs were separated from uninfected cells along PLS-DA ( R 2 X = 0.163, 0.11, and 0.182 at 6, 24, and 48 hpi, respectively). ( C ) OPLS-DA score plots (left) and corresponding coefficient loading plots (right) derived from 1 H NMR spectra of infected and uninfected cells at 48 hpi. Infected cells were separated from uninfected cells along OPLS-DA 1 ( R 2 X = 0.0872). The color scaling map on the right-hand side of the coefficient loading plot shows the significance of metabolite variations between infected and uninfected cells. Peaks oriented upward (positive direction) and downward (negative direction) indicate metabolites that are more or less abundant, respectively, in infected cells compared to control cells. The red and blue colors denote increased and decreased levels of metabolites, respectively. The peak height is expressed in arbitrary units (a.u.) relative to the total peak contribution. UN indicates unknown metabolite.
Figure Legend Snippet: Metabolomic profiling revealed distinct changes in metabolites between T. gondii -infected and control cells. ( A ) PCA score plots of metabolites of infected and uninfected BMECs at 6, 24, and 48 hpi. Infected cells were slightly separated from uninfected cells along PC1 ( R 2 X = 0.262, 0.309, and 0.272 for 6, 24, and 48 hpi, respectively). Each point in the plot represents one replicate 1 H NMR spectra. Gray and red circles denote control and infected samples, respectively. ( B ) PLS-DA score plots (top row) and cross-validation plots (bottom row) of the metabolites. Infected BMECs were separated from uninfected cells along PLS-DA ( R 2 X = 0.163, 0.11, and 0.182 at 6, 24, and 48 hpi, respectively). ( C ) OPLS-DA score plots (left) and corresponding coefficient loading plots (right) derived from 1 H NMR spectra of infected and uninfected cells at 48 hpi. Infected cells were separated from uninfected cells along OPLS-DA 1 ( R 2 X = 0.0872). The color scaling map on the right-hand side of the coefficient loading plot shows the significance of metabolite variations between infected and uninfected cells. Peaks oriented upward (positive direction) and downward (negative direction) indicate metabolites that are more or less abundant, respectively, in infected cells compared to control cells. The red and blue colors denote increased and decreased levels of metabolites, respectively. The peak height is expressed in arbitrary units (a.u.) relative to the total peak contribution. UN indicates unknown metabolite.

Techniques Used: Infection, Nuclear Magnetic Resonance, Derivative Assay

14) Product Images from "Non-invasively predicting differentiation of pancreatic cancer through comparative serum metabonomic profiling"

Article Title: Non-invasively predicting differentiation of pancreatic cancer through comparative serum metabonomic profiling

Journal: BMC Cancer

doi: 10.1186/s12885-017-3703-9

The PCA ( a ) and PLS-DA ( b ) scores plots based on 1 H NMR data of serums from PDAC groups. P, Panc-1; B, BxPC-3; SW, SW1990
Figure Legend Snippet: The PCA ( a ) and PLS-DA ( b ) scores plots based on 1 H NMR data of serums from PDAC groups. P, Panc-1; B, BxPC-3; SW, SW1990

Techniques Used: Nuclear Magnetic Resonance

15) Product Images from "Authentication of Meat and Meat Products Using Triacylglycerols Profiling and by DNA Analysis"

Article Title: Authentication of Meat and Meat Products Using Triacylglycerols Profiling and by DNA Analysis

Journal: Foods

doi: 10.3390/foods9091269

PCA and PLS-DA plots created from ions related to triacylglycerols present in hexane extracts of meat products (green), chicken (blue), pork (red) and beef (yellow). Group 1—chicken ham samples; group 2—meat products containing 70% of beef; group 3—pork meat products containing mechanically separated chicken meat and the rest of the green points represent meat products based on pork meat.
Figure Legend Snippet: PCA and PLS-DA plots created from ions related to triacylglycerols present in hexane extracts of meat products (green), chicken (blue), pork (red) and beef (yellow). Group 1—chicken ham samples; group 2—meat products containing 70% of beef; group 3—pork meat products containing mechanically separated chicken meat and the rest of the green points represent meat products based on pork meat.

Techniques Used:

16) Product Images from "Geographical and Varietal Traceability of Chinese Jujubes Based on Physical and Nutritional Characteristics"

Article Title: Geographical and Varietal Traceability of Chinese Jujubes Based on Physical and Nutritional Characteristics

Journal: Foods

doi: 10.3390/foods10102270

Principal component analysis (PCA), partial least squares-discriminant analysis (PLS-DA), and orthogonal partial least squares-discriminant analysis (OPLS-DA) of Chinese jujube samples in five regions with the eight main quality parameters, and the OPLS-DA model of the five categories of Chinese jujubes samples with the training set and testing set: ( a ) PCA; ( b ) PLS-DA; ( c ) OPLS-DA; ( d ) OPLS-DA model with training set and testing set.
Figure Legend Snippet: Principal component analysis (PCA), partial least squares-discriminant analysis (PLS-DA), and orthogonal partial least squares-discriminant analysis (OPLS-DA) of Chinese jujube samples in five regions with the eight main quality parameters, and the OPLS-DA model of the five categories of Chinese jujubes samples with the training set and testing set: ( a ) PCA; ( b ) PLS-DA; ( c ) OPLS-DA; ( d ) OPLS-DA model with training set and testing set.

Techniques Used:

Principal component analysis (PCA), partial least squares-discriminant analysis (PLS-DA), and orthogonal partial least squares-discriminant analysis (OPLS-DA) of Chinese jujube samples in six varieties with the eight main quality parameters, and the OPLS-DA model of the six categories of Chinese jujubes samples with the training set and testing set: ( a ) PCA; ( b ) PLS-DA; ( c ) OPLS-DA; ( d ) OPLS-DA model with training set and testing set.
Figure Legend Snippet: Principal component analysis (PCA), partial least squares-discriminant analysis (PLS-DA), and orthogonal partial least squares-discriminant analysis (OPLS-DA) of Chinese jujube samples in six varieties with the eight main quality parameters, and the OPLS-DA model of the six categories of Chinese jujubes samples with the training set and testing set: ( a ) PCA; ( b ) PLS-DA; ( c ) OPLS-DA; ( d ) OPLS-DA model with training set and testing set.

Techniques Used:

17) Product Images from "Metabolomic Study of High-Fat Diet-Induced Obese (DIO) and DIO Plus CCl4-Induced NASH Mice and the Effect of Obeticholic Acid"

Article Title: Metabolomic Study of High-Fat Diet-Induced Obese (DIO) and DIO Plus CCl4-Induced NASH Mice and the Effect of Obeticholic Acid

Journal: Metabolites

doi: 10.3390/metabo11060374

The metabolomic analysis of liver, serum and intestine content. ( A ) PCA score plots of liver, serum and intestine content. ( B ) PLS-DA score plots of liver, serum and intestine content. ( C ) Model validation using a permutation test with 200 cycles of liver, serum and intestine content.
Figure Legend Snippet: The metabolomic analysis of liver, serum and intestine content. ( A ) PCA score plots of liver, serum and intestine content. ( B ) PLS-DA score plots of liver, serum and intestine content. ( C ) Model validation using a permutation test with 200 cycles of liver, serum and intestine content.

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18) Product Images from "Molecular Docking and Multivariate Analysis of Xanthones as Antimicrobial and Antiviral Agents"

Article Title: Molecular Docking and Multivariate Analysis of Xanthones as Antimicrobial and Antiviral Agents

Journal: Molecules

doi: 10.3390/molecules200713165

Discrimination of simple xanthones by antifungal activity against A. flavus based on docking scores. ( a ) PCA score plot grouped according to HCA; ( b ) PLS-DA score plot employing antifungal activity as classification variable (group 1: highest activity; group 2: medium activity; group 3: lowest activity).
Figure Legend Snippet: Discrimination of simple xanthones by antifungal activity against A. flavus based on docking scores. ( a ) PCA score plot grouped according to HCA; ( b ) PLS-DA score plot employing antifungal activity as classification variable (group 1: highest activity; group 2: medium activity; group 3: lowest activity).

Techniques Used: Activity Assay, High Content Screening

19) Product Images from "Fusarium inhibition by wild populations of the medicinal plant Salvia africana-lutea L. linked to metabolomic profiling"

Article Title: Fusarium inhibition by wild populations of the medicinal plant Salvia africana-lutea L. linked to metabolomic profiling

Journal: BMC Complementary and Alternative Medicine

doi: 10.1186/1472-6882-14-99

Score plots of the PCA (A) (6 axes, R 2 X 0.995) and PLS-DA (B) (6 axes, Q 2 cum 0.89, R 2 X cum 0.88, R 2 Y cum 0.97) on 1 H NMR data (entire spectrum) of samples from the 5 sites.
Figure Legend Snippet: Score plots of the PCA (A) (6 axes, R 2 X 0.995) and PLS-DA (B) (6 axes, Q 2 cum 0.89, R 2 X cum 0.88, R 2 Y cum 0.97) on 1 H NMR data (entire spectrum) of samples from the 5 sites.

Techniques Used: Nuclear Magnetic Resonance

20) Product Images from "Metabolic effects of basic fibroblast growth factor in streptozotocin-induced diabetic rats: A 1H NMR-based metabolomics investigation"

Article Title: Metabolic effects of basic fibroblast growth factor in streptozotocin-induced diabetic rats: A 1H NMR-based metabolomics investigation

Journal: Scientific Reports

doi: 10.1038/srep36474

Multivariate analysis based on serum metabolic profiles of the control (CON), diabetic (DM) and bFGF-treated (bFGF) rats: ( A ) PLS-DA score plot. ( B ) Permutation test (200 cycles, R 2 = 0.880, Q 2 = 0.854). ( C ) NMR spectrum colored with VIP values.
Figure Legend Snippet: Multivariate analysis based on serum metabolic profiles of the control (CON), diabetic (DM) and bFGF-treated (bFGF) rats: ( A ) PLS-DA score plot. ( B ) Permutation test (200 cycles, R 2 = 0.880, Q 2 = 0.854). ( C ) NMR spectrum colored with VIP values.

Techniques Used: Nuclear Magnetic Resonance

Multivariate analysis based on fecal metabolic profiles of the control (CON), diabetic (DM) and bFGF-treated (bFGF) rats: ( A ) PLS-DA score plot. ( B ) Permutation test (200 cycles, R 2 = 0.692, Q 2 = 0.392). ( C ) NMR spectrum colored with VIP values.
Figure Legend Snippet: Multivariate analysis based on fecal metabolic profiles of the control (CON), diabetic (DM) and bFGF-treated (bFGF) rats: ( A ) PLS-DA score plot. ( B ) Permutation test (200 cycles, R 2 = 0.692, Q 2 = 0.392). ( C ) NMR spectrum colored with VIP values.

Techniques Used: Nuclear Magnetic Resonance

21) Product Images from "Urinary metabolomic changes and microbiotic alterations in presenilin1/2 conditional double knockout mice"

Article Title: Urinary metabolomic changes and microbiotic alterations in presenilin1/2 conditional double knockout mice

Journal: Journal of Translational Medicine

doi: 10.1186/s12967-021-03032-9

Urinary metabolic profiling (n = 6) of PS cDKO mice and WT mice of 2 months and 6 months. PCA score plot ( A ), PLS-DA ( B )
Figure Legend Snippet: Urinary metabolic profiling (n = 6) of PS cDKO mice and WT mice of 2 months and 6 months. PCA score plot ( A ), PLS-DA ( B )

Techniques Used: Mouse Assay

22) Product Images from "Intrafollicular interleukin-8, interleukin-12, and adrenomedullin are the promising prognostic markers of oocyte and embryo quality in women with endometriosis"

Article Title: Intrafollicular interleukin-8, interleukin-12, and adrenomedullin are the promising prognostic markers of oocyte and embryo quality in women with endometriosis

Journal: Journal of Assisted Reproduction and Genetics

doi: 10.1007/s10815-016-0782-5

Multivariate analysis. Score scatterplot of t1 versus t2 after applying a PCA and b PLS-DA to various intrafollicular cytokines and angiogenic growth factors in women with endometriosis ( blue ) and controls ( green ). c Results from the permutation test
Figure Legend Snippet: Multivariate analysis. Score scatterplot of t1 versus t2 after applying a PCA and b PLS-DA to various intrafollicular cytokines and angiogenic growth factors in women with endometriosis ( blue ) and controls ( green ). c Results from the permutation test

Techniques Used:

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    Umetrics squares discriminant analysis pls da
    The scores plot at 6 h (A) and 24 h (B) from the <t>SIMCA</t> <t>PLS</t> training set modeling using the 41 metabolites. VIP plots display the contribution of each metabolite to the modeling at 6 h (C) and 24 h (D). Each dot in the score plots represents one animal labeled as dose compound followed by high dose (H), time point (1 for 6 h and 2 for 24 h) and animal number, for example APAPH14 is animal #4 in the APAP high dose group at 6 h; while APAPH27 is animal #7 in the APAP high dose group at 24 h.
    Squares Discriminant Analysis Pls Da, supplied by Umetrics, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Umetrics partial least squares discriminant analysis pls da
    Comparison of metabolic composition of serum. (A) <t>PCA</t> (R 2 X = 0.642, Q 2 = 0.178) and (B) <t>PLS-DA</t> (R 2 Y = 0.915, Q 2 = 0.700) models of serum metabolite concentrations of sham C57BL/6 female mice compared with ovariectomized mice with and without Fosamax treatment for 23 weeks. Permutation testing revealed that the model was valid, with all values of the permuted R 2 Y and Q 2 data being significantly less than the original model (p
    Partial Least Squares Discriminant Analysis Pls Da, supplied by Umetrics, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/partial least squares discriminant analysis pls da/product/Umetrics
    Average 86 stars, based on 1 article reviews
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    Umetrics discriminant analysis pls da
    <t>PLS‐DA</t> scores plot showing group separation between HF patients due to non‐ischemic cardiomyopathy and controls at rest (t 0 ) colored by NYHA class (A) and loadings plot colored by metabolite ontology group (B).
    Discriminant Analysis Pls Da, supplied by Umetrics, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    The scores plot at 6 h (A) and 24 h (B) from the SIMCA PLS training set modeling using the 41 metabolites. VIP plots display the contribution of each metabolite to the modeling at 6 h (C) and 24 h (D). Each dot in the score plots represents one animal labeled as dose compound followed by high dose (H), time point (1 for 6 h and 2 for 24 h) and animal number, for example APAPH14 is animal #4 in the APAP high dose group at 6 h; while APAPH27 is animal #7 in the APAP high dose group at 24 h.

    Journal: Computational and Structural Biotechnology Journal

    Article Title: Identification of a metabolic biomarker panel in rats for prediction of acute and idiosyncratic hepatotoxicity

    doi: 10.1016/j.csbj.2014.08.001

    Figure Lengend Snippet: The scores plot at 6 h (A) and 24 h (B) from the SIMCA PLS training set modeling using the 41 metabolites. VIP plots display the contribution of each metabolite to the modeling at 6 h (C) and 24 h (D). Each dot in the score plots represents one animal labeled as dose compound followed by high dose (H), time point (1 for 6 h and 2 for 24 h) and animal number, for example APAPH14 is animal #4 in the APAP high dose group at 6 h; while APAPH27 is animal #7 in the APAP high dose group at 24 h.

    Article Snippet: The resulting normalized data for all 41 metabolites was further subjected to partial least squares discriminant analysis (PLS-DA) using SIMCA v. 13 (MKS Umetrics AB, Sweden).

    Techniques: Labeling

    The scores plot from the Simca PLS training set modeling using 6 metabolites at 6 h (A), 7 metabolites at 24 h (B), and 20 metabolites at both 6 h (C) and 24 h (D). The metabolites were chosen based on the VIP value from the Simca PLS modeling ( Fig. 1 C D). Animal labeling is the same as Fig. 1 .

    Journal: Computational and Structural Biotechnology Journal

    Article Title: Identification of a metabolic biomarker panel in rats for prediction of acute and idiosyncratic hepatotoxicity

    doi: 10.1016/j.csbj.2014.08.001

    Figure Lengend Snippet: The scores plot from the Simca PLS training set modeling using 6 metabolites at 6 h (A), 7 metabolites at 24 h (B), and 20 metabolites at both 6 h (C) and 24 h (D). The metabolites were chosen based on the VIP value from the Simca PLS modeling ( Fig. 1 C D). Animal labeling is the same as Fig. 1 .

    Article Snippet: The resulting normalized data for all 41 metabolites was further subjected to partial least squares discriminant analysis (PLS-DA) using SIMCA v. 13 (MKS Umetrics AB, Sweden).

    Techniques: Labeling

    Multivariate data analysis of 1 H NMR spectra obtained from COPD patients and healthy controls. Scores scatter plots generated from applying (A) PCA, (C) PLS-DA and (E) OPLS-DA to the 1 H NMR spectra of serum. The corresponding scores plots derived from 1 H NMR spectra of urine are shown in (B), (D) and (F), respectively.

    Journal: PLoS ONE

    Article Title: Metabonomic Profiling of Serum and Urine by 1H NMR-Based Spectroscopy Discriminates Patients with Chronic Obstructive Pulmonary Disease and Healthy Individuals

    doi: 10.1371/journal.pone.0065675

    Figure Lengend Snippet: Multivariate data analysis of 1 H NMR spectra obtained from COPD patients and healthy controls. Scores scatter plots generated from applying (A) PCA, (C) PLS-DA and (E) OPLS-DA to the 1 H NMR spectra of serum. The corresponding scores plots derived from 1 H NMR spectra of urine are shown in (B), (D) and (F), respectively.

    Article Snippet: After normalization, principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA) and orthogonal projections to latent structures (OPLS)-DA were performed using SIMCA-P+ software version 11.0 (Umetrics, Umea, Sweden).

    Techniques: Nuclear Magnetic Resonance, Generated, Derivative Assay

    Comparison of metabolic composition of serum. (A) PCA (R 2 X = 0.642, Q 2 = 0.178) and (B) PLS-DA (R 2 Y = 0.915, Q 2 = 0.700) models of serum metabolite concentrations of sham C57BL/6 female mice compared with ovariectomized mice with and without Fosamax treatment for 23 weeks. Permutation testing revealed that the model was valid, with all values of the permuted R 2 Y and Q 2 data being significantly less than the original model (p

    Journal: PLoS ONE

    Article Title: An NMR Metabolomic Study on the Effect of Alendronate in Ovariectomized Mice

    doi: 10.1371/journal.pone.0106559

    Figure Lengend Snippet: Comparison of metabolic composition of serum. (A) PCA (R 2 X = 0.642, Q 2 = 0.178) and (B) PLS-DA (R 2 Y = 0.915, Q 2 = 0.700) models of serum metabolite concentrations of sham C57BL/6 female mice compared with ovariectomized mice with and without Fosamax treatment for 23 weeks. Permutation testing revealed that the model was valid, with all values of the permuted R 2 Y and Q 2 data being significantly less than the original model (p

    Article Snippet: Multivariate data analysis (Principal Component Analysis (PCA) and Partial Least Squares-Discriminant Analysis (PLS-DA)) was performed on log10 - transformed metabolite concentrations using SIMCA-P (version 13.0, Umetrics, Umeå, Sweden) as described in Slupsky .

    Techniques: Mouse Assay

    PLS‐DA scores plot showing group separation between HF patients due to non‐ischemic cardiomyopathy and controls at rest (t 0 ) colored by NYHA class (A) and loadings plot colored by metabolite ontology group (B).

    Journal: Esc Heart Failure

    Article Title: Metabolic profiles in heart failure due to non‐ischemic cardiomyopathy at rest and under exercise) Metabolic profiles in heart failure due to non‐ischemic cardiomyopathy at rest and under exercise

    doi: 10.1002/ehf2.12133

    Figure Lengend Snippet: PLS‐DA scores plot showing group separation between HF patients due to non‐ischemic cardiomyopathy and controls at rest (t 0 ) colored by NYHA class (A) and loadings plot colored by metabolite ontology group (B).

    Article Snippet: Multivariate analysis including principal component analysis (PCA) and partial least squares ‐discriminant analysis (PLS‐DA) was applied using Umetrics SIMCA P+ 12 (MKS Data Analytics Solutions).

    Techniques: