package v3.5.1 Search Results


prcomp  (RStudio)
90
RStudio prcomp
Quantitative proteomic analysis of developmentally timed pupal brains reveals a role for Nab2 in neurodevelopment. A , principal component <t>analysis</t> <t>(PCA)</t> of proteomic data from 24 h after puparium formation Drosophila brains from ten biological replicates of control , Nab2 ex3 , and Nab2 oe flies (control = C155>Gal4, w 1118 ; Nab2 ex3 = C155>Gal4;;Nab2 ex3 ; Nab2 oe = C155>Gal4;Nab2 EP3716 ;Nab2 ex3 ) show results cluster based on the genotype and that Nab2 ex3 and Nab2 oe are distinct from control and each other. PCA was performed in RStudio using <t>prcomp</t> (default stats package v3.5.1), and summed peptide intensities were used as the input. B and C , volcano plots show proteins differentially expressed in each Nab2 genotype compared with the control [ B , Nab2 ex3 (346; 188 down and 158 up) and C , Nab2 oe compared with the control (514; 285 down and 229 up)]. Ten biological replicates (n = 10) per genotype (20 brains per pooled biological replicate) with 30 technical replicates in total. Significance thresholds: log 2 (≥0.32 and ≤−0.32) and −log 10 ( p -value) ≥1.3; thresholds were based on power calculation and instrumental limits. Protein abundance change (down or up) indicated on each side of the plot (log 2 Nab2 ex3 /Cont or Nab2 oe /Cont: gray = not significant, blue ≤ −0.32, red ≥ 0.32). The number of differentially expressed proteins to total detected proteins is shown atop the graph; 346 of 4302 Nab2 ex3 proteins are differentially expressed ( B ) and 514 of 4302 Nab2 oe proteins are differentially expressed ( C ). D – G , the enriched gene ontology terms from FlyEnrichr database for biological process are shown for proteins increased log 2 ( Nab2 ex3 /Cont) ≥0.32 in panel D Nab2 ex3 and log 2 ( Nab2 oe /Cont) in panel E Nab2 oe and decreased log 2 ( Nab2 ex3 /Cont) ≤−0.32 in panel F Nab2 ex3 and log 2 ( Nab2 oe /Cont) in panel G Nab2 oe . The bars shown correspond to the top ten c-scores (c-score = ln(adj p -val) ∗ z-score) in each dataset (adjusted p -value <0.05) ( , , ).
Prcomp, supplied by RStudio, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/package+v3%2E5%2E1/pmc08260979-41-6-4?v=RStudio
Average 90 stars, based on 1 article reviews
prcomp - by Bioz Stars, 2026-07
90/100 stars
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biomod2 package v3.5.1  (RStudio)
90
RStudio biomod2 package v3.5.1
Quantitative proteomic analysis of developmentally timed pupal brains reveals a role for Nab2 in neurodevelopment. A , principal component <t>analysis</t> <t>(PCA)</t> of proteomic data from 24 h after puparium formation Drosophila brains from ten biological replicates of control , Nab2 ex3 , and Nab2 oe flies (control = C155>Gal4, w 1118 ; Nab2 ex3 = C155>Gal4;;Nab2 ex3 ; Nab2 oe = C155>Gal4;Nab2 EP3716 ;Nab2 ex3 ) show results cluster based on the genotype and that Nab2 ex3 and Nab2 oe are distinct from control and each other. PCA was performed in RStudio using <t>prcomp</t> (default stats package v3.5.1), and summed peptide intensities were used as the input. B and C , volcano plots show proteins differentially expressed in each Nab2 genotype compared with the control [ B , Nab2 ex3 (346; 188 down and 158 up) and C , Nab2 oe compared with the control (514; 285 down and 229 up)]. Ten biological replicates (n = 10) per genotype (20 brains per pooled biological replicate) with 30 technical replicates in total. Significance thresholds: log 2 (≥0.32 and ≤−0.32) and −log 10 ( p -value) ≥1.3; thresholds were based on power calculation and instrumental limits. Protein abundance change (down or up) indicated on each side of the plot (log 2 Nab2 ex3 /Cont or Nab2 oe /Cont: gray = not significant, blue ≤ −0.32, red ≥ 0.32). The number of differentially expressed proteins to total detected proteins is shown atop the graph; 346 of 4302 Nab2 ex3 proteins are differentially expressed ( B ) and 514 of 4302 Nab2 oe proteins are differentially expressed ( C ). D – G , the enriched gene ontology terms from FlyEnrichr database for biological process are shown for proteins increased log 2 ( Nab2 ex3 /Cont) ≥0.32 in panel D Nab2 ex3 and log 2 ( Nab2 oe /Cont) in panel E Nab2 oe and decreased log 2 ( Nab2 ex3 /Cont) ≤−0.32 in panel F Nab2 ex3 and log 2 ( Nab2 oe /Cont) in panel G Nab2 oe . The bars shown correspond to the top ten c-scores (c-score = ln(adj p -val) ∗ z-score) in each dataset (adjusted p -value <0.05) ( , , ).
Biomod2 Package V3.5.1, supplied by RStudio, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/package+v3%2E5%2E1/pmc10995821-72-3-14?v=RStudio
Average 90 stars, based on 1 article reviews
biomod2 package v3.5.1 - by Bioz Stars, 2026-07
90/100 stars
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r studio v.3.5.1  (RStudio)
90
RStudio r studio v.3.5.1
Quantitative proteomic analysis of developmentally timed pupal brains reveals a role for Nab2 in neurodevelopment. A , principal component <t>analysis</t> <t>(PCA)</t> of proteomic data from 24 h after puparium formation Drosophila brains from ten biological replicates of control , Nab2 ex3 , and Nab2 oe flies (control = C155>Gal4, w 1118 ; Nab2 ex3 = C155>Gal4;;Nab2 ex3 ; Nab2 oe = C155>Gal4;Nab2 EP3716 ;Nab2 ex3 ) show results cluster based on the genotype and that Nab2 ex3 and Nab2 oe are distinct from control and each other. PCA was performed in RStudio using <t>prcomp</t> (default stats package v3.5.1), and summed peptide intensities were used as the input. B and C , volcano plots show proteins differentially expressed in each Nab2 genotype compared with the control [ B , Nab2 ex3 (346; 188 down and 158 up) and C , Nab2 oe compared with the control (514; 285 down and 229 up)]. Ten biological replicates (n = 10) per genotype (20 brains per pooled biological replicate) with 30 technical replicates in total. Significance thresholds: log 2 (≥0.32 and ≤−0.32) and −log 10 ( p -value) ≥1.3; thresholds were based on power calculation and instrumental limits. Protein abundance change (down or up) indicated on each side of the plot (log 2 Nab2 ex3 /Cont or Nab2 oe /Cont: gray = not significant, blue ≤ −0.32, red ≥ 0.32). The number of differentially expressed proteins to total detected proteins is shown atop the graph; 346 of 4302 Nab2 ex3 proteins are differentially expressed ( B ) and 514 of 4302 Nab2 oe proteins are differentially expressed ( C ). D – G , the enriched gene ontology terms from FlyEnrichr database for biological process are shown for proteins increased log 2 ( Nab2 ex3 /Cont) ≥0.32 in panel D Nab2 ex3 and log 2 ( Nab2 oe /Cont) in panel E Nab2 oe and decreased log 2 ( Nab2 ex3 /Cont) ≤−0.32 in panel F Nab2 ex3 and log 2 ( Nab2 oe /Cont) in panel G Nab2 oe . The bars shown correspond to the top ten c-scores (c-score = ln(adj p -val) ∗ z-score) in each dataset (adjusted p -value <0.05) ( , , ).
R Studio V.3.5.1, supplied by RStudio, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/package+v3%2E5%2E1/pmc07211879__rsos191700_review_history-280-11-13?v=RStudio
Average 90 stars, based on 1 article reviews
r studio v.3.5.1 - by Bioz Stars, 2026-07
90/100 stars
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ggplot2 v.3.5.1 package  (RStudio)
90
RStudio ggplot2 v.3.5.1 package
Quantitative proteomic analysis of developmentally timed pupal brains reveals a role for Nab2 in neurodevelopment. A , principal component <t>analysis</t> <t>(PCA)</t> of proteomic data from 24 h after puparium formation Drosophila brains from ten biological replicates of control , Nab2 ex3 , and Nab2 oe flies (control = C155>Gal4, w 1118 ; Nab2 ex3 = C155>Gal4;;Nab2 ex3 ; Nab2 oe = C155>Gal4;Nab2 EP3716 ;Nab2 ex3 ) show results cluster based on the genotype and that Nab2 ex3 and Nab2 oe are distinct from control and each other. PCA was performed in RStudio using <t>prcomp</t> (default stats package v3.5.1), and summed peptide intensities were used as the input. B and C , volcano plots show proteins differentially expressed in each Nab2 genotype compared with the control [ B , Nab2 ex3 (346; 188 down and 158 up) and C , Nab2 oe compared with the control (514; 285 down and 229 up)]. Ten biological replicates (n = 10) per genotype (20 brains per pooled biological replicate) with 30 technical replicates in total. Significance thresholds: log 2 (≥0.32 and ≤−0.32) and −log 10 ( p -value) ≥1.3; thresholds were based on power calculation and instrumental limits. Protein abundance change (down or up) indicated on each side of the plot (log 2 Nab2 ex3 /Cont or Nab2 oe /Cont: gray = not significant, blue ≤ −0.32, red ≥ 0.32). The number of differentially expressed proteins to total detected proteins is shown atop the graph; 346 of 4302 Nab2 ex3 proteins are differentially expressed ( B ) and 514 of 4302 Nab2 oe proteins are differentially expressed ( C ). D – G , the enriched gene ontology terms from FlyEnrichr database for biological process are shown for proteins increased log 2 ( Nab2 ex3 /Cont) ≥0.32 in panel D Nab2 ex3 and log 2 ( Nab2 oe /Cont) in panel E Nab2 oe and decreased log 2 ( Nab2 ex3 /Cont) ≤−0.32 in panel F Nab2 ex3 and log 2 ( Nab2 oe /Cont) in panel G Nab2 oe . The bars shown correspond to the top ten c-scores (c-score = ln(adj p -val) ∗ z-score) in each dataset (adjusted p -value <0.05) ( , , ).
Ggplot2 V.3.5.1 Package, supplied by RStudio, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/package+v3%2E5%2E1/pm39943045-329-11-16?v=RStudio
Average 90 stars, based on 1 article reviews
ggplot2 v.3.5.1 package - by Bioz Stars, 2026-07
90/100 stars
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slice-o-matic  (TomoVision Inc)
90
TomoVision Inc slice-o-matic
Quantitative proteomic analysis of developmentally timed pupal brains reveals a role for Nab2 in neurodevelopment. A , principal component <t>analysis</t> <t>(PCA)</t> of proteomic data from 24 h after puparium formation Drosophila brains from ten biological replicates of control , Nab2 ex3 , and Nab2 oe flies (control = C155>Gal4, w 1118 ; Nab2 ex3 = C155>Gal4;;Nab2 ex3 ; Nab2 oe = C155>Gal4;Nab2 EP3716 ;Nab2 ex3 ) show results cluster based on the genotype and that Nab2 ex3 and Nab2 oe are distinct from control and each other. PCA was performed in RStudio using <t>prcomp</t> (default stats package v3.5.1), and summed peptide intensities were used as the input. B and C , volcano plots show proteins differentially expressed in each Nab2 genotype compared with the control [ B , Nab2 ex3 (346; 188 down and 158 up) and C , Nab2 oe compared with the control (514; 285 down and 229 up)]. Ten biological replicates (n = 10) per genotype (20 brains per pooled biological replicate) with 30 technical replicates in total. Significance thresholds: log 2 (≥0.32 and ≤−0.32) and −log 10 ( p -value) ≥1.3; thresholds were based on power calculation and instrumental limits. Protein abundance change (down or up) indicated on each side of the plot (log 2 Nab2 ex3 /Cont or Nab2 oe /Cont: gray = not significant, blue ≤ −0.32, red ≥ 0.32). The number of differentially expressed proteins to total detected proteins is shown atop the graph; 346 of 4302 Nab2 ex3 proteins are differentially expressed ( B ) and 514 of 4302 Nab2 oe proteins are differentially expressed ( C ). D – G , the enriched gene ontology terms from FlyEnrichr database for biological process are shown for proteins increased log 2 ( Nab2 ex3 /Cont) ≥0.32 in panel D Nab2 ex3 and log 2 ( Nab2 oe /Cont) in panel E Nab2 oe and decreased log 2 ( Nab2 ex3 /Cont) ≤−0.32 in panel F Nab2 ex3 and log 2 ( Nab2 oe /Cont) in panel G Nab2 oe . The bars shown correspond to the top ten c-scores (c-score = ln(adj p -val) ∗ z-score) in each dataset (adjusted p -value <0.05) ( , , ).
Slice O Matic, supplied by TomoVision Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/package+v3%2E5%2E1/pmc09921698__12967_2023_3901_MOESM1_ESM-2-17-18?v=TomoVision+Inc
Average 90 stars, based on 1 article reviews
slice-o-matic - by Bioz Stars, 2026-07
90/100 stars
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correlate 0.84 package  (RStudio)
90
RStudio correlate 0.84 package
Quantitative proteomic analysis of developmentally timed pupal brains reveals a role for Nab2 in neurodevelopment. A , principal component <t>analysis</t> <t>(PCA)</t> of proteomic data from 24 h after puparium formation Drosophila brains from ten biological replicates of control , Nab2 ex3 , and Nab2 oe flies (control = C155>Gal4, w 1118 ; Nab2 ex3 = C155>Gal4;;Nab2 ex3 ; Nab2 oe = C155>Gal4;Nab2 EP3716 ;Nab2 ex3 ) show results cluster based on the genotype and that Nab2 ex3 and Nab2 oe are distinct from control and each other. PCA was performed in RStudio using <t>prcomp</t> (default stats package v3.5.1), and summed peptide intensities were used as the input. B and C , volcano plots show proteins differentially expressed in each Nab2 genotype compared with the control [ B , Nab2 ex3 (346; 188 down and 158 up) and C , Nab2 oe compared with the control (514; 285 down and 229 up)]. Ten biological replicates (n = 10) per genotype (20 brains per pooled biological replicate) with 30 technical replicates in total. Significance thresholds: log 2 (≥0.32 and ≤−0.32) and −log 10 ( p -value) ≥1.3; thresholds were based on power calculation and instrumental limits. Protein abundance change (down or up) indicated on each side of the plot (log 2 Nab2 ex3 /Cont or Nab2 oe /Cont: gray = not significant, blue ≤ −0.32, red ≥ 0.32). The number of differentially expressed proteins to total detected proteins is shown atop the graph; 346 of 4302 Nab2 ex3 proteins are differentially expressed ( B ) and 514 of 4302 Nab2 oe proteins are differentially expressed ( C ). D – G , the enriched gene ontology terms from FlyEnrichr database for biological process are shown for proteins increased log 2 ( Nab2 ex3 /Cont) ≥0.32 in panel D Nab2 ex3 and log 2 ( Nab2 oe /Cont) in panel E Nab2 oe and decreased log 2 ( Nab2 ex3 /Cont) ≤−0.32 in panel F Nab2 ex3 and log 2 ( Nab2 oe /Cont) in panel G Nab2 oe . The bars shown correspond to the top ten c-scores (c-score = ln(adj p -val) ∗ z-score) in each dataset (adjusted p -value <0.05) ( , , ).
Correlate 0.84 Package, supplied by RStudio, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/package+v3%2E5%2E1/10__53539_slash_squjs__splisspp1___9-99-7-10?v=RStudio
Average 90 stars, based on 1 article reviews
correlate 0.84 package - by Bioz Stars, 2026-07
90/100 stars
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solve software package  (BioNano Genomics)
90
BioNano Genomics solve software package
Quantitative proteomic analysis of developmentally timed pupal brains reveals a role for Nab2 in neurodevelopment. A , principal component <t>analysis</t> <t>(PCA)</t> of proteomic data from 24 h after puparium formation Drosophila brains from ten biological replicates of control , Nab2 ex3 , and Nab2 oe flies (control = C155>Gal4, w 1118 ; Nab2 ex3 = C155>Gal4;;Nab2 ex3 ; Nab2 oe = C155>Gal4;Nab2 EP3716 ;Nab2 ex3 ) show results cluster based on the genotype and that Nab2 ex3 and Nab2 oe are distinct from control and each other. PCA was performed in RStudio using <t>prcomp</t> (default stats package v3.5.1), and summed peptide intensities were used as the input. B and C , volcano plots show proteins differentially expressed in each Nab2 genotype compared with the control [ B , Nab2 ex3 (346; 188 down and 158 up) and C , Nab2 oe compared with the control (514; 285 down and 229 up)]. Ten biological replicates (n = 10) per genotype (20 brains per pooled biological replicate) with 30 technical replicates in total. Significance thresholds: log 2 (≥0.32 and ≤−0.32) and −log 10 ( p -value) ≥1.3; thresholds were based on power calculation and instrumental limits. Protein abundance change (down or up) indicated on each side of the plot (log 2 Nab2 ex3 /Cont or Nab2 oe /Cont: gray = not significant, blue ≤ −0.32, red ≥ 0.32). The number of differentially expressed proteins to total detected proteins is shown atop the graph; 346 of 4302 Nab2 ex3 proteins are differentially expressed ( B ) and 514 of 4302 Nab2 oe proteins are differentially expressed ( C ). D – G , the enriched gene ontology terms from FlyEnrichr database for biological process are shown for proteins increased log 2 ( Nab2 ex3 /Cont) ≥0.32 in panel D Nab2 ex3 and log 2 ( Nab2 oe /Cont) in panel E Nab2 oe and decreased log 2 ( Nab2 ex3 /Cont) ≤−0.32 in panel F Nab2 ex3 and log 2 ( Nab2 oe /Cont) in panel G Nab2 oe . The bars shown correspond to the top ten c-scores (c-score = ln(adj p -val) ∗ z-score) in each dataset (adjusted p -value <0.05) ( , , ).
Solve Software Package, supplied by BioNano Genomics, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/package+v3%2E5%2E1/pm39843533-94-23-23?v=BioNano+Genomics
Average 90 stars, based on 1 article reviews
solve software package - by Bioz Stars, 2026-07
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simplot software package  (Simplot Science)
86
Simplot Science simplot software package
Quantitative proteomic analysis of developmentally timed pupal brains reveals a role for Nab2 in neurodevelopment. A , principal component <t>analysis</t> <t>(PCA)</t> of proteomic data from 24 h after puparium formation Drosophila brains from ten biological replicates of control , Nab2 ex3 , and Nab2 oe flies (control = C155>Gal4, w 1118 ; Nab2 ex3 = C155>Gal4;;Nab2 ex3 ; Nab2 oe = C155>Gal4;Nab2 EP3716 ;Nab2 ex3 ) show results cluster based on the genotype and that Nab2 ex3 and Nab2 oe are distinct from control and each other. PCA was performed in RStudio using <t>prcomp</t> (default stats package v3.5.1), and summed peptide intensities were used as the input. B and C , volcano plots show proteins differentially expressed in each Nab2 genotype compared with the control [ B , Nab2 ex3 (346; 188 down and 158 up) and C , Nab2 oe compared with the control (514; 285 down and 229 up)]. Ten biological replicates (n = 10) per genotype (20 brains per pooled biological replicate) with 30 technical replicates in total. Significance thresholds: log 2 (≥0.32 and ≤−0.32) and −log 10 ( p -value) ≥1.3; thresholds were based on power calculation and instrumental limits. Protein abundance change (down or up) indicated on each side of the plot (log 2 Nab2 ex3 /Cont or Nab2 oe /Cont: gray = not significant, blue ≤ −0.32, red ≥ 0.32). The number of differentially expressed proteins to total detected proteins is shown atop the graph; 346 of 4302 Nab2 ex3 proteins are differentially expressed ( B ) and 514 of 4302 Nab2 oe proteins are differentially expressed ( C ). D – G , the enriched gene ontology terms from FlyEnrichr database for biological process are shown for proteins increased log 2 ( Nab2 ex3 /Cont) ≥0.32 in panel D Nab2 ex3 and log 2 ( Nab2 oe /Cont) in panel E Nab2 oe and decreased log 2 ( Nab2 ex3 /Cont) ≤−0.32 in panel F Nab2 ex3 and log 2 ( Nab2 oe /Cont) in panel G Nab2 oe . The bars shown correspond to the top ten c-scores (c-score = ln(adj p -val) ∗ z-score) in each dataset (adjusted p -value <0.05) ( , , ).
Simplot Software Package, supplied by Simplot Science, 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/product/package+v3%2E5%2E1/pmc13001373-97-15-15?v=Simplot+Science
Average 86 stars, based on 1 article reviews
simplot software package - by Bioz Stars, 2026-07
86/100 stars
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drc package  (RStudio)
90
RStudio drc package
Quantitative proteomic analysis of developmentally timed pupal brains reveals a role for Nab2 in neurodevelopment. A , principal component <t>analysis</t> <t>(PCA)</t> of proteomic data from 24 h after puparium formation Drosophila brains from ten biological replicates of control , Nab2 ex3 , and Nab2 oe flies (control = C155>Gal4, w 1118 ; Nab2 ex3 = C155>Gal4;;Nab2 ex3 ; Nab2 oe = C155>Gal4;Nab2 EP3716 ;Nab2 ex3 ) show results cluster based on the genotype and that Nab2 ex3 and Nab2 oe are distinct from control and each other. PCA was performed in RStudio using <t>prcomp</t> (default stats package v3.5.1), and summed peptide intensities were used as the input. B and C , volcano plots show proteins differentially expressed in each Nab2 genotype compared with the control [ B , Nab2 ex3 (346; 188 down and 158 up) and C , Nab2 oe compared with the control (514; 285 down and 229 up)]. Ten biological replicates (n = 10) per genotype (20 brains per pooled biological replicate) with 30 technical replicates in total. Significance thresholds: log 2 (≥0.32 and ≤−0.32) and −log 10 ( p -value) ≥1.3; thresholds were based on power calculation and instrumental limits. Protein abundance change (down or up) indicated on each side of the plot (log 2 Nab2 ex3 /Cont or Nab2 oe /Cont: gray = not significant, blue ≤ −0.32, red ≥ 0.32). The number of differentially expressed proteins to total detected proteins is shown atop the graph; 346 of 4302 Nab2 ex3 proteins are differentially expressed ( B ) and 514 of 4302 Nab2 oe proteins are differentially expressed ( C ). D – G , the enriched gene ontology terms from FlyEnrichr database for biological process are shown for proteins increased log 2 ( Nab2 ex3 /Cont) ≥0.32 in panel D Nab2 ex3 and log 2 ( Nab2 oe /Cont) in panel E Nab2 oe and decreased log 2 ( Nab2 ex3 /Cont) ≤−0.32 in panel F Nab2 ex3 and log 2 ( Nab2 oe /Cont) in panel G Nab2 oe . The bars shown correspond to the top ten c-scores (c-score = ln(adj p -val) ∗ z-score) in each dataset (adjusted p -value <0.05) ( , , ).
Drc Package, supplied by RStudio, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/package+v3%2E5%2E1/pmc07821297-88-11-14?v=RStudio
Average 90 stars, based on 1 article reviews
drc package - by Bioz Stars, 2026-07
90/100 stars
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ggplot v3.5.1  (RStudio)
90
RStudio ggplot v3.5.1
Quantitative proteomic analysis of developmentally timed pupal brains reveals a role for Nab2 in neurodevelopment. A , principal component <t>analysis</t> <t>(PCA)</t> of proteomic data from 24 h after puparium formation Drosophila brains from ten biological replicates of control , Nab2 ex3 , and Nab2 oe flies (control = C155>Gal4, w 1118 ; Nab2 ex3 = C155>Gal4;;Nab2 ex3 ; Nab2 oe = C155>Gal4;Nab2 EP3716 ;Nab2 ex3 ) show results cluster based on the genotype and that Nab2 ex3 and Nab2 oe are distinct from control and each other. PCA was performed in RStudio using <t>prcomp</t> (default stats package v3.5.1), and summed peptide intensities were used as the input. B and C , volcano plots show proteins differentially expressed in each Nab2 genotype compared with the control [ B , Nab2 ex3 (346; 188 down and 158 up) and C , Nab2 oe compared with the control (514; 285 down and 229 up)]. Ten biological replicates (n = 10) per genotype (20 brains per pooled biological replicate) with 30 technical replicates in total. Significance thresholds: log 2 (≥0.32 and ≤−0.32) and −log 10 ( p -value) ≥1.3; thresholds were based on power calculation and instrumental limits. Protein abundance change (down or up) indicated on each side of the plot (log 2 Nab2 ex3 /Cont or Nab2 oe /Cont: gray = not significant, blue ≤ −0.32, red ≥ 0.32). The number of differentially expressed proteins to total detected proteins is shown atop the graph; 346 of 4302 Nab2 ex3 proteins are differentially expressed ( B ) and 514 of 4302 Nab2 oe proteins are differentially expressed ( C ). D – G , the enriched gene ontology terms from FlyEnrichr database for biological process are shown for proteins increased log 2 ( Nab2 ex3 /Cont) ≥0.32 in panel D Nab2 ex3 and log 2 ( Nab2 oe /Cont) in panel E Nab2 oe and decreased log 2 ( Nab2 ex3 /Cont) ≤−0.32 in panel F Nab2 ex3 and log 2 ( Nab2 oe /Cont) in panel G Nab2 oe . The bars shown correspond to the top ten c-scores (c-score = ln(adj p -val) ∗ z-score) in each dataset (adjusted p -value <0.05) ( , , ).
Ggplot V3.5.1, supplied by RStudio, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/package+v3%2E5%2E1/pmc11868764-50-13-18?v=RStudio
Average 90 stars, based on 1 article reviews
ggplot v3.5.1 - by Bioz Stars, 2026-07
90/100 stars
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r v3 5 1  (STATA Corporation)
99
STATA Corporation r v3 5 1
Quantitative proteomic analysis of developmentally timed pupal brains reveals a role for Nab2 in neurodevelopment. A , principal component <t>analysis</t> <t>(PCA)</t> of proteomic data from 24 h after puparium formation Drosophila brains from ten biological replicates of control , Nab2 ex3 , and Nab2 oe flies (control = C155>Gal4, w 1118 ; Nab2 ex3 = C155>Gal4;;Nab2 ex3 ; Nab2 oe = C155>Gal4;Nab2 EP3716 ;Nab2 ex3 ) show results cluster based on the genotype and that Nab2 ex3 and Nab2 oe are distinct from control and each other. PCA was performed in RStudio using <t>prcomp</t> (default stats package v3.5.1), and summed peptide intensities were used as the input. B and C , volcano plots show proteins differentially expressed in each Nab2 genotype compared with the control [ B , Nab2 ex3 (346; 188 down and 158 up) and C , Nab2 oe compared with the control (514; 285 down and 229 up)]. Ten biological replicates (n = 10) per genotype (20 brains per pooled biological replicate) with 30 technical replicates in total. Significance thresholds: log 2 (≥0.32 and ≤−0.32) and −log 10 ( p -value) ≥1.3; thresholds were based on power calculation and instrumental limits. Protein abundance change (down or up) indicated on each side of the plot (log 2 Nab2 ex3 /Cont or Nab2 oe /Cont: gray = not significant, blue ≤ −0.32, red ≥ 0.32). The number of differentially expressed proteins to total detected proteins is shown atop the graph; 346 of 4302 Nab2 ex3 proteins are differentially expressed ( B ) and 514 of 4302 Nab2 oe proteins are differentially expressed ( C ). D – G , the enriched gene ontology terms from FlyEnrichr database for biological process are shown for proteins increased log 2 ( Nab2 ex3 /Cont) ≥0.32 in panel D Nab2 ex3 and log 2 ( Nab2 oe /Cont) in panel E Nab2 oe and decreased log 2 ( Nab2 ex3 /Cont) ≤−0.32 in panel F Nab2 ex3 and log 2 ( Nab2 oe /Cont) in panel G Nab2 oe . The bars shown correspond to the top ten c-scores (c-score = ln(adj p -val) ∗ z-score) in each dataset (adjusted p -value <0.05) ( , , ).
R V3 5 1, supplied by STATA Corporation, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Quantitative proteomic analysis of developmentally timed pupal brains reveals a role for Nab2 in neurodevelopment. A , principal component <t>analysis</t> <t>(PCA)</t> of proteomic data from 24 h after puparium formation Drosophila brains from ten biological replicates of control , Nab2 ex3 , and Nab2 oe flies (control = C155>Gal4, w 1118 ; Nab2 ex3 = C155>Gal4;;Nab2 ex3 ; Nab2 oe = C155>Gal4;Nab2 EP3716 ;Nab2 ex3 ) show results cluster based on the genotype and that Nab2 ex3 and Nab2 oe are distinct from control and each other. PCA was performed in RStudio using <t>prcomp</t> (default stats package v3.5.1), and summed peptide intensities were used as the input. B and C , volcano plots show proteins differentially expressed in each Nab2 genotype compared with the control [ B , Nab2 ex3 (346; 188 down and 158 up) and C , Nab2 oe compared with the control (514; 285 down and 229 up)]. Ten biological replicates (n = 10) per genotype (20 brains per pooled biological replicate) with 30 technical replicates in total. Significance thresholds: log 2 (≥0.32 and ≤−0.32) and −log 10 ( p -value) ≥1.3; thresholds were based on power calculation and instrumental limits. Protein abundance change (down or up) indicated on each side of the plot (log 2 Nab2 ex3 /Cont or Nab2 oe /Cont: gray = not significant, blue ≤ −0.32, red ≥ 0.32). The number of differentially expressed proteins to total detected proteins is shown atop the graph; 346 of 4302 Nab2 ex3 proteins are differentially expressed ( B ) and 514 of 4302 Nab2 oe proteins are differentially expressed ( C ). D – G , the enriched gene ontology terms from FlyEnrichr database for biological process are shown for proteins increased log 2 ( Nab2 ex3 /Cont) ≥0.32 in panel D Nab2 ex3 and log 2 ( Nab2 oe /Cont) in panel E Nab2 oe and decreased log 2 ( Nab2 ex3 /Cont) ≤−0.32 in panel F Nab2 ex3 and log 2 ( Nab2 oe /Cont) in panel G Nab2 oe . The bars shown correspond to the top ten c-scores (c-score = ln(adj p -val) ∗ z-score) in each dataset (adjusted p -value <0.05) ( , , ).
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Quantitative proteomic analysis of developmentally timed pupal brains reveals a role for Nab2 in neurodevelopment. A , principal component analysis (PCA) of proteomic data from 24 h after puparium formation Drosophila brains from ten biological replicates of control , Nab2 ex3 , and Nab2 oe flies (control = C155>Gal4, w 1118 ; Nab2 ex3 = C155>Gal4;;Nab2 ex3 ; Nab2 oe = C155>Gal4;Nab2 EP3716 ;Nab2 ex3 ) show results cluster based on the genotype and that Nab2 ex3 and Nab2 oe are distinct from control and each other. PCA was performed in RStudio using prcomp (default stats package v3.5.1), and summed peptide intensities were used as the input. B and C , volcano plots show proteins differentially expressed in each Nab2 genotype compared with the control [ B , Nab2 ex3 (346; 188 down and 158 up) and C , Nab2 oe compared with the control (514; 285 down and 229 up)]. Ten biological replicates (n = 10) per genotype (20 brains per pooled biological replicate) with 30 technical replicates in total. Significance thresholds: log 2 (≥0.32 and ≤−0.32) and −log 10 ( p -value) ≥1.3; thresholds were based on power calculation and instrumental limits. Protein abundance change (down or up) indicated on each side of the plot (log 2 Nab2 ex3 /Cont or Nab2 oe /Cont: gray = not significant, blue ≤ −0.32, red ≥ 0.32). The number of differentially expressed proteins to total detected proteins is shown atop the graph; 346 of 4302 Nab2 ex3 proteins are differentially expressed ( B ) and 514 of 4302 Nab2 oe proteins are differentially expressed ( C ). D – G , the enriched gene ontology terms from FlyEnrichr database for biological process are shown for proteins increased log 2 ( Nab2 ex3 /Cont) ≥0.32 in panel D Nab2 ex3 and log 2 ( Nab2 oe /Cont) in panel E Nab2 oe and decreased log 2 ( Nab2 ex3 /Cont) ≤−0.32 in panel F Nab2 ex3 and log 2 ( Nab2 oe /Cont) in panel G Nab2 oe . The bars shown correspond to the top ten c-scores (c-score = ln(adj p -val) ∗ z-score) in each dataset (adjusted p -value <0.05) ( , , ).

Journal: The Journal of Biological Chemistry

Article Title: The RNA-binding protein Nab2 regulates the proteome of the developing Drosophila brain

doi: 10.1016/j.jbc.2021.100877

Figure Lengend Snippet: Quantitative proteomic analysis of developmentally timed pupal brains reveals a role for Nab2 in neurodevelopment. A , principal component analysis (PCA) of proteomic data from 24 h after puparium formation Drosophila brains from ten biological replicates of control , Nab2 ex3 , and Nab2 oe flies (control = C155>Gal4, w 1118 ; Nab2 ex3 = C155>Gal4;;Nab2 ex3 ; Nab2 oe = C155>Gal4;Nab2 EP3716 ;Nab2 ex3 ) show results cluster based on the genotype and that Nab2 ex3 and Nab2 oe are distinct from control and each other. PCA was performed in RStudio using prcomp (default stats package v3.5.1), and summed peptide intensities were used as the input. B and C , volcano plots show proteins differentially expressed in each Nab2 genotype compared with the control [ B , Nab2 ex3 (346; 188 down and 158 up) and C , Nab2 oe compared with the control (514; 285 down and 229 up)]. Ten biological replicates (n = 10) per genotype (20 brains per pooled biological replicate) with 30 technical replicates in total. Significance thresholds: log 2 (≥0.32 and ≤−0.32) and −log 10 ( p -value) ≥1.3; thresholds were based on power calculation and instrumental limits. Protein abundance change (down or up) indicated on each side of the plot (log 2 Nab2 ex3 /Cont or Nab2 oe /Cont: gray = not significant, blue ≤ −0.32, red ≥ 0.32). The number of differentially expressed proteins to total detected proteins is shown atop the graph; 346 of 4302 Nab2 ex3 proteins are differentially expressed ( B ) and 514 of 4302 Nab2 oe proteins are differentially expressed ( C ). D – G , the enriched gene ontology terms from FlyEnrichr database for biological process are shown for proteins increased log 2 ( Nab2 ex3 /Cont) ≥0.32 in panel D Nab2 ex3 and log 2 ( Nab2 oe /Cont) in panel E Nab2 oe and decreased log 2 ( Nab2 ex3 /Cont) ≤−0.32 in panel F Nab2 ex3 and log 2 ( Nab2 oe /Cont) in panel G Nab2 oe . The bars shown correspond to the top ten c-scores (c-score = ln(adj p -val) ∗ z-score) in each dataset (adjusted p -value <0.05) ( , , ).

Article Snippet: PCA was performed in RStudio using prcomp (default stats package v3.5.1), and summed peptide intensities were used as the input.

Techniques: Control, Quantitative Proteomics