Journal: BMC Plant Biology

Article Title: Integration of proteomic and transcriptomic profiles reveals multiple levels of genetic regulation of salt tolerance in cotton

doi: 10.1186/s12870-018-1350-1

Figure Lengend Snippet: Schematic overview of proteomic and transcriptomic data generation and analysis workflow. Step 1: differential expression analysis of proteomic and Step 2: differential expression analysis of mRNA-seq data. Step 3: AS (alternative splicing) analysis using TopHat software and alternatively spliced differentially expressed genes (AS-DEGs) were obtained. Step 4: mapping of all proteins from the proteomic to mRNA-seq data and output of the two target groups. Among them, Group A contains translation repression and/or transcriptional degradation targets (contains differentially expressed genes and proteins whose levels were unchanged, both genes and proteins that were differentially expressed or no proteomic data). Group B contains potential targets of miRNA translational repression (differentially abundant proteins whose mRNA did not change or no mRNA data). Step 5: genome-wide analysis of differentially expressed conserved and novel miRNAs in both cotton genotypes under control and salt stress conditions. Step 6: psRNATarget analysis of both groups against miRNAs DE in the opposite direction combined with Group A and B data

Article Snippet: Scatterplots and Pearson correlation coefficients (r values) between proteins and mRNA expression ratios were constructed and calculated, respectively, using GraphPad Prism version 6 (GraphPad Software, Inc., San Diego, CA) with two-tailed t-tests.

Techniques: Quantitative Proteomics, Alternative Splicing, Software, Genome Wide, Control

Journal: BMC Plant Biology

Article Title: Integration of proteomic and transcriptomic profiles reveals multiple levels of genetic regulation of salt tolerance in cotton

doi: 10.1186/s12870-018-1350-1

Figure Lengend Snippet: Hierarchical clustering analysis of mRNA-seq and proteomic data based on expression data. Heatmap of the proteins and mRNA expression ratios that have the same ( a , c ) or opposite ( b , d ) change tendencies after 4 h and 24 h of salt treatment, respectively. The expression profiles shown in the left and right panels are based on standardized log 2 ratio values. The minimum and maximum displayed log 2 ratios are ±3 for the transcriptomic data and ± 0.5 for the proteomics data. Black represents no significant change in expression. The KEGG pathway of genes/proteins showing significance are represented by various symbols behind the gene ID

Article Snippet: Scatterplots and Pearson correlation coefficients (r values) between proteins and mRNA expression ratios were constructed and calculated, respectively, using GraphPad Prism version 6 (GraphPad Software, Inc., San Diego, CA) with two-tailed t-tests.

Techniques: Expressing

Journal: Journal of Translational Medicine

Article Title: Type 1 diabetic mellitus patients with increased atherosclerosis risk display decreased CDKN2A/2B/2BAS gene expression in leukocytes

doi: 10.1186/s12967-019-1977-1

Figure Lengend Snippet: Correlation studies between of CDKN2A/2B/2BAS genes and transcription factors involved in T cell differentiation. Correlation of CDKN2A(p16 Ink4a ) a , CDKN2A(p14 Arf ) b , CDKN2B c , and CDKN2BAS d mRNA levels with RORC and FOXP3 mRNA levels. Statistical analysis was performed using non-parametric Spearman correlation coefficient

Article Snippet: Differences were assessed by Student ́s t-test or Mann–Whitney U test and correlation studies by the Spearman correlation coefficient (GraphPad Prism 5.03, CA, USA).

Techniques: Cell Differentiation

Journal: Journal of Translational Medicine

Article Title: Type 1 diabetic mellitus patients with increased atherosclerosis risk display decreased CDKN2A/2B/2BAS gene expression in leukocytes

doi: 10.1186/s12967-019-1977-1

Figure Lengend Snippet: Correlation studies in all human subjects. Correlation of CDKN2A/2B/2BAS mRNA levels with a SOCS1 and b SOCS3 mRNA levels. Statistical analysis was performed using non-parametric Spearman correlation coefficient

Article Snippet: Differences were assessed by Student ́s t-test or Mann–Whitney U test and correlation studies by the Spearman correlation coefficient (GraphPad Prism 5.03, CA, USA).

Techniques: