rma-normalized expression values  (Biotechnology Information)

Journal: EBioMedicine

Article Title: Trefoil factor(s) and CA19.9: A promising panel for early detection of pancreatic cancer

doi: 10.1016/j.ebiom.2019.03.056

Figure Lengend Snippet: Differential expression of TFF1, TFF2, and TFF3 in PC genomic datasets. (a) Representative box and whisker plots depict the comparison of normalized expression of TFF1–3 mRNA in GSE43288 dataset across normal pancreas (n = 3), PC precursor lesions i.e. PanIN (n = 13) and pancreatic tumor (PC) tissues (n = 4). (b) Representative box and whisker plots comparing normalized expression of TFF1–3 mRNA in GSE16515 dataset across normal pancreas (n = 16), and pancreatic tumor tissues ( n = 36). The interquartile range (IQR) for TFF1–3 expression is presented by box and whisker plot (horizontal line represents the 25th percentile, median and 75th percentile and whisker represents 5th and 95th percentile). Publicly available datasets were obtained from Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/ ). Significantly elevated expression of all the TFFs were observed in pancreatic tumors. Further, the elevation in TFFs was found to be significantly higher across precursor lesions of PC. P values were determined using the Mann-Whitney U test (two-tailed). Red triangle represents outlier value.

Article Snippet: The normalized gene expression values (RMA) for TFFs in normal, PanIN, and PC were plotted using MedCalc software.

Techniques: Quantitative Proteomics, Whisker Assay, Comparison, Expressing, Gene Expression, MANN-WHITNEY, Two Tailed Test

Journal: EBioMedicine

Article Title: Trefoil factor(s) and CA19.9: A promising panel for early detection of pancreatic cancer

doi: 10.1016/j.ebiom.2019.03.056

Figure Lengend Snippet: Differential expression of TFF1–3 in tissues from precursor lesions, PC tissues from spontaneous PC mouse models and human PC. (a) Immunohistochemical analysis for individual TFF were performed on pancreatic tissue microarrays (TMAs) containing normal pancreatic tissue adjacent to tumor (NAT) (TFF1, n = 39;TFF2, n = 8; TFF3, n = 41), pancreatic cancer precursor lesions (PanIN I, II and III), (TFF1, n = 32;TFF2, n = 16; TFF3, n = 10) well-differentiated (WD) (TFF1, n = 13;TFF2, n = 13; TFF3, n = 11), moderately-differentiated (MD) (TFF1, n = 40;TFF2, n = 40; TFF3, n = 121) and poorly-differentiated (PD) (TFF1, n = 9;TFF2, n = 9;TFF3, n = 10) pancreatic tumor tissues. No expression of TFF1, TFF2, and TFF3 were observed in normal pancreatic ducts while elevated expression was observed in the ductal compartment across a spectrum of precursor lesions as well as various stages of pancreatic tumor differentiation. Scale bar for upper represents 500 μm and lower panel magnification represents 100 μm. Corresponding box and whisker plot representing quantitative H-score for TFFs expression across NAT, PanINs and pancreatic tumor tissues. Significant overexpression of TFFs was observed in pancreatic tumor tissues in comparison to normal pancreas. *** P < .0005, ** P < .005, * P < .05, determined by Welch t-Test. (b) Immunohistochemical analysis of all mouse TFF (mTFF1, mTFF2, & mTFF3) protein expression levels throughout the progression of PC in the spontaneous Kras G12D Pdx1-Cre (KC) mouse model, from 10 weeks to 30 weeks. Expression of TFF1, TFF2, and TFF3 was progressively increased from 10 to 30 weeks. Scale bars are 100 μm ( n = 3 animals/age groups).The interquartile range (IQR) for TFFs expression is presented by corresponding box and whisker plot (Middle horizontal line represents the median value). * P < .05 is determined by student t-test.

Article Snippet: The normalized gene expression values (RMA) for TFFs in normal, PanIN, and PC were plotted using MedCalc software.

Techniques: Quantitative Proteomics, Immunohistochemical staining, Expressing, Whisker Assay, Over Expression, Comparison