For each gene, we computed a score of tissue-specificity TSg,t = (eg,t – Q3g)/(Q3g – Q1g), where eg,t is the expression of gene g in tissue t, Q1g and Q3g are the first and third quartiles in the distribution of expression values for gene g across all tissues.
The majority of the genes extracted from the literature were confirmed in our data, thus indicating that the pathological scoring of tissue components was robust (see Table S2).
The work-up and scoring of tissue sections was carried out in a blinded fashion as described previously [ 10].
Because no pathologist can tell which piece of tissue came from which victim without DNA testing, forensic scientists may test scores of tissues that turn out to be from the same person.
For this purpose, we take the mean of the ratio of the weighted differences between the tm-score of a single tissue and the tm-scores of tissues.
In our study, there were no deviations in the quality scores of tissue-specific DNA samples from KT538 (Additional file 1: Table S6).
For semi-quantitative analysis, the score of each tissue section was based on both the proportion of positively stained tumor cells and the intensity of staining.
In the LLS (maximum value of 35) each lobe contributes a maximum score of 5 (tissue damage in the entire lobe).
Since all of the 3+ IHC positive UFPE cases were also positive by FISH, there was no false positive result that might affect therapeutic decision based on HER2 IHC score of UFPE tissue.
Samples were taken from different joint areas after 6, 12, 24 and 48 weeks, and gene expression levels of common cartilage molecules were quantified in relation to the histological grading (modified Mankin score) of adjacent tissue.
To this end, we compared classic measures of bleomycin-induced lung fibrosis (fibrosis score of lung tissue sections, TVD, and lung collagen) between mice that did or did not undergo lung function testing prior to sacrifice.
