Sections were scored for cellular location (nuclear versus cytosolic), intensity (from 0 to 3), and percent of area involved (from 0 to 100%), and an H score was calculated multiplying the intensity by the extent of the staining signal.
Cells were scored for cellular senescence on the basis of a large flat cellular morphology (n = 4 lines from each genotype, **p < 0.01).
Week 1 and 2 sections were scored for cellular infiltration and synovial hyperplasia from 0 (normal) to 3 (severe) as previously [ 21].
Frequently reported histological predictors of a poor renal outcome include WHO class IV histopathology [ 4, 33, 34], high activity index scores and chronicity index scores [ 4, 18, 35], high index scores for cellular crescents [ 35, 36], glomerular sclerosis [ 4, 35], interstitial fibrosis [ 4, 35- 37], and tubular atrophy [ 4, 35].
In fact, enrichment scores of "cell division" and "cell cycle" related genes constituted 56.87% of the total score for the "cellular process" for the up-regulated genes found in FF samples and 63.2% of the up-regulated genes found in FFPE sample.
The averaged intensity score of cellular VEGF for the MSeA-treated tumor was 1.0 (weak staining), while as the same score for the non-MSeA treated control tumor was greater than 2.0 (dark brown cytoplasm staining).
Figure 6(i) and Figure 6 ii) show hierarchical clustering of the enrichment scores for the "cellular process" category under the broad term "Biological process" for FF and FFPE samples respectively.
Two independent observers (MG, RB) unaware of the treatment scored the sections for cellular infiltration and hyperplasia (0: no, 1: mild, 2: moderate, 3: severe alterations), cartilage destruction and bone erosion (0: no erosion, 1: erosion of < 10%, 2: of 10 to 25%, 3: of 25 to 50%, and 4: of > 50% of cartilage and bone).
For quality control, another domain expert was asked to second-score a subset of the annotations for cellular component, a particularly complex class.
Quantitative colony sizes derived from SGA analysis can be used to measure cellular fitness and score for genetic interactions, such as synthetic lethality.
