Question

All RNAs from cancerous human lung cells were isolated and quantified using RNA-Seq and compared to all RNAs from normal lung cells. The data from both cell types (normal and cancerous) were analyzed, and the RNA data below show the results obtained for six different RNAs. The values are expressed in relative FPKM units (Fragments per Kilobase Million). The higher the FPKM value the higher the relative abundance of that RNA and the lower the FPKM value the lower the relative abundance of that RNA. The numbers in the "Cancerous" and "Normal" columns of table below indicate the relative FPKM value for each RNA from those cell types. Finally, the ratio (last column) is calculated with the FPKM value in Cancerous cells divided by FPKM value in normal cells. Ratio values significantly higher than 1.0 (e.g., 3.5 or 8.3) indicate RNAs that are expressed at higher amounts in cancerous cells than normal cells. Ratio values around 1.0 (e.g., 1.15 or 0.93) indicate RNAs that are roughly equal in abundance between both cell types. Finally, Ratio values significantly lower than 1.0 (e.g., 0.12 or 0.05) indicate RNAs that are expressed at lower amounts in cancerous cells versus normal cells. Note, ratio values need have at least two fold higher >2.0) or two fold lower (<0.5) than 1.0 to be considered statistically significant change in expression. Thus, ratios of 1.23 or 0.75 would not be significantly different from 1.0, and you would conclude no significant change for that RNA in cancerous versus normal cells. a. (2 pt) Identify those RNAs (if any) in the list below that have a significant change in abundance in the cancerous lung cells versus normal lung cells. In your answer, for each RNA in table below, describe the following: (1) based on FPKM values is the RNA normally expressed at a relative high (many hundreds to thousands FPKM), low (tens of FPKM), or intermediate (a hundred to several hundred FPKM) amounts in the Normal Cells? (2) is there a significant change (>2 fold increase or decrease) in RNA abundance in cancerous versus normal cells? FPKM Values Cancerous Normal Cancer/Normal Ratio 624 3994 RNAS p/5Ink 4b 18S rRNA MOESIN CYCLIN DI NF2 CDK4 TRANSFERRIN RECEPTOR 4233 125 699 789 0.07 1.06 0.16 5.30 0.09 132 198 2.43 114 128

Answer 1

a)

1) Based on the FPKM values in RNA at relatively high FPKM are

CYCLIN D1 - FPKM value 699 in cancerous cells, ratio - 5.30

CDK₄ - FPKM value 56 in cancerous cells, ratio - 2.43

Intermidiate FPKM are

TRANSFERRIN RECEPTOR - FPKM value - 114, ratio - 0.89

18s rRNA -FPKM value 4233 in cancerous cells, ratio -1.06

low FPKM

p15Ink4b - FPKM value 43, ratio - 0.07

MOESIN - FPKM value - 125, ratio - 0.16

NF2 - FPKM value- 18, ratio - 0.09

2) yes there is grater than 2 fold increse in the all cancerous cells vs normal cells.

yes there is significant change in cancerous cells than normal cells.