2.4. Generation of a novel hypoxia gene signature and calculation of hypoxia score

Our novel hypoxia gene signature was built using robust rank aggregation (RRA)algorithm 13 from the microarray data of hypoxia‐treated HUH7, SNU‐182 and HLF cells. Up‐regulated (fold change > 1.5) mRNAs with P < .05 were selected from the RRA output. 21 mRNAs were included after qRT‐PCR validation under acute, chronic and intermittent hypoxia conditions. To estimate the hypoxia exposure, the hypoxia score was calculated using gene set variation analysis (GSVA). 14 We also compared our 21‐gene hypoxia signature with seven other published hypoxia gene signatures including Buffa’s signature, 9 Eustace's signature, 10 Ragnum’s signature, 11 Sorensen's signature, 15 winter’s signature 16 and Malenstein’s signature. 12 Hypoxia scores based on these seven signatures were also calculated by GSVA. The gene lists of 21‐gene signature were shown in Table S1.

Note: The content above has been extracted from a research article, so it may not display correctly.

Please log in to submit your questions online.
Your question will be posted on the Bio-101 website. We will send your questions to the authors of this protocol and Bio-protocol community members who are experienced with this method. you will be informed using the email address associated with your Bio-protocol account.

We use cookies on this site to enhance your user experience. By using our website, you are agreeing to allow the storage of cookies on your computer.