Comparative Transcriptomic Analysis To Understand The Role Of Melanin In Melanoma

Melanin is a pigment found in most living organisms and is produced by a process called melanogenesis. This pigment is produced in specialized groups of cells called melanocytes and their function is to protect us against UV radiation. But did you know that melanoma caused by melanocyte mutations accounts for about 9000 deaths a year in the United States alone? To investigate this topic further, Gautam Chauhan, a Research Fellow at Pine Biotech performed a research project that aims to evaluate the risk of signature genes with the potential of developing melanoma by comparing two dark-skin samples with two light-skin


Gautam Chauhan is a student of B.Sc.(Hons) Zoology at Amity Institute of Biotechnology, Amity University, Noida, India. Being a research enthusiast by nature, Gautam opted for the AUUP Bioinformatics Research Fellowship Program at Pine Biotech. He completed his research project under the guidance of Dr. Sohini Singh, Assistant Professor, Amity Institute of Biotechnology, Amity University, Noida; Dr. Raghavendran Lakshminarayanan, Research Consultant and Mentor at Pine Biotech and Mr. Elia Brodsky, CEO of Pine Biotech. 


Before starting his research project, Gautam completed an introductory course on Course 1: Introduction to Bioinformatics to cover the fundamental concepts of bioinformatics. Then, he went on to complete intermediate courses such as Course 5: Transcriptomics and Course 9: Designing a Bioinformatics Research Project. Having gained a strong foundation in bioinformatics, transcriptomics and how to design a research project, he further went on to complete the following example projects: 


  1. Project 01: COVID-19 Origin & Pathogenesis of SARS-COV2
  2. Project 02: Ebolavirus: Deadly Mutations
  3. Project 03: TCGA Liver Cancer - Precision Oncology
  4. Project 04: EV-D68 and Acute flaccid myelitis in Kids
  5. Project 05: Modeling Cancer Precision Medicine
  6. Project 06: Patient-Derived Xenograft Models
  7. Project 07: Changing Immune Response in Cancer
  8. Project 08: Spodoptera frugiperda (fall armyworm)
  9. Project 09: Drought stress and resistance in potato


To view Gautam’s OmicsLogic student profile and learn more about the various courses and projects he has completed, visit the link -  


After completing his coursework and example projects, he began to work on his own research project titled - “Comparative Transcriptomic Analysis To Understand The Role Of Melanin In Melanoma”. For the research project, the difference in melanocytes with other major types of skin cells at the level of the complete transcriptome was compared. The transcriptomic data were obtained from Sequence Read Archive (SRA) and consisted of 4 samples: 2 dark-skinned and 2 light-skinned. To perform the analysis, the RNA-Seq Pipeline and Differential Gene Expression Pipeline that is available on the T-BioInfo platform were used.    


T-Bioinfo Server

Fig - Bulk RNA Seq Pipeline on the Tauber Bioinformatics Server


After conducting the analysis, it was observed that 8 out of 10 genes of the light-skin samples were expressed at a higher fold (>1 fold in absolute scale) for at least one of the samples implying that lighter skin individuals have potential risk factors associated with the development of melanoma. Further, it was observed that the pattern is not uniform, i.e., only one of the samples exhibits this behavior, and it was mentioned that this could be due to inter-sample variability. Upregulation of the FOXM1 gene (which is known to play a key role in cell cycle progression) in dark-skin samples was also observed during the course of the research analysis. He concluded that one needs more samples to clearly identify the trends and verify the validity of the hub genes identified from melanoma cell lines. 


Here is what Gautam had to say about his research fellowship experience: 

My experience with Pine Biotech has been amazing. I got to learn a lot about various interesting topics and got hands-on experience in the world of omics. My mentors have always been supportive, they helped me a lot throughout my project and provided me with extensive support. Through my project, I gained a lot of knowledge regarding my research topic and it was an interesting learning experience for me to work on the project


To learn more about his research project, visit the link - 

Research Fellowship Certificate


Feeling motivated to work on your own research project? Then don't miss the chance to register yourself for the Bioinformatics Research Fellowship Program

Bioinformatics Research Fellowship


The Bioinformatics Research Fellowship Program is a structured program that guides students through various areas of Big Data Bioinformatics Research using practical examples. During this program, we go through several high-quality research publications and learn about applications of computational biology in projects these publications describe. This allows beginners to try computational biology techniques on public domain data, making it possible to work with large files and extract meaningful information from patient samples, animal models, cell lines, and microbiota. The program provides support and mentorship, therefore it is an intensive research program involving training tasks, access to our online sessions and a guide on the implementation of learned skills to proposed research ideas. 


To learn more about the program, please visit the link: