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Bioinformatics analysis of rna sequence data for potential biomarker discovery

Author: 
Supreetha, K. V., Shambhu, M. G. and Kusum Paul
Subject Area: 
Life Sciences
Abstract: 

Normal and disease-specific genes can be identified by making use of the existing microarray and RNA (NGS) sequencing data. The study attempts to identify potential biomarkers for the mammalian testis. Available NGS analysis database and software were first compiled and compared. NGS data corresponding to normal human and mouse testes have been collected after careful selection. The read data were aligned using Top Hat tool and ‘Cufflinks’ & ‘Cuffcompare’ tools were then used to obtain the transcript-specific FPKM values. The processed data were compared across different reports, and a score has been assigned to identify the consistent transcripts. The final transcript list was then compared to the microarray data from MgEx-Tdb. The top-scoring transcripts have been identified as the potential biomarkers for the normal human testis. In addition, potential marker transcripts have also been identified for specific testis cell types in the mouse. These in turn could help in detecting any abnormality, and also assist in research towards male contraception. This study has identified four genes which are ACTB, SMC6, PCMT1, SON along with their transcripts as potential biomarkers for normal human and mouse testis. Only certain transcripts show higher expression in normal testis condition and hence genes-transcript pairs can be good biomarkers.

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