Transcriptomics
What is transcriptomics?
Transcriptomics is the analysis of all the RNA expressed in any given cell (the transcriptome). This allows us to study all DNA that is being transcribed since not all DNA transcribed is used to code for proteins, some have structural and regulatory roles within the cell. Transcriptome analysis can allow researchers to identify when and where different genes are being expressed in an organism, which can give an insight into function [1].
What can transcriptomics tell us about RASSF1A?
GEO DataSets: Geo DataSets combines various forms of genomic data and allows you to search based on a gene, disease or phenotype to find relevant data [2]. When I carried out a search I found a dataset which looked at Peptidyl-prolyl cis/trans isomerase Pin1 deficiency effect on prostate cancer cells in humans [3]. On the right shows a cluster analysis of the results which shows if expression is high (pink) or low (green) when comparing two different types of prostate cancer cells [4]. GEO Profiles: GEO Profiles can be found within the datasets. These show expression for specific genes that have been studied in the data [2]. On the right is the expression profile for RASSF1A from the dataset [5]. You can see in the data that expression of the RASSF1A gene is much lower in LNCaP cells than in DU145 prostate cancer cells. Looking into these cells further it can be seenthat that LNCaP cells express the prostate specific antigen while the DU145 cells do not. This may have some implication into the difference in expression of RASSF1A |
References
[1] National Human Genome Research Institute, Transcriptome, https://www.genome.gov/13014330/
[2] GEO Overview https://www.ncbi.nlm.nih.gov/geo/info/overview.html
[3] GEO DataSet https://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS5805
[4] GEO DataSet, Cluster Analysis https://www.ncbi.nlm.nih.gov/geo/gds/analyze/analyze.cgi?ID=GDS5805
[5] GEO Profile, RASSF1A https://www.ncbi.nlm.nih.gov/geo/tools/profileGraph.cgi?ID=GDS5805:8087640
[2] GEO Overview https://www.ncbi.nlm.nih.gov/geo/info/overview.html
[3] GEO DataSet https://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS5805
[4] GEO DataSet, Cluster Analysis https://www.ncbi.nlm.nih.gov/geo/gds/analyze/analyze.cgi?ID=GDS5805
[5] GEO Profile, RASSF1A https://www.ncbi.nlm.nih.gov/geo/tools/profileGraph.cgi?ID=GDS5805:8087640