Transcriptome comparison

Table 2 Comparison of Transcriptomic, Proteomic, and Metabonomic Changes Observed in Mice After Administration of Acetaminophen...

In the whole biosphere, it is estimated that there are about 100000 compounds with a molecular weight lower than about 1000 Da produced in living species. In a human, the metabolome is estimated to be no higher than about 3000 compounds. In comparison, the number of genes is 25 000 to 30 000, the number of transcripts is 100 000 to 200 000 and it is estimated that there are up to 1000 000 different proteins, including post-translational modifications. Because the metabolome is composed of a limited number of compounds, metabolomics provides data that are less complex and more quantitative than genomics, transcriptomics and proteomics. 

Recent comparison of gene expression profiles of von Hippel-lindau-i- versus von Hippel-lindau-ceU lines obtained from the clear cell RCC subtype identified proteins that might serve as candidate molecular markers. Inactivation of VHL is a hallmark in most sporadic clear cell RCC and it occurs early in renal carcinogenesis (Skates and Iliopoulus., 2004 Latifet al, 1993). Furthermore, the profile of secreted proteins could be directly AQ4 determined by analyzing comparatively the genomic and proteomic patterns of these cell lines as well as their conditioned tissue culture supernatants (Ferguson et al, 2004). A combination of cDNA microarray and proteome analyses appears reasonable since not every difference at the transcriptome level will translate into differences at the protein level, whereas posttranscriptional/posttranslational modifications were not detectable by tran-scriptomics. 

Piper, M.D., Daran-Lapujade, P., Bro, C., Regenberg, B., Knudsen, S., Nielsen, J. and Pronk, J.T. (2002) Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J. Biol. Chem. 277, 37001-37008. 

Jennings P, Weiland C, Limonciel A, Bloch KM, Radford R, Aschauer L, McMorrow T, Wilmes A, Pfaller W, Ahr HJ, Slattery C, Lock EA, Ryan MP, Ellinger-Ziegelbauer H (2012) Transcriptomic alterations induced by Ochratoxin A in rat and human renal proximal tubular in vitro models and comparison to a rat in vivo model. Arch Toxicol 86(4) 571-589. doi 10.1007/s00204-011-0780-4... 

Jennings P et al (2009) Inter-laboratory comparison of human renal proximal tubule (HK-2) transcriptome alterations due to Cyclosporine A exposure and medium exhaustion. Toxicol In Vitro 23(3) 486 99... 

Jennings P et al (2012) Transcriptomic alterations induced by Ochratoxin A in rat and human renal proximal tubular in vitro models and comparison to a rat in vivo model. Arch Toxicol 86(4) 571-589... 

Boutros PC, Yan R, Moffat ID, Pohjanvirta R, Okey AB (2008) Transcriptomic responses to 2, 3, 7,8-tetrachlOTodibenzo-p-dioxin (TCDD) in liver comparison of rat and mouse. BMC Genom 9 419... 

---