A cut-off based approach for gene expression analysis of formalin-fixed and paraffin-embedded tissue samples.

Microarray analysis of formalin-fixed and paraffin-embedded (FFPE) tissue seems to be of importance for the detection of molecular marker sets in prostate cancer (PC). The compromised RNA integrity of FFPE tissue results in a high degree of variability at the probe level of microarray data as shown by degradation plot. We tested methods that reduce the variability by including all probes within 300 nucleotides, within 600 nucleotides, or up to a calculated breakpoint with reference to the 3'-end.

Herbivory-induced changes in the small-RNA transcriptome and phytohormone signaling in Nicotiana attenuata.

Phytohormones mediate the perception of insect-specific signals and the elicitation of defenses during insect attack. Large-scale changes in a plant's transcriptome ensue, but how these changes are regulated remains unknown. Silencing of RNA-directed RNA polymerase 1 (RdR1) makes Nicotiana attenuata highly susceptible to insect herbivores, suggesting that defense elicitation is under the direct control of small-RNAs (smRNAs).

Argonaute--a database for gene regulation by mammalian microRNAs.

MicroRNAs (miRNAs) constitute a recently discovered class of small non-coding RNAs that regulate expression of target genes either by decreasing the stability of the target mRNA or by translational inhibition. They are involved in diverse processes, including cellular differentiation, proliferation and apoptosis. Recent evidence also suggests their importance for cancerogenesis.