Abstract: Several embryonic cellular mechanism including cell
cycle, growth and apoptosis are regulated by phosphatidylinositol-3-
kinase (PI3K)/Akt signaling pathway. The goal of present study is to
determine the effects of annatto (Bixa orellana)-derived δ-tocotrienol
(δ-TCT) on the regulations of PI3K/Akt genes in murine morula.
Twenty four 6-8 week old (23-25g) female balb/c mice were
randomly divided into four groups (G1-G4; n=6). Those groups were
subjected to the following treatments for 7 consecutive days: G1
(control) received tocopherol stripped corn oil, G2 was given 60
mg/kg/day of δ-TCT mixture (contains 90% delta & 10% gamma
isomers), G3 was given 60 mg/kg/day of pure δ-TCT (>98% purity)
and G4 received 60 mg/kg/day α-TOC. On Day 8, females were
superovulated with 5 IU Pregnant Mare’s Serum Gonadotropin
(PMSG) for 48 hours followed with 5 IU human Chorionic
Gonadotropin (hCG) before mated with males at the ratio of 1:1.
Females were sacrificed by cervical dislocation for embryo collection
48 hours post-coitum. About fifty morulas from each group were
used in the gene expression analyses using Affymetrix QuantiGene
Plex 2.0 Assay. Present data showed a significant increase (p
Abstract: Gene expression profiling is rapidly evolving into a
powerful technique for investigating tumor malignancies. The
researchers are overwhelmed with the microarray-based platforms
and methods that confer them the freedom to conduct large-scale
gene expression profiling measurements. Simultaneously,
investigations into cross-platform integration methods have started
gaining momentum due to their underlying potential to help
comprehend a myriad of broad biological issues in tumor diagnosis,
prognosis, and therapy. However, comparing results from different
platforms remains to be a challenging task as various inherent
technical differences exist between the microarray platforms. In this
paper, we explain a simple ratio-transformation method, which can
provide some common ground for cDNA and Affymetrix platform
towards cross-platform integration. The method is based on the
characteristic data attributes of Affymetrix- and cDNA- platform. In
the work, we considered seven childhood leukemia patients and their
gene expression levels in either platform. With a dataset of 822
differentially expressed genes from both these platforms, we carried
out a specific ratio-treatment to Affymetrix data, which subsequently
showed an improvement in the relationship with the cDNA data.
Abstract: Sense-antisense gene pair (SAGP) is a pair of two oppositely transcribed genes sharing a common region on a chromosome. In the mammalian genomes, SAGPs can be organized in more complex sense-antisense gene architectures (CSAGA) in which at least one gene could share loci with two or more antisense partners. Many dozens of CSAGAs can be found in the human genome. However, CSAGAs have not been systematically identified and characterized in context of their role in human diseases including cancers. In this work we characterize the structural-functional properties of a cluster of 5 genes –TMEM97, IFT20, TNFAIP1, POLDIP2 and TMEM199, termed TNFAIP1 / POLDIP2 module. This cluster is organized as CSAGA in cytoband 17q11.2. Affymetrix U133A&B expression data of two large cohorts (410 atients, in total) of breast cancer patients and patient survival data were used. For the both studied cohorts, we demonstrate (i) strong and reproducible transcriptional co-regulatory patterns of genes of TNFAIP1/POLDIP2 module in breast cancer cell subtypes and (ii) significant associations of TNFAIP1/POLDIP2 CSAGA with amplification of the CSAGA region in breast cancer, (ii) cancer aggressiveness (e.g. genetic grades) and (iv) disease free patient-s survival. Moreover, gene pairs of this module demonstrate strong synergetic effect in the prognosis of time of breast cancer relapse. We suggest that TNFAIP1/ POLDIP2 cluster can be considered as a novel type of structural-functional gene modules in the human genome.