Microarray

Meta-analysis of differentially expressed genes in autism based on gene expression data

L. F. Ning, Yu, Y. Q., GuoJi, E. T., Kou, C. G., Wu, Y. H., Shi, J. P., Ai, L. Z., and Yu, Q., “Meta-analysis of differentially expressed genes in autism based on gene expression data”, vol. 14, pp. 2146-2155, 2015.

The purpose of this study was to identify differentially expressed (DE) genes and biological processes associated with changes in gene expression in autism. We performed a meta-analysis using new publicly available Gene Expression Omnibus (GEO) datasets of autism. We performed Gene Ontology (GO) enrichment analyses and pathway analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG). Ten GEO datasets, including 364 cases and 248 controls, were available for the meta-analysis.

Abnormal gene expression profile reveals the common key signatures associated with clear cell renal cell carcinoma: a meta-analysis

H. J. Zhang, Sun, Z. Q., Qian, W. Q., and Sheng, L., “Abnormal gene expression profile reveals the common key signatures associated with clear cell renal cell carcinoma: a meta-analysis”, vol. 14, pp. 2216-2224, 2015.

The aims of this study were to identify the common gene signatures of clear cell renal cell carcinoma (CCRCC), and to expand the respective protein-protein interaction networks associated with CCRCC regulation. For the latter, we utilized multiple gene expression data sets from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO), with which we could analyze the aberrant gene expression patterns at the transcriptome level that distinguish cancer from normal samples.

Identification and functional analysis of differentially expressed genes related to obesity using DNA microarray

J. Y. Du, Yang, H., Tian, D. R., Wang, Q. M., and He, L., “Identification and functional analysis of differentially expressed genes related to obesity using DNA microarray”, vol. 13, pp. 64-72, 2014.

We looked for differentially expressed genes at different stages of preadipocyte differentiation and examined their functions, based on DNA microarrays of preadipocytes obtained from healthy subjects undergoing cosmetic liposuction. We downloaded gene expression profile GSE25910 from the Gene Expression Omnibus database and identified the differentially expressed genes with packages in R language. The selected differentially expressed genes were further analyzed using bioinformatics methods.

MicroRNAs function primarily in the pathogenesis of human anencephaly via the mitogen-activated protein kinase signaling pathway

W. D. Zhang, Yu, X., Fu, X., Huang, S., Jin, S. J., Ning, Q., and Luo, X. P., “MicroRNAs function primarily in the pathogenesis of human anencephaly via the mitogen-activated protein kinase signaling pathway”, vol. 13, pp. 1015-1029, 2014.

Anencephaly is one of the most serious forms of neural tube defects (NTDs), a group of congenital central nervous system (CNS) malformations. MicroRNAs (miRNAs) are involved in diverse biological processes via the post-transcriptional regulation of target mRNAs. Although miRNAs play important roles in the development of mammalian CNS, their function in human NTDs remains unknown.

Systematic review of accuracy of prenatal diagnosis for abnormal chromosome diseases by microarray technology

H. B. Xu, Yang, H., Liu, G., and Chen, H., “Systematic review of accuracy of prenatal diagnosis for abnormal chromosome diseases by microarray technology”, vol. 13, pp. 9115-9121, 2014.

The accuracy of prenatal diagnosis for abnormal chromosome diseases by chromosome microarray technology and karyotyping were compared. A literature search was carried out in the MEDLINE database with the keywords “chromosome” and “karyotype” and “genetic testing” and “prenatal diagnosis” and “oligonucleotide array sequence”. The studies obtained were filtered by using the QUADAS tool, and studies conforming to the quality standard were fully analyzed.

Transcriptomic profiles of Japanese medaka (Oryzias latipes) in response to alkalinity stress

Z. L. Yao, Wang, H., Chen, L., Zhou, K., Ying, C. Q., and Lai, Q. F., “Transcriptomic profiles of Japanese medaka (Oryzias latipes) in response to alkalinity stress”, vol. 11, pp. 2200-2246, 2012.

Oryzias latipes (Adrianichthyidae), known as Japanese medaka or Japanese killifish, is a small 2-4 cm long fish common in rice paddies in coastal Southeast Asia and is also a popular aquarium fish. It has been widely used as a research model because of its small size and because it is very easy to rear. Alkalinity stress is considered to be one of the major stressors on fish in saline-alkaline water.

Isolation and identification of the immune-relevant ribosomal protein L10 (RPL10/QM-like gene) from the large yellow croaker Pseudosciaena crocea (Pisces: Sciaenidae)

X. Chen, Su, Y. Q., Wang, J., Liu, M., Niu, S. F., Zhong, S. P., and Qiu, F., “Isolation and identification of the immune-relevant ribosomal protein L10 (RPL10/QM-like gene) from the large yellow croaker Pseudosciaena crocea (Pisces: Sciaenidae)”, vol. 11, pp. 3755-3765, 2012.

In order to investigate the immune role of ribosomal protein L10 (RPL10/QM-like gene) in marine fish, we challenged the large yellow croaker Pseudosciaena (= Larimichthys) crocea, the most important marine fish culture species in China, by injection with a mixture of the bacteria Vibrio harveyi and V. parahaemolyticus (3:1 in volume). Microarray analysis and real-time PCR were performed 24 and 48 h post-challenge to isolate and identify the QM-like gene from the gill P. crocea (designated PcQM).

Comparative and joint analyses of gene expression profiles under drought and rewatering in Arabidopsis

Z. H. Xu and Wu, W. R., “Comparative and joint analyses of gene expression profiles under drought and rewatering in Arabidopsis”, vol. 12, pp. 3622-3629, 2013.

Drought is a major limiting factor in crop production. Rewatering is a process opposite to drought, allowing plants to recover to their normal physiological state. To understand more thoroughly the set of genes involved in plant response to drought, we comparatively and jointly analyzed the microarray data of drought and rewatering experiments in Arabidopsis. A total of 3833 differentially expressed genes (DEGs) were identified. Among them, ~74% were proven to be co-regulated by drought and rewatering.

Aberrant gene expression profiles in hepatocellular carcinoma detected by microdissection

Y. M. Wei, Li, Y. Y., Zhang, Y. C., and Nie, Y. Q., “Aberrant gene expression profiles in hepatocellular carcinoma detected by microdissection”, vol. 12, pp. 5527-5536, 2013.

The aim of this study was to identify genomic aberrations in hepatocellular carcinoma (HCC) by using laser capture microdissection (LCM) combined with microarray analysis. Samples were procured by LCM from HCC and patient-matched normal liver tissue surgically resected from 4 patients. RNA was isolated from the samples and reverse transcribed into cDNA. After 2-cycle linear amplification and 2-color fluorescent labeling, the cRNA was hybridized onto a whole genome microarray. All genes expressed in the normal and HCC samples were counted and analyzed.

Molecular characterisation of a der(Y)t(Xp;Yp) with Xp functional disomy and sex reversal

F. Ashton, O’Connor, R., Love, J. M., Doherty, E., Aftimos, S., George, A., and Love, D. R., “Molecular characterisation of a der(Y)t(Xp;Yp) with Xp functional disomy and sex reversal”, vol. 9. pp. 1815-1823, 2010.

Sex reversal due to duplication of the Xp21 dosage-sensitive sex reversal locus results in XY females with gonadal dysgenesis. Pure Xp disomy (without a concurrent loss of genetic material) can occur by translocation or interstitial duplication. The case reported here is the rare form with a t(Xp;Yp). The combination of conventional clinical cytogenetic techniques, microsatellite analysis and high-density microarrays identified the X-chromosome breakpoint as centromeric of the NR0B1 gene and its control elements.

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