Comparative and Functional Analysis of Testis-Specific Genes

Liu, Fu Jun; Jin, Shao Hua; Li, Ning; Liu, Xin; Wang, Haiyan; Li, Jianyuan

doi:10.1248/bpb.34.28

Cited by 25 publications

(18 citation statements)

References 22 publications

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“…As described in our previous studies (Liu et al, 2011(Liu et al, , 2012c, some testis-specific proteins could become cancer/testis antigens specifically expressed in certain cancers. These proteins could be used as potential cancer vaccine targets.…”

Section: Discussionsupporting

confidence: 51%

“…Of the 14 tissues examined, thyroid cancer tissue has the highest number of cancer tissue-specific proteins (103), including the well-known thyroid specific proteins TG and TPO (González et al, 2002). Of the normal tissues, the testis has the largest number of tissue-specific proteins, which reflects the complex protein expression and regulation in the testis (Liu et al, 2011(Liu et al, , 2012cHua et al, 2013). These proteins may be potential cancer biomarkers and/or physiologic treatment targets, and further studies are warranted to evaluate their underlying functions.…”

Section: Discussionmentioning

confidence: 99%

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Novel bioinformatic identification of differentially expressed tissue-specific and cancer-related proteins from the Human Protein Atlas for biomarker discovery

2015

Genet. Mol. Res.

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ABSTRACT. Identification of cancer-associated and tissue-specific proteins is important for research on carcinogenesis mechanisms and biomarker discovery. Here we performed a new strategy to identify candidate cancer proteins by mining immunohistochemistry protein profiles. Proteins with quantitative values from 14 normal tissues and their corresponding cancer tissues were compared and analyzed using bioinformatics. The final results included identification of tissue-specific proteins and differentially expressed proteins in different cancer types that are primarily involved in energy metabolism and cell invasion. From the tissue-specific proteins, secreted and membrane proteins were further screened and functionally clustered. These primarily belonged to the gene families of endogenous ligands, cluster of differentiation molecules, and solute carriers, and were mainly involved in the processes of cell motility, hormone metabolism, adhesion, and transport. Further studies are warranted to validate the candidates identified herein and substantiate the suggested enriched functions. The results 4557-4565 (2015) from this study might provide a reliable resource to study underlying carcinogenesis mechanisms and discover potential cancer targets for the development of therapeutic targets and of early diagnosis and disease response markers.

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Section: Discussionsupporting

confidence: 51%

Section: Discussionmentioning

confidence: 99%

Novel bioinformatic identification of differentially expressed tissue-specific and cancer-related proteins from the Human Protein Atlas for biomarker discovery

2015

Genet. Mol. Res.

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“…To eliminate the difference caused by the unequal number of ESTs in each selected libraries, DDD uses the Fisher Exact Test [13] to restrict the output for statistically significant differences (P ≤ 0.05). This approach has proven to be very useful in the study of organ-specific genes in mammal [14] and cancer cells [15]. Despite these works, some work of in silico expression studies have been conducted in wheat [16,17].…”

Section: Introductionmentioning

confidence: 99%

Screening and identification of seed-specific genes using digital differential display tools combined with microarray data from common wheat

Yang

Hua

et al. 2011

BMC Genomics

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BackgroundWheat is one of the most important cereal crops for human beings, with seeds being the tissue of highly economic value. Various morphogenetic and metabolic processes are exclusively associated with seed maturation. The goal of this study was to screen and identify genes specifically expressed in the developing seed of wheat with an integrative utilization of digital differential display (DDD) and available online microarray databases.ResultsA total of 201 unigenes were identified as the results of DDD screening and microarray database searching. The expressions of 6 of these were shown to be seed-specific by qRT-PCR analysis. Further GO enrichment analysis indicated that seed-specific genes were mainly associated with defense response, response to stress, multi-organism process, pathogenesis, extracellular region, nutrient reservoir activity, enzyme inhibitor activity, antioxidant activity and oxidoreductase activity. A comparison of this set of genes with the rice (Oryza sativa) genome was also performed and approximately three-fifths of them have rice counterparts. Between the counterparts, around 63% showed similar expression patterns according to the microarray data.ConclusionsIn conclusion, the DDD screening combined with microarray data analysis is an effective strategy for the identification of seed-specific expressed genes in wheat. These seed-specific genes screened during this study will provide valuable information for further studies about the functions of these genes in wheat.

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“…Highly-expressed human testicular and epididymal genes from a previous study (10–12) were compared with the present data. The overlapping epididymal genes were further characterized using microarray annotation (http://humanet.scbit.org/index.jsp).…”

Section: Methodsmentioning

confidence: 98%

Functional analysis of human cancer-associated genes and their association with the testes and epididymis

Hua¹,

Wang²,

Liu³

2013

Oncology Letters

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Human cancer-associated UniGene sets (NCBI GeneBank) provide a platform for identifying differentially-expressed genes in human cancers. The present study identified and characterized a set of human cancer-associated genes using the Digital Differential Display (DDD) and functional analysis tools. A total of 1,904 genes were differentially expressed in 15 cancer types, including genes that had been previously shown to be specific in certain human cancers. A total of 274 genes were uniquely expressed in certain cancer types, including 37 genes that were highly expressed in the human testes and epididymis. These genes mainly functioned as ribosomal proteins, enzymes, receptors, secretory proteins and cell adhesion molecules. The most common domains that were encoded by the cancer-associated genes were those of cytochrome P450 CYP2D6, serpin and apolipoprotein A-I. A further gene ontology (GO) enrichment analysis revealed seven major functional clusters, which corresponded to the enriched pathways involved in cancer. The present study provides a source of cancer-associated genes and their functions. The results provide new insights into cancer biology and the involvement of highly-expressed epididymal genes in cancer biomarkers.

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Comparative and Functional Analysis of Testis-Specific Genes

Cited by 25 publications

References 22 publications

Novel bioinformatic identification of differentially expressed tissue-specific and cancer-related proteins from the Human Protein Atlas for biomarker discovery

Novel bioinformatic identification of differentially expressed tissue-specific and cancer-related proteins from the Human Protein Atlas for biomarker discovery

Screening and identification of seed-specific genes using digital differential display tools combined with microarray data from common wheat

Functional analysis of human cancer-associated genes and their association with the testes and epididymis

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