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Gene function prediction

He Wang, Yanmei Chen, Xinzhong Li, Guojun Chen, Lintao Zhong, Gangbing Chen, Yulin Liao, Wangjun Liao, Jianping Bin
Alternative splicing (AS) drives determinative changes during mouse heart development. Recent high-throughput technological advancements have facilitated genome-wide AS, while its analysis in human foetal heart transition to the adult stage has not been reported. Here, we present a high-resolution global analysis of AS transitions between human foetal and adult hearts. RNA-sequencing data showed extensive AS transitions occurred between human foetal and adult hearts, and AS events occurred more frequently in protein-coding genes than in long non-coding RNA (lncRNA)...
October 18, 2016: Scientific Reports
Liang Li, Jian-Wei Zhang, Gregory Jenkins, Fang Xie, Erin E Carlson, Brooke L Fridley, William R Bamlet, Gloria M Petersen, Robert R McWilliams, Liewei Wang
BACKGROUND: Pancreatic cancer is a rapidly fatal disease with gemcitabine remaining the first-line therapy. We performed a genotype-phenotype association study to identify biomarkers for predicting gemcitabine treatment outcome. MATERIALS AND METHODS: We selected the top 200 single nucleotide polymorphisms (SNPs) identified from our previous genome-wide association study to associate with overall survival using 400 patients treated with/or without gemcitabine, followed by imputation analysis for regions around the identified SNPs and a replication study using an additional 537 patients by the TaqMan genotyping assay...
October 4, 2016: Pharmacogenetics and Genomics
Chuan-Xin Wu, Jing Cheng, Yun-Ying Wang, Jiao-Jiao Wang, Hui Guo, Hang Sun
INTRODUCTION: The aim of this study was to clarify the miRNA expression profiles of RAW264.7 macrophages infected by Candida albicans to elucidate the roles of differentially expressed miRNAs and to further explore the mechanisms underlying the immune response to C. albicans infection. METHODS: High-throughput miRNA microarray analysis was performed to detect differentially expressed miRNAs in control and C. albicans-infected RAW264.7 cells. Quantitative real-time PCR analysis was used to verify the microarray results...
October 5, 2016: Shock
Shanmei Du, Helou Li, Xiaochun Sun, Dongsheng Li, Yong Yang, Zehua Tao, Qian Li, Kui Liu
MicroRNA (miRNA) is a type of endogenous non‑coding RNA implicated in various cellular processes. Studies have shown that miR-124 is involved in the malignant progression of cancer, but little is known concerning its potential role in breast cancer. Therefore, the purpose of this study was to conduct a functional analysis of miR-124 in breast cancer, and to identify its target genes in this disease. To this end, we used quantitative real-time PCR to examine the expression level of miR-124 in breast cancer tissue specimens and cell lines...
October 11, 2016: Oncology Reports
Yuan-Yuan Zhang, Si-Han Huang, Hua-Rong Zhou, Cong-Jie Chen, Li-Hong Tian, Jian-Zhen Shen
HOX antisense intergenic RNA (HOTAIR), a long non-coding RNA, plays an important role in the development of many types of cancers. Its function in acute leukemia (AL), however, has not been examined. The present study investigated the role of HOTAIR and its downstream genes in AL, and determined whether it could act as a molecular marker for prediction of leukemia development and prognosis. Real-time quantitative PCR was used to examine the expression of each gene in the HOTAIR signaling pathway in AL patients...
October 4, 2016: Oncology Reports
Wei Zhang, Jianzhou Liu, Jianxin Qiu, Xiaoliang Fu, Qisheng Tang, Fan Yang, Zhiguang Zhao, He Wang
MicroRNAs (miRNAs) have emerged as important regulators in cancer that are implicated in regulation of various cellular processes. miR-382 has been proposed as a tumor suppressor by several recent studies. However, the function of miR-382 in prostate cancer remains unknown. In this study, we aimed to investigate the potential function of miR-382 in prostate cancer. We found that miR-382 was significantly decreased in prostate cancer specimens and cancer cell lines. The overexpression of miR-382 in prostate cancer cells markedly inhibited cell proliferation, migration, and invasion...
October 3, 2016: Oncology Reports
Maksim Kitsak, Amitabh Sharma, Jörg Menche, Emre Guney, Susan Dina Ghiassian, Joseph Loscalzo, Albert-László Barabási
Genes carrying mutations associated with genetic diseases are present in all human cells; yet, clinical manifestations of genetic diseases are usually highly tissue-specific. Although some disease genes are expressed only in selected tissues, the expression patterns of disease genes alone cannot explain the observed tissue specificity of human diseases. Here we hypothesize that for a disease to manifest itself in a particular tissue, a whole functional subnetwork of genes (disease module) needs to be expressed in that tissue...
October 17, 2016: Scientific Reports
Jing-Yi Li, Li-Li Zheng, Ting-Ting Wang, Min Hu
BACKGROUND: Melanoma is a type of cancer that develops from the pigment-containing cells. Until now, its pathological mechanisms remain largely unknown. The aim of this study was to identify metastasis-related microRNA (miRNAs) and gain an understanding of the biological functions in the metastasis of melanoma. METHODS: We searched the PubMed and Gene Expression Omnibus database to collect miRNA expression profiling datasets about melanoma, with key words of "melanoma", "miRNA", "microarray", and "gene expression profiling"...
2016: Chinese Medical Journal
Qijiang Jin, Xin Hu, Xin Li, Bei Wang, Yanjie Wang, Hongwei Jiang, Neil Mattson, Yingchun Xu
Trehalose-6-phosphate synthase (TPS) plays a key role in plant carbohydrate metabolism and the perception of carbohydrate availability. In the present work, the publicly available Nelumbo nucifera (lotus) genome sequence database was analyzed which led to identification of nine lotus TPS genes (NnTPS). It was found that at least two introns are included in the coding sequences of NnTPS genes. When the motif compositions were analyzed we found that NnTPS generally shared the similar motifs, implying that they have similar functions...
2016: Frontiers in Plant Science
Wenwu Ye, Yang Wang, Brett M Tyler, Yuanchao Wang
Comparative genomic analysis is useful for identifying genes affected by evolutionary selection and for studying adaptive variation in gene functions. In Phytophthora sojae, a model oomycete plant pathogen, the related study is lacking. We compared sequence data among four isolates of P. sojae, which represent its four major genotypes. These isolates exhibited >99.688%, >99.864%, and >98.981% sequence identities at genome, gene, and non-gene regions, respectively. One hundred and fifty-three positive selection and 139 negative selection candidate genes were identified...
2016: Frontiers in Microbiology
Xuan Liang, Hecheng Li, Delai Fu, Tie Chong, Ziming Wang, Zhaolun Li
MicroRNAs (miRNAs) have been known to be implicated in tumorigenic programs. miR-1297 has been reported to be dysregulated and involved in cancer progression in many types of human cancers. However, the expression level and the role of miR-1297 in prostate cancer remain unclear. Herein, we aimed to investigate the potential role and molecular mechanism of miR-1297 in prostate cancer progression. We found that miR-1297 was significantly downregulated in human prostate cancer specimens as well as in several prostate cancer cell lines...
October 13, 2016: Biochemical and Biophysical Research Communications
Jezkova Eva, Kajo Karol, Zubor Pavol, Grendar Marian, Malicherova Bibiana, Mendelova Andrea, Dokus Karol, Lasabova Zora, Plank Lukas, Danko Jan
Breast cancer is a heterogeneous disease with very different responses to therapy and different length of survival. In many cases, however, the determination of the stage and histopathological characteristics of breast cancer is insufficient to predict prognosis and response to treatment for the vast heterogeneity of the disease. To understand the molecular signature of subtypes of breast cancer, we attempted to identify the methylation status of key tumour suppressor gene Ras association (RalGDS/AF-6) domain family member 1 isoform a (RASSF1A) and a member of the paired-like homeodomain transcription factor family which functions in left-right asymmetry development (PITX2) and to correlate results with known clinicopathological features of breast cancer...
October 15, 2016: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
Teija Ojala, Pia K S Laine, Terhi Ahlroos, Jarna Tanskanen, Saara Pitkänen, Tuomas Salusjärvi, Matti Kankainen, Soile Tynkkynen, Lars Paulin, Petri Auvinen
Propionibacterium freudenreichii is a commercially important bacterium that is essential for the development of the characteristic eyes and flavor of Swiss-type cheeses. These bacteria grow actively and produce large quantities of flavor compounds during cheese ripening at warm temperatures but also appear to contribute to the aroma development during the subsequent cold storage of cheese. Here, we advance our understanding of the role of P. freudenreichii in cheese ripening by presenting the 2.68-Mbp annotated genome sequence of P...
September 26, 2016: International Journal of Food Microbiology
Blaz Skrlj, Tanja Kunej
BACKGROUND: Protein-protein interactions (PPI) play an important role in function of all organisms and enable understanding of underlying metabolic processes. Computational predictions of PPIs are an important aspect in proteomics, as experimental methods may result in high degree of false positive results and are more expensive. Although there are many databases collecting predicted PPIs, exploration of genetics information underlying PPI interactions has not been investigated thoroughly...
October 4, 2016: Computers in Biology and Medicine
Olympia Gianfrancesco, Vivien J Bubb, John P Quinn
Many facets of human behaviour are likely to have developed in part due to evolutionary changes in the regulation of neuropeptide and other brain-related genes. This has allowed species-specific expression patterns and unique epigenetic modulation in response to our environment, regulating response not only at the molecular level, but also contributing to differences in behaviour between individuals. As such, genetic variants or epigenetic changes that may alter neuropeptide gene expression are predicted to play a role in behavioural conditions and psychiatric illness...
October 11, 2016: Neuropeptides
Mathijs van de Vrie, Jeroen K Deegens, Michael Eikmans, Johan van der Vlag, Luuk B Hilbrands
Urine represents a non-invasive source in which proteins and nucleic acids can be assessed. Such analytes may function as biomarkers to monitor kidney graft pathology at every desired frequency, thereby providing a time window to prevent graft damage by therapeutic intervention. Recently, several proteins have been measured in urine as markers of graft injury. However, the specificity is limited, and measuring urinary proteins generally lacks the potential to predict early kidney graft damage. Currently, urinary mRNA and microRNA are being investigated to evaluate the prognostic value of changes in gene expression during the initial stages of graft damage...
October 15, 2016: American Journal of Transplantation
Tao Shi, Kun Wang, Pingfang Yang
microRNAs (miRNAs) are important noncoding small RNAs that regulate mRNAs in eukaryotes. However, under which circumstances different miRNAs/miRNA families exhibit different evolutionary trajectories in plants remains unclear. In this study, we sequenced the small RNAs and degradome from a basal eudicot, sacred lotus (Nelumbo nucifera or lotus), to identify miRNAs and their targets. Combining with public miRNAs, we predicted 57 pre-eudicot miRNA families from different evolutionary stages. We found that miRNA families featuring older age, higher copy and target number tend to show lower propensity for miRNA family loss (PGL) and stronger signature of purifying selection during divergence of temperate and tropical lotus...
October 15, 2016: Plant Journal: for Cell and Molecular Biology
Timothy J Hohman, Logan Dumitrescu, Nancy J Cox, Angela L Jefferson
Preclinical Alzheimer's disease (AD) is characterized by amyloid deposition in the absence of overt clinical impairment. There is substantial heterogeneity in the long-term clinical outcomes among amyloid positive individuals, yet limited work has focused on identifying molecular factors driving resilience from amyloid-related cognitive impairment. We apply a recently developed predicted gene expression analysis (PrediXcan) to identify genes that modify the association between baseline amyloid deposition and longitudinal cognitive changes...
October 14, 2016: Brain Imaging and Behavior
Jing Wu, Qian Li, Nina Wang, Hong Wei, Chao Li, Guibin Yang
BACKGROUND: MicroRNAs, targeting mRNAs of cancer-associated genes, are often aberrantly expressed in human gastric cancer (GC). AIM: We have examined the possible role and mechanisms of miRNA regulation of Prdx-6 in the development and progression of H. pylori-related gastric mucosal lesions. METHODS: First, miR-24-3p was predicted to target Prdx-6, and this negative regulation was validated by luciferase reporter analyses, Western blot, and quantitative RT-PCR...
October 14, 2016: Digestive Diseases and Sciences
Christina Backes, Tim Kehl, Daniel Stöckel, Tobias Fehlmann, Lara Schneider, Eckart Meese, Hans-Peter Lenhof, Andreas Keller
In the last decade, miRNAs and their regulatory mechanisms have been intensively studied and many tools for the analysis of miRNAs and their targets have been developed. We previously presented a dictionary on single miRNAs and their putative target pathways. Since then, the number of miRNAs has tripled and the knowledge on miRNAs and targets has grown substantially. This, along with changes in pathway resources such as KEGG, leads to an improved understanding of miRNAs, their target genes and related pathways...
October 13, 2016: Nucleic Acids Research
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