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gene set enrichment

Xuebin Qi, Qu Zhang, Yaoxi He, Lixin Yang, Xiaoming Zhang, Peng Shi, Linping Yang, Zhengheng Liu, Fuheng Zhang, Fengyun Liu, Shiming Liu, Tianyi Wu, Chaoying Cui, Ouzhuluobu, Caijuan Bai, Baimakangzhuo, Jianlin Han, Shengguo Zhao, Chunnian Liang, Bing Su
Yak is one of the largest native mammalian species at the Himalayas, the highest plateau area in the world with an average elevation of more than 4,000 meters above the sea level. Yak is well adapted to high altitude environment with a set of physiological features for a more efficient blood flow for oxygen delivery under hypobaric hypoxia. Yet, the genetic mechanism underlying its adaptation remains elusive. We conducted a cross-tissue, cross-altitude and cross-species study to characterize the transcriptomic landscape of domestic yaks...
December 4, 2018: Genome Biology and Evolution
Zhongyu Wang, Qian Song, Zuyi Yang, Jianing Chen, Jun Shang, Wen Ju
The kidney renal papillary cell carcinoma (KIRP) is a relatively rare type of kidney cancer. There has been no investigation to find a robust signature to predict the survival outcome of KIRP patients in the aspect of tumor immunology. In this study, 285 KIRP samples from The Cancer Genome Atlas (TCGA) were randomly divided into training and testing set. A total of 1534 immune-related genes from The Immunology Database and Analysis Portal (ImmPort) were used as candidates to construct the signature. Using univariate Cox analysis, we evaluated the relationship between overall survival and immune-related genes expression and found 272 immune-related genes with predicting prognostic ability...
December 5, 2018: Cancer Medicine
Dong-Mei Wu, Shan Wang, Xin Wen, Xin-Rui Han, Yong-Jian Wang, Shao-Hua Fan, Zi-Feng Zhang, Qun Shan, Jun Lu, Yuan-Lin Zheng
AIMS: We aimed to explore the impact of long noncoding RNA (lncRNA) nuclear enriched abundant transcript 1 (NEAT1) on cell proliferation, invasion, and migration of glioma. METHODS: Differentially expressed genes were screened out from Gene Expression Omnibus data set based on the microarray analysis. The expression levels of lncRNA NEAT1, miR-139-5p, and CDK6 in glioma cells and tissues were examined by quantitative reverse transcription polymerase chain reaction, and the protein level of CDK6 in glioma cells was determined by western blot and immunohistochemistry...
December 4, 2018: Journal of Cellular Physiology
Niu Yu, Jin-Chang Yang, Guang-Tian Yin, Rong-Sheng Li, Wen-Tao Zou
Terpenes serve important physiological and ecological functions in plants. Sindora glabra trees accumulate copious amounts of sesquiterpene-rich oleoresin in the stem. A transcriptome approach was used to determine the unique terpene biosynthesis pathway and to explore the different regulatory mechanisms responsible for the variation of terpene content among individuals. Analysis of de novo- assembled contigs revealed a complete set of genes for terpene biosynthesis. A total of 23,261 differentially expressed unigenes (DEGs) were discovered between high and low oil-yielding plants...
2018: Frontiers in Plant Science
Xin He, Wenlu Li, Xiaogong Liang, Xuan Zhu, Lei Zhang, Yu Huang, Teng Yu, Shu Li, Zhigang Chen
BACKGROUND/AIMS: IGF2BP2 has been reported to serve as an oncogene in various solid cancers. However, the role of IGF2BP2 in acute myelocytic leukemia (AML) is still unknown. METHODS: Public databases Gene Omnibus was used to evaluate the expression of IGF2BP2 in AML patients and healthy controls. In addition, primary cells from these two populations were prepared by Ficoll density centrifugation. Rt-qPCR and western blot were used to detect IGF2BP2 expression in the primary cells from these two populations...
December 4, 2018: Cellular Physiology and Biochemistry
Wenjin Yan, Zheng Hao, Shuyan Tang, Jin Dai, Liming Zheng, Pengjun Yu, Wenqiang Yan, Xiao Han, Xingquan Xu, Dongquan Shi, Shiro Ikegawa, Huajian Teng, Qing Jiang
Developmental dysplasia of the hip (DDH) is one of the most common congenital malformations and covers a spectrum of hip disorders from mild dysplasia to irreducible dislocation. The pathological mechanisms of DDH are poorly understood, which hampers the development of diagnostic tools and treatments. To gain insight into its disease mechanism, we explored the potential biological processes that underlie DDH by integrating pathway analysis tools and performing a genome-wide association study (GWAS). A total of 406 DDH-associated genes (P< 0...
December 3, 2018: Clinical Genetics
Marianna Grinberg, Regina M Stöber, Wiebke Albrecht, Karolina Edlund, Markus Schug, Patricio Godoy, Cristina Cadenas, Rosemarie Marchan, Alfonso Lampen, Albert Braeuning, Thorsten Buhrke, Marcel Leist, Axel Oberemm, Birte Hellwig, Hennicke Kamp, Iain Gardner, Sylvia Escher, Olivier Taboureau, Alejandro Aguayo-Orozco, Agapios Sachinidis, Heidrun Ellinger-Ziegelbauer, Jörg Rahnenführer, Jan G Hengstler
Transcriptomics is developing into an invaluable tool in toxicology. The aim of this study was, using a transcriptomics approach, to identify genes that respond similar to many different chemicals (including drugs and industrial compounds) in both rat liver in vivo and in cultivated hepatocytes. For this purpose, we analyzed Affymetrix microarray expression data from 162 compounds that were previously tested in a concentration-dependent manner in rat livers in vivo and in rat hepatocytes cultivated in sandwich culture...
December 3, 2018: Archives of Toxicology
Upendra Raj Bhattarai, Fengjiao Li, Mandira Katuwal Bhattarai, Abolfazl Masoudi, Dun Wang
The tree-top disease is an altered behavioral state, displayed by baculovirus-infected lepidopteran larvae, and characterized by climbing to an elevated position before death. The detailed molecular mechanism underlying this phenomenal behavior change has not been reported yet. Our study focused on the transcriptomic changes in the host larvae due to baculovirus infection from pre-symptomatic to tree-top disease stage. Enrichment map visualization of the gene sets grouped based on the functional annotation similarity revealed 34 enriched pathways in signaling mechanism cluster during LdMNPV induced tree-top disease in third instar Lymantria dispar asiatica larvae...
December 3, 2018: Scientific Reports
Huimei Wang, Qiqi Xie, Wen Ou-Yang, Mingwei Zhang
Idiopathic pulmonary fibrosis (IPF), characterized by irreversible scarring and progressive destruction of the lung tissue, is one of the most common types of idiopathic interstitial pneumonia worldwide. However, there are no reliable candidates for curative therapies. Hence, elucidation of the mechanisms of IPF genesis and exploration of potential biomarkers and prognostic indicators are essential for accurate diagnosis and treatment of IPF. Recently, efficient microarray and bioinformatics analyses have promoted an understanding of the molecular mechanisms of disease occurrence and development, which is necessary to explore genetic alternations and identify potential diagnostic biomarkers...
December 2, 2018: Journal of Cellular Biochemistry
Jia Yu, Feixue Wang, Xijing Zhan, Xin Wang, Feng Zuo, Yuxi Wei, Jun Qi, Yin Liu
Loop-mediated isothermal amplification (LAMP) is a specific, sensitive, and easy-to-perform nucleic acid analytical technique with wide application for diagnosis of disease. Recently, LAMP combined with use of a lateral chromatographic flow dipstick (LFD) has been widely used in nucleic acid detection. However, the LFD mechanism has not been systematically analyzed, and the optimal combination of labeled primers has not been adequately evaluated. We analyzed the LAMP mechanism and discovered that the labeled loop primers played a significant role in the LFD assay...
December 1, 2018: Analytical and Bioanalytical Chemistry
Wenwu He, Linxin Chen, Kun Yuan, Qiuxi Zhou, Lin Peng, Yongtao Han
Background: Esophageal squamous cell carcinoma (ESCC) is a common malignancy with high mortality. Because of the lack of clarity in the relevant genes and mechanisms involved, and the current difficulty for oncotherapy in providing therapeutic solutions, there is an urgent need to study this matter. While gene probe studies have been used to select the most virulent genes and pathways, paucity of case controls during gene screening and lack of conclusive results to expound the etiology and pathogenesis of the disease, have reduced study reliability...
October 2018: Journal of Thoracic Disease
Suhu Liu, Anna E Marneth, Gabriela Alexe, Sarah R Walker, Helen I Gandler, Darwin Q Ye, Katherine Labella, Radhika Mathur, Patricia A Toniolo, Michelle Tillgren, Prafulla C Gokhale, David Barbie, Ann Mullally, Kimberly Stegmaier, David A Frank
To identify novel therapeutic targets in acute myeloid leukemia (AML), we examined kinase expression patterns in primary AML samples. We found that the serine/threonine kinase IKBKE, a noncanonical IkB kinase, is expressed at higher levels in myeloid leukemia cells compared with normal hematopoietic cells. Inhibiting IKBKE, or its close homolog TANK-binding kinase 1 (TBK1), by either short hairpin RNA knockdown or pharmacological compounds, induces apoptosis and reduces the viability of AML cells. Using gene expression profiling and gene set enrichment analysis, we found that IKBKE/TBK1-sensitive AML cells typically possess an MYC oncogenic signature...
December 11, 2018: Blood Advances
Nicole R Laferriere, Wendy E Kurata, Cary T Grayson, Kelsey M Stecklow, Lisa M Pierce
Gulf War Illness (GWI) is a chronic, multisymptom illness that continues to affect up to 30% of veterans deployed to the Persian Gulf during the 1990-1991 Gulf War. After nearly 30 years, useful treatments for GWI are lacking and underlying cellular and molecular mechanisms involved in its pathobiology remain poorly understood, although exposures to pyridostigmine bromide (PB) and pesticides are consistently identified to be among the strongest risk factors. Alleviation of the broad range of symptoms manifested in GWI, which involve the central nervous system, the neuroendocrine system, and the immune system likely requires therapies that are able to activate and inactivate a large set of orchestrated genes...
November 29, 2018: Neurotoxicology
Filomene G Morrison, Mark W Miller, Mark W Logue, Michele Assef, Erika J Wolf
There is increasing evidence that epigenetic factors play a critical role in posttraumatic stress disorder (PTSD), by mediating the impact of environmental exposures to trauma on the regulation of gene expression. DNA methylation is one epigenetic mark that has been highly studied in PTSD. This review will begin by providing an overview of DNA methylation (DNAm) methods, and will then highlight two major biological systems that have been identified in the epigenetic regulation in PTSD: (a) the immune system and (b) the stress response system...
November 29, 2018: Progress in Neuro-psychopharmacology & Biological Psychiatry
Judith C Sporn, Eriko Katsuta, Li Yan, Kazuaki Takabe
BACKGROUND: MicroRNA-9 (miR-9) was found to play an important role in a variety of different cancers and can adopt either tumor suppressor or oncogenic activity. Most studies have suggested an oncogenic role in breast cancer. We were interested in the relationship of miR-9 expression and survival in breast cancer and hypothesized that high expression of miR-9 was associated with worse prognosis in breast cancer patients. MATERIALS AND METHODS: We utilized The Cancer Genome Atlas containing genetic and molecular data, clinical profiles, and survival information for 985 breast cancers...
January 2019: Journal of Surgical Research
Steven Mullenbrock, Fei Liu, Suzanne Szak, Xiaoping Hronowski, Benbo Gao, Peter Juhasz, Chao Sun, Mei Liu, Helen McLaughlin, Qiurong Xiao, Carol Feghali-Bostwick, Timothy S Zheng
Fibroblasts/myofibroblasts are the key effector cells responsible for excessive extracellular matrix (ECM) deposition and fibrosis progression in both idiopathic pulmonary fibrosis (IPF) and systemic sclerosis (SSc) patient lungs, thus it is critical to understand the transcriptomic and proteomic programs underlying their fibrogenic activity. We conducted the first integrative analysis of the fibrotic programming in these cells at the levels of gene and microRNA (miRNA) expression, as well as deposited ECM protein to gain insights into how fibrotic transcriptional programs culminate in aberrant ECM protein production/deposition...
November 29, 2018: Genes
Nao Nagai, Hiroto Ohguchi, Ryo Nakaki, Yoshihiro Matsumura, Yasuharu Kanki, Juro Sakai, Hiroyuki Aburatani, Takashi Minami
Endothelial cell (EC) plasticity in pathological settings has recently been recognized as a driver of disease progression. Endothelial-to-mesenchymal transition (EndMT), in which ECs acquire mesenchymal properties, has been described for a wide range of pathologies, including cancer. However, the mechanism regulating EndMT in the tumor microenvironment and the contribution of EndMT in tumor progression are not fully understood. Here, we found that combined knockdown of two ETS family transcription factors, ERG and FLI1, induces EndMT coupled with dynamic epigenetic changes in ECs...
November 30, 2018: PLoS Genetics
Jiayu Chen, Kent E Hutchison, Angela D Bryan, Francesca M Filbey, Vince D Calhoun, Eric D Claus, Dongdong Lin, Jing Sui, Yuhui Du, Jingyu Liu
Alcohol use disorder (AUD) is a devastating public health problem in which both genetic and environmental factors play a role. Growing evidence supports that epigenetic regulation is one major mechanism in neuroadaptation that contributes to development of AUD. Meanwhile, epigenetic patterns can be modified by various stimuli including exercise. Thus, it is an intriguing question whether exercise can lead to methylation changes that are opposite to those related to drinking. We herein conducted a comparative study to explore this issue...
2018: Frontiers in Psychiatry
Jeroen G J van Rooij, Lieke H H Meeter, Shami Melhem, Diana A T Nijholt, Tsz Hang Wong, Annemieke Rozemuller, Andre G Uitterlinden, Joyce G van Meurs, John C van Swieten
Knowledge about the molecular mechanisms driving Alzheimer's disease (AD) is still limited. To learn more about AD biology, we performed whole transcriptome sequencing on the hippocampus of 20 AD cases and 10 age- and sex-matched cognitively healthy controls. We observed 2716 differentially expressed genes, of which 48% replicated in a second data set of 84 AD cases and 33 controls. We used an integrative network-based approach for combining transcriptomic and protein-protein interaction data to find differentially expressed gene modules that may reflect key processes in AD biology...
October 29, 2018: Neurobiology of Aging
Qiulan Luo, Bian Chao, Ming Tao, Yu Huang, Yihong Zheng, Yunyun Lv, Li Jia, Chaogang Wang, Xinxin You, Bin Jia, Junmin Xu, Jiancheng Li, Ze Li, Qiong Shi, Zhangli Hu
Haematococcus pluvialis is a freshwater species of Chlorophyta, family Haematococcaceae. It is well known for its capacity to synthesize high amounts of astaxanthin, which is a strong antioxidant that has been utilized in aquaculture and cosmetics. To improve astaxanthin yield and to establish genetic resources for H. pluvialis, we performed whole-genome sequencing, assembly, and annotation of this green microalga. A total of 83.1 Gigabases (Gb) of raw reads were sequenced. After filtering the raw reads, we subsequently generated a draft assembly with a genome size of 669...
November 29, 2018: Genome Biology and Evolution
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