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https://www.readbyqxmd.com/read/29332824/dithiothreitol-based-protein-equalization-technology-to-unravel-biomarkers-for-bladder-cancer
#1
J E Araújo, H López-Fernández, M S Diniz, Pedro M Baltazar, Luís Campos Pinheiro, Fernando Calais da Silva, Mylène Carrascal, Paula Videira, H M Santos, J L Capelo
This study aimed to assess the benefits of dithiothreitol (DTT)-based sample treatment for protein equalization to assess potential biomarkers for bladder cancer. The proteome of plasma samples of patients with bladder carcinoma, patients with lower urinary tract symptoms (LUTS) and healthy volunteers, was equalized with dithiothreitol (DTT) and compared. The equalized proteomes were interrogated using two-dimensional gel electrophoresis and matrix assisted laser desorption ionization time of flight mass spectrometry...
April 1, 2018: Talanta
https://www.readbyqxmd.com/read/29329366/delineating-differential-regulatory-signatures-of-the-human-transcriptome-in-the-choriodecidua-and-myometrium-at-term-labor
#2
Sylvia Lui, Cyntia Duval, Farkhondeh Farrokhnia, Sylvie Girard, Lynda K Harris, Clare L Tower, Adam Stevens, Rebecca L Jones
Background: Preterm deliveries remain the leading cause of neonatal morbidity and mortality. Current therapies target only myometrial contractions and are largely ineffective. As labor involves multiple coordinated events across maternal and fetal tissues, identifying fundamental regulatory pathways of normal term labor is vital to understanding successful parturition and consequently labor pathologies. We aimed to identify transcriptomic signatures of human normal term labor of two tissues: in the fetal-facing choriodecidua and the maternal myometrium...
January 10, 2018: Biology of Reproduction
https://www.readbyqxmd.com/read/29328449/bioinformatics-analysis-to-screen-key-genes-implicated-in-the-differentiation-of-induced-pluripotent-stem-cells-to-hepatocytes
#3
Rui Lin, Yufeng Wang, Kun Ji, Zhongyan Liu, Shuai Xiao, Dehua Zhou, Quanning Chen, Baomin Shi
Due to the lack of potential organs, hepatocellular transplantation has been considered for treating end-stage liver disease. Induced pluripotent stem cells (iPSCs) are reverted from somatic cells and are able to differentiate into hepatocytes. The present study aimed to investigate the mechanisms underlying iPSC differentiation to hepatocytes. GSE66076 was downloaded from the Gene Expression Omnibus; this database includes data from 3 undifferentiated (T0), 3 definitive endoderm (T5), and 3 early hepatocyte (T24) samples across hepatic‑directed differentiation of iPSCs...
January 5, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29328442/identification-of-differentially-expressed-genes-and-regulatory-relationships-in-huntington-s-disease-by-bioinformatics-analysis
#4
Xiaoyu Dong, Shuyan Cong
Huntington's disease (HD) is an inherited, progressive neurodegenerative disease caused by a CAG expansion in the huntingtin (HTT) gene; various dysfunctions of biological processes in HD have been proposed. However, at present the exact pathogenesis of HD is not fully understood. The present study aimed to explore the pathogenesis of HD using a computational bioinformatics analysis of gene expression. GSE11358 was downloaded from the Gene Expression Omnibus andthe differentially expressed genes (DEGs) in the mutant HTT knock‑in cell model STHdhQ111/Q111 were predicted...
January 9, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29328395/bioinformatic-identification-of-chemoresistance-associated-micrornas-in-breast-cancer-based-on-microarray-data
#5
Ya-Wen Wang, Weiguo Zhang, Rong Ma
Breast cancer is the most commonly diagnosed cancer among females, and chemoresistance constitutes a major clinical obstacle to the treatment of this disease. MicroRNAs (miRNAs) are related to human cancer development, progression and drug resistance. To identify breast cancer chemoresistance-associated miRNAs, miRNA microarray dataset GSE71142, including five chemoresistant breast cancer tissues and five chemosensitive tissues, was downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed miRNAs (DE-miRNAs) were obtained by t-test and the potential target genes were predicted by miRWalk2...
January 10, 2018: Oncology Reports
https://www.readbyqxmd.com/read/29328361/logistic-regression-analysis-for-the-identification-of-the-metastasis-associated-signaling-pathways-of-osteosarcoma
#6
Yang Liu, Wei Sun, Xiaojun Ma, Yuedong Hao, Gang Liu, Xiaohui Hu, Houlai Shang, Pengfei Wu, Zexue Zhao, Weidong Liu
Osteosarcoma (OS) is the most common histological type of primary bone cancer. The present study was designed to identify the key genes and signaling pathways involved in the metastasis of OS. Microarray data of GSE39055 were downloaded from the Gene Expression Omnibus database, which included 19 OS biopsy specimens before metastasis (control group) and 18 OS biopsy specimens after metastasis (case group). After the differentially expressed genes (DEGs) were identified using the Linear Models for Microarray Analysis package, hierarchical clustering analysis and unsupervised clustering analysis were performed separately, using orange software and the self-organization map method...
January 2, 2018: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29323532/identification-of-cdk2-as-a-novel-target-in-treatment-of-prostate-cancer
#7
Xifeng Yin, Jun Yu, Yang Zhou, Chengyue Wang, Zhimin Jiao, Zhounan Qian, Hao Sun, Binghai Chen
AIM: This study aims the potential gene involved in the metastasis of prostate cancer (Pca). METHODS: PubMed GEO datasets (GSE6605 and GSE6606) were downloaded. We used multiple bioinformatics methods to screen differentially expressed genes in Pca. Gene network was built by STRING and visualized by Cytoscape. All of the hub genes were analyzed by cBioPortal. Inhibition of CDK2 including siRNA, inhibitor and cas9-induced CDK2 knockout was followed by an invasion assay...
January 11, 2018: Future Oncology
https://www.readbyqxmd.com/read/29322790/integrated-network-analysis-to-identify-the-key-genes-transcription-factors-and-micrornas-involved-in-hepatocellular-carcinoma
#8
S Q Shi, J-J Ke, Q S Xu, W Q Wu, Y Y Wan
HCC (hepatocellular carcinoma), which can be induced by cirrhosis and viral hepatitis infection, is the most frequent form of liver cancer. This study is performed to investigate the mechanisms of HCC. GSE57957 was obtained from Gene Expression Omnibus database, including 39 HCC samples and 39 adjacent non-tumorous samples. The DEGs (differentially expressed genes) were screened using the limma package in R, and then were conducted with enrichment analysis using "BioCloud" platform. Using STRING database, WebGestalt tool, as well as ITFP and TRANSFAC databases, PPI (protein-protein interaction) pairs, miRNA (microRNA)-target pairs, and TF (transcription factor)-target pairs separately were predicted...
2018: Neoplasma
https://www.readbyqxmd.com/read/29307852/global-gene-expression-analysis-of-knockdown-triosephosphate-isomerase-tpi-gene-in-human-gastric-cancer-cell-line-mgc-803
#9
Ping Ouyang, Bode Lin, Jinlin Du, Haiyan Pan, Haibing Yu, Rongwei He, Zhigang Huang
Our preview studies showed TPI gene which encodes the Triosephosphate isomerase was overexpressed in human gastric cancer (GC) tissues. However, the potential molecular mechanisms how TPI influences the GC development is not clear. Here, we performed global gene expression profiling for TPI knockdown using microarrays in human GC cell line MGC-803 cells. The differentially expressed genes (DEGs) were identified using reverse transcription-quantitative polymerase chain reaction analysis. Then the DEGs were analyzed by an online software WebGestalt to perform the functional analysis, pathway analysis and network analysis...
January 4, 2018: Gene
https://www.readbyqxmd.com/read/29305979/target-gene-screening-and-evaluation-of-prognostic-values-in-non-small-cell-lung-cancers-by-bioinformatics-analysis
#10
Junjie Piao, Jie Sun, Yang Yang, Tiefeng Jin, Liyan Chen, Zhenhua Lin
BACKGROUND: Non-small cell lung cancer (NSCLC) is the major leading cause of cancer-related deaths worldwide. This study aims to explore molecular mechanism of NSCLC. METHODS: Microarray dataset was obtained from the Gene Expression Omnibus (GEO) database, and analyzed by using GEO2R. Functional and pathway enrichment analysis were performed based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Then, STRING, Cytoscape and MCODE were applied to construct the Protein-protein interaction (PPI) network and screen hub genes...
January 3, 2018: Gene
https://www.readbyqxmd.com/read/29286604/protein-protein-interaction-network-analysis-for-a-biomarker-panel-related-to-human-esophageal-adenocarcinoma
#11
Majid Rezaei-Tavirani, Sina Rezaei-Taviran, Mansouri Mansouri, Mohammad Rostami-Nejad, Mostafa Rezaei-Tavirani
Background: Esophageal adenocarcinoma (EAC) is one of the mostlethal cancers in the world with a very poor prognosis. Identification of molecular diagnostic methods is an important goal. Since protein-protein interaction (PPI) network analysis is a suitable method for molecular assessment, in the present research a PPI network related to EAC was targeted. Material and Method: Cytoscape software and its applications including STRING DB, Cluster ONE and ClueGO were applied to analyze the PPI network. Result: Among 182 EAC-related proteins which were identified, 129 were included in a main connected component...
December 29, 2017: Asian Pacific Journal of Cancer Prevention: APJCP
https://www.readbyqxmd.com/read/29286140/identification-of-key-genes-implicated-in-the-suppressive-function-of-human-foxp3-cd25-cd4-regulatory-t-cells-through-the-analysis-of-time%C3%A2-series-data
#12
Xiaofeng Bai, Hua Shi, Mingxi Yang, Yuanlin Wang, Zhaolin Sun, Shuxiong Xu
Human forkhead box P3 (FOXP3)+ cluster of differentiation (CD)25+CD4+ regulatory T cells (Tregs) are a type of T cell that express CD4, CD25 and FOXP3, which are critical for maintaining immune homeostasis. The present study aimed to determine the mechanisms underlying Treg function. The GSE11292 dataset was downloaded from the Gene Expression Omnibus, which included data from Treg cells at 19 time points (0‑360 min) with an equal interval of 20 min, and corresponding repeated samples. However, data for Treg cells at time point 120 min were missing...
December 29, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29286097/identification-of-key-genes-associated-with-congenital-heart-defects-in-embryos-of-diabetic-mice
#13
Nan Lin, Yan Cai, Linlin Zhang, Yahang Chen
Maternal diabetes has been reported to be a critical factor for congenital heart defects (CHD) in offspring. The present study aimed to screen the key genes that may be involved in CHD in offspring of diabetic mothers. The present study obtained the gene expression profile of GSE32078, including three embryonic heart tissue samples at embryonic day 13.5 (E13.5), three embryonic heart tissue samples at embryonic day 15.5 (E15.5) from diabetic mice and their respective controls from normal mice. The cut‑off criterion of P<0...
December 20, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29276392/integrative-analysis-of-lncrnas-and-mirnas-with-coding-rnas-associated-with-cerna-crosstalk-network-in-triple-negative-breast-cancer
#14
Naijun Yuan, Guijuan Zhang, Fengjie Bie, Min Ma, Yi Ma, Xuefeng Jiang, Yurong Wang, Xiaoqian Hao
Triple negative breast cancer (TNBC) is a particular subtype of breast malignant tumor with poorer prognosis than other molecular subtypes. Currently, there is increasing focus on long non-coding RNAs (lncRNAs), which can act as competing endogenous RNAs (ceR-NAs) and suppress miRNA functions involved in post-transcriptional regulatory networks in the tumor. Therefore, to investigate specific mechanisms of TNBC carcinogenesis and improve treatment efficiency, we comprehensively integrated expression profiles, including data on mRNAs, lncRNAs and miRNAs obtained from 116 TNBC tissues and 11 normal tissues from The Cancer Genome Atlas...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/29249532/omega-3-pufa-modulate-lipogenesis-er-stress-and-mitochondrial-dysfunction-markers-in-nash-proteomic-and-lipidomic-insight
#15
Lívia Samara Dos Reis Rodrigues Okada, Claudia P Oliveira, José Tadeu Stefano, Monize Aydar Nogueira, Ismael Dale Cotrim Guerreiro da Silva, Fernanda Bertucce Cordeiro, Venâncio Avancini Ferreira Alves, Raquel Susana Torrinhas, Flair José Carrilho, Puneet Puri, Dan L Waitzberg
BACKGROUND & AIMS: Currently there is no FDA-approved therapy for nonalcoholic steatohepatitis (NASH). Increased n-6/n-3 polyunsaturated fatty acids (PUFA) ratio can induce endoplasmic reticulum (ER) stress and mitochondrial dysfunction that characterize NASH. Our recent study with n-3 PUFA showed improvement in individual histologic parameters like steatosis, ballooning and lobular inflammation. We hypothesized that n-3 PUFA therapy mediated improvement in histologic parameters is modulated by lipidomic and proteomic changes...
September 7, 2017: Clinical Nutrition: Official Journal of the European Society of Parenteral and Enteral Nutrition
https://www.readbyqxmd.com/read/29249121/matrix-metalloproteinase-1-a-better-biomarker-for-squamous-cell-carcinoma-by-multiple-microarray-analyses
#16
Li-Qiang Zheng, Rui Wang, Su-Min Chi, Cheng-Xin Li
BACKGROUND: The present study aimed to validate MMP1 role in the development of squamous cell carcinoma (SCC) by bioinformatics methods. METHODS: Gene expression data of 10 GSE series (5 HNSCCs and 5 cSCCs) were obtained from the Gene Expression Omnibus (GEO) database and used to identify differentially expressed genes (DEGs). RESULTS: Higher expression of MMP1 was found rank number one in 9/10 GSE series of SCC. MMP1 was mainly focused on Gene Ontology (GO) terms of collagen catabolic process, extracellular matrix disassembly...
December 15, 2017: Giornale Italiano di Dermatologia e Venereologia: Organo Ufficiale, Società Italiana di Dermatologia e Sifilografia
https://www.readbyqxmd.com/read/29241710/new-insights-into-the-gene-expression-associated-to-amyotrophic-lateral-sclerosis
#17
REVIEW
Daniela Recabarren-Leiva, Marcelo Alarcón
Amyotrophic lateral sclerosis (ALS) is the most prevalent neuromuscular disease worldwide. It is a lethal and progressive neurodegenerative disease, principally affecting motor neurons; patient clinical characteristics are muscle weakness, dysphagia and respiratory failure. The mean age is related to family history (40years, familial ALS or FALS) or with no family history (50years), but it is more common in people aged 60-69years. The cause of ALS is not known and it is not known yet why it affects some people and not others...
December 11, 2017: Life Sciences
https://www.readbyqxmd.com/read/29240723/identi%C3%AF-cation-of-key-genes-and-pathways-in-tongue-squamous-cell-carcinoma-using-bioinformatics-analysis
#18
Huayong Zhang, Jianmin Liu, Xiaoyan Fu, Ankui Yang
BACKGROUND Tongue squamous cell carcinoma (TSCC) is a major type of oral cancers and has remained an intractable cancer over the past decades. The aim of this study was to identify differentially expressed genes (DEGs) during TSCC and reveal their potential mechanisms. MATERIAL AND METHODS The gene expression profiles of GSE13601 were downloaded from the GEO database. The GSE13601 dataset contains 57 samples, including 31 tongue SCC samples and 26 matched normal mucosa samples. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses were performed; Cytoscape software was used for the protein-protein interaction (PPI) network and module analysis of the DEGs...
December 14, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/29225431/insights-from-the-protein-protein-interaction-network-analysis-of-mycobacterium-tuberculosis-toxin-antitoxin-systems
#19
Zoozeal Thakur, Renu Dharra, Vandana Saini, Ajit Kumar, Promod K Mehta
Protein-protein interaction (PPI) network analysis is a powerful strategy to understand M. tuberculosis (Mtb) system level physiology in the identification of hub proteins. In the present study, the PPI network of 79 Mtb toxin-antitoxin (TA) systems comprising of 167 nodes and 234 edges was investigated. The topological properties of PPI network were examined by 'Network analyzer' a cytoscape plugin app and STRING database. The key enriched biological processes and the molecular functions of Mtb TA systems were analyzed by STRING...
2017: Bioinformation
https://www.readbyqxmd.com/read/29209625/prediction-and-validation-of-hub-genes-associated-with-colorectal-cancer-by-integrating-ppi-network-and-gene-expression-data
#20
Yongfu Xiong, Wenxian You, Rong Wang, Linglong Peng, Zhongxue Fu
Although hundreds of colorectal cancer- (CRC-) related genes have been screened, the significant hub genes still need to be further identified. The aim of this study was to identify the hub genes based on protein-protein interaction network and uncover their clinical value. Firstly, 645 CRC patients' data from the Tumor Cancer Genome Atlas were downloaded and analyzed to screen the differential expression genes (DEGs). And then, the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis was performed, and PPI network of the DEGs was constructed by Cytoscape software...
2017: BioMed Research International
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