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Ingenuity pathway analysis

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https://www.readbyqxmd.com/read/28653025/proteomics-data-on-map-kinase-kinase-3-knock-out-bone-marrow-derived-macrophages-exposed-to-cigarette-smoke-extract
#1
Roshni Srivastava, Praveen Mannam, Navin Rauniyar, TuKiet T Lam, Ruiyan Luo, Patty J Lee, Anup Srivastava
This data article reports changes in the phosphoproteome and total proteome of cigarette smoke extract (CSE) exposed WT and MAP Kinase Kinase 3 knock out (MKK3(-/-)) bone marrow derived macrophages (BMDM). The dataset generated is helpful for understanding the mechanism of CSE induced inflammation and the role of MAP kinase signaling pathway. The cellular proteins were labeled with isobaric tags for relative and absolute quantitation (iTRAQ®) reagents and analyzed by LC-MS/MS. The standard workflow module for iTRAQ® quantification within the Proteome Discoverer was utilized for the data analysis...
August 2017: Data in Brief
https://www.readbyqxmd.com/read/28651487/identification-of-genes-and-pathways-related-to-lymphovascular-invasion-in-breast-cancer-patients-a-bioinformatics-analysis-of-gene-expression-profiles
#2
Sukhontip Klahan, Henry Sung-Ching Wong, Shih-Hsin Tu, Wan-Hsuan Chou, Yan-Feng Zhang, Thien-Fiew Ho, Chih-Yi Liu, Shih-Ying Yih, Hsing Fang Lu, Sean Chun-Chang Chen, Chi-Cheng Huang, Wei-Chiao Chang
Surgery is the most effective treatment for breast cancer patients. However, some patients developed recurrence and distant metastasis after surgery. Adjuvant therapy is considered for high-risk patients depending on several prognostic markers, and lymphovascular invasion has become one of such prognostic markers that help physicians to identify the risk for distant metastasis and recurrence. However, the mechanism of lymphovascular invasion in breast cancer remains unknown. This study aims to unveil the genes and pathways that may involve in lymphovascular invasion in breast cancer...
June 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28649315/effects-of-a-social-stimulus-on-gene-expression-in-a-mouse-model-of-fragile-x-syndrome
#3
Tiffany D Rogers, Allison M J Anacker, Travis M Kerr, C Gunnar Forsberg, Jing Wang, Bing Zhang, Jeremy Veenstra-VanderWeele
BACKGROUND: People with fragile X syndrome (FXS) often have deficits in social behavior, and a substantial portion meet criteria for autism spectrum disorder. Though the genetic cause of FXS is known to be due to the silencing of FMR1, and the Fmr1 null mouse model representing this lesion has been extensively studied, the contributions of this gene and its protein product, FMRP, to social behavior are not well understood. METHODS: Fmr1 null mice and wildtype littermates were exposed to a social or non-social stimulus...
2017: Molecular Autism
https://www.readbyqxmd.com/read/28645527/inhibition-of-17beta-hydroxysteroid-dehydrogenase-type-7-modulates-breast-cancer-protein-profile-and-enhances-apoptosis-by-down-regulating-grp78
#4
Xiao-Qiang Wang, Juliette A Aka, Tang Li, Dan Xu, Charles J Doillon, Sheng-Xiang Lin
17beta-hydroxysteroid dehydrogenase type 7 (17β-HSD7) promotes breast cancer cell growth via dual-catalytic activity by modulating estradiol and DHT. Here, we clarified the expression pattern of 17β-HSD7 in postmenopausal luminal A type breast cancer with The Cancer Genome Atlas (TCGA) cohort. The impact of 17β-HSD7 inhibition on the proteome of MCF-7 cells was investigated and on cell apoptosis was revealed. MCF-7 cells were treated with an efficient inhibitor of 17β-HSD7 or with vehicle, and a differential proteomics study was performed using two-dimensional (2D) gel electrophoresis followed by mass spectrometry and ingenuity pathway analysis (IPA)...
June 20, 2017: Journal of Steroid Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28636987/combination-of-calr-and-pdia3-is-a-potential-prognostic-biomarker-for-non-small-cell-lung-cancer
#5
Ke Wang, Hao Li, Ruo Chen, Yang Zhang, Xiu-Xuan Sun, Wan Huang, Huijie Bian, Zhi-Nan Chen
Proteomic-based approaches for biomarker discovery are promising strategies used in cancer research. In this study, we performed quantitative proteomic analysis on 16 paired samples of non-small cell lung cancer (NSCLC) and adjacent non-tumor lung tissues using label-free quantitative proteomics and liquid chromatography-tandem mass spectrometry/mass spectrometry (LC-MS/MS) to identify differentially expressed proteins. A total of 91 proteins were differentially expressed in NSCLC compared with adjacent non-tumor lung tissues among 4047 identified proteins (fold change > 1...
June 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28633944/gene-expression-analysis-identify-a-metabolic-and-cell-function-alterations-as-a-hallmark-of-obesity-without-metabolic-syndrome-in-peripheral-blood-a-pilot-study
#6
Daniel Antonio de Luis, Raquel Almansa, Rocío Aller, Olatz Izaola, E Romero
BACKGROUND: Understanding molecular basis involved in overweight is an important first step in developing therapeutic pathways against excess in body weight gain. OBJECTIVE: The purpose of our pilot study was to evaluate the gene expression profiles in the peripheral blood of obese patients without other metabolic complications. DESIGN: A sample of 17 obese patients without metabolic syndrome and 15 non obese control subjects was evaluated in a prospective way...
June 10, 2017: Clinical Nutrition: Official Journal of the European Society of Parenteral and Enteral Nutrition
https://www.readbyqxmd.com/read/28628668/dose-dependent-effects-of-gamma-radiation-on-the-early-zebrafish-development-and-gene-expression
#7
Selma Hurem, Leonardo Martín Martín, Dag Anders Brede, Eystein Skjerve, Rasoul Nourizadeh-Lillabadi, Ole Christian Lind, Terje Christensen, Vidar Berg, Hans-Christian Teien, Brit Salbu, Deborah Helen Oughton, Peter Aleström, Jan Ludvig Lyche
Ionizing radiation from natural sources or anthropogenic activity has the potential to cause oxidative stress or genetic damage in living organisms, through the ionization and excitation of molecules and the subsequent production of free radicals and reactive oxygen species (ROS). The present work focuses on radiation-induced biological effects using the zebrafish (Danio rerio) vertebrate model. Changes in developmental traits and gene expression in zebrafish were assessed after continuous external gamma irradiation (0...
2017: PloS One
https://www.readbyqxmd.com/read/28621308/inhalation-toxicity-of-indoor-air-pollutants-in-drosophila-melanogaster-using-integrated-transcriptomics-and-computational-behavior-analyses
#8
Hyun-Jeong Eom, Yuedan Liu, Gyu-Suk Kwak, Muyoung Heo, Kyung Seuk Song, Yun Doo Chung, Tae-Soo Chon, Jinhee Choi
We conducted an inhalation toxicity test on the alternative animal model, Drosophila melanogaster, to investigate potential hazards of indoor air pollution. The inhalation toxicity of toluene and formaldehyde was investigated using comprehensive transcriptomics and computational behavior analyses. The ingenuity pathway analysis (IPA) based on microarray data suggests the involvement of pathways related to immune response, stress response, and metabolism in formaldehyde and toluene exposure based on hub molecules...
June 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28614626/ptprs-and-per3-methylation-levels-are-associated-with-childhood-obesity-results-from-a-genome-wide-methylation-analysis
#9
M Samblas, F I Milagro, M L Mansego, A Marti, J A Martinez
BACKGROUND: The global prevalence of childhood overweight and obesity has increased in the last years. Epigenetic dysregulation affecting gene expression could be a determinant in early-life obesity onset and accompanying complications. OBJECTIVE: The aim of the present investigation was to analyse the putative association between DNA methylation and childhood obesity. METHODS: DNA was isolated from white blood cells of 24 children obtained from the GENOI study and was hybridized in a 450K methylation array...
June 14, 2017: Pediatric Obesity
https://www.readbyqxmd.com/read/28610954/feedback-regulation-of-aldoa-activates-the-hif-1%C3%AE-mmp9-axis-to-promote-lung-cancer-progression
#10
Yu-Chan Chang, Yung-Chieh Chan, Wei-Ming Chang, Yuan-Feng Lin, Chih-Jen Yang, Chia-Yi Su, Ming-Shyan Huang, Alexander T H Wu, Michael Hsiao
Distant metastasis and recurrence are the greatest challenges in the clinical management of lung cancer. Despite advances in targeted therapies, high mortality rates persist. Therefore, alternative therapeutic interventions are urgently required. Accumulating evidence indicates that normalizing tumor metabolism may be a way to increase therapeutic efficacy and to reduce tumor malignancy. Here, we analyzed integrated transcriptomics data and an shRNA library against glycolytic enzymes and found that elevated Aldolase A expression is highly correlated with metastatic potential and a poor prognosis in patients with non-small cell lung cancer (NSCLC)...
June 10, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28604807/brain-derived-neurotrophic-factor-bdnf-trkb-signaling-modulates-cancer-endothelial-cells-interaction-and-affects-the-outcomes-of-triple-negative-breast-cancer
#11
Yi-Fang Tsai, Ling-Ming Tseng, Chih-Yi Hsu, Muh-Hwa Yang, Jen-Hwey Chiu, Yi-Ming Shyr
AIMS: There is good evidence that the tumor microenvironment plays an important role in cancer metastasis and progression. Our previous studies have shown that brain-derived neurotrophic factor (BDNF) participates in the process of metastasis and in the migration of cancer cells. The aim of this study was to investigate the role of BDNF on the tumor cell microenvironment, namely, the cancer cell-endothelial cell interaction of TNBC cells. METHODS: We conducted oligoneucleotide microarray analysis of potential biomarkers that are able to differentiate recurrent TNBC from non-recurrent TNBC...
2017: PloS One
https://www.readbyqxmd.com/read/28598000/peptidomic-analysis-of-maternal-serum-to-identify-biomarker-candidates-for-prenatal-diagnosis-of-tetralogy-of-fallot
#12
Bin Zhuang, Yin Hu, Xuemei Fan, Mengmeng Li, Jingai Zhu, Heng Liu, Li Cao, Dong Liang, Jingjing Zhang, Zhangbin Yu, Shuping Han
Tetralogy of Fallot (TOF) is the most common form of cyanotic congenital heart disease. To identify endogenous peptides possibly involved in the progression of TOF, we performed comparative peptidomic profiling of maternal serum between normal fetuses and fetuses suffering from TOF. A total of 278 differentially expressed peptides, including 94 over-expressed peptides and 184 under-expressed peptides, originating from 227 protein precursors were identified by Liquid Chromatography/Mass Spectrometry (LC/MS) in maternal serum of fetuses with TOF compared to normal controls...
June 9, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28592827/a-comprehensive-characterisation-of-the-metabolic-profile-of-varicose-veins-implications-in-elaborating-plausible-cellular-pathways-for-disease-pathogenesis
#13
Muzaffar A Anwar, Kyrillos N Adesina-Georgiadis, K Spagou, P A Vorkas, J V Li, Joseph Shalhoub, Elaine Holmes, Alun H Davies
Metabolic phenotypes reflect both the genetic and environmental factors which contribute to the development of varicose veins (VV). This study utilises analytical techniques to provide a comprehensive metabolic picture of VV disease, with the aim of identifying putative cellular pathways of disease pathogenesis. VV (n = 80) and non-VV (n = 35) aqueous and lipid metabolite extracts were analysed using 600 MHz (1)H Nuclear Magnetic Resonance spectroscopy and Ultra-Performance Liquid Chromatography Mass Spectrometry...
June 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28590090/motile-hepatocellular-carcinoma-cells-preferentially-secret-sugar-metabolism-regulatory-proteins-via-exosomes
#14
Jing Zhang, Shaohua Lu, Ye Zhou, Kun Meng, Zhipeng Chen, Yizhi Cui, Yunfeng Shi, Qing-Yu He, Tong Wang
Exosomes are deliverers of critically functional proteins, capable of transforming target cells in numerous cancers, including hepatocellular carcinoma (HCC). We hypothesize that the motility of HCC cells can be featured by comparative proteome of exosomes. Hence, we performed the super-SILAC-based MS analysis on the exosomes secreted by three human HCC cell lines, including the non-motile Hep3B cell, and the motile 97H and LM3 cells. Over 1400 exosomal proteins were confidently quantified in each MS analysis with highly biological reproducibility...
June 7, 2017: Proteomics
https://www.readbyqxmd.com/read/28579740/applying-multivariate-adaptive-splines-to-identify-genes-with-expressions-varying-after-diagnosis-in-microarray-experiments
#15
REVIEW
Fenghai Duan, Ye Xu
PURPOSE: To analyze a microarray experiment to identify the genes with expressions varying after the diagnosis of breast cancer. METHODS: A total of 44 928 probe sets in an Affymetrix microarray data publicly available on Gene Expression Omnibus from 249 patients with breast cancer were analyzed by the nonparametric multivariate adaptive splines. Then, the identified genes with turning points were grouped by K-means clustering, and their network relationship was subsequently analyzed by the Ingenuity Pathway Analysis...
2017: Cancer Informatics
https://www.readbyqxmd.com/read/28577936/association-between-dna-methylation-and-coronary-heart-disease-or-other-atherosclerotic-events-a-systematic-review
#16
REVIEW
Alba Fernández-Sanlés, Sergi Sayols-Baixeras, Isaac Subirana, Irene R Degano, Roberto Elosua
BACKGROUND AND AIMS: The aim of this study was to perform a systematic review of the association between DNA methylation and coronary heart disease (CHD) or related atherosclerotic traits. METHODS: A systematic review was designed. The condition of interest was DNA methylation, and the outcome was CHD or other atherosclerosis-related traits. Three DNA methylation approaches were considered: global methylation, candidate-gene, and epigenome-wide association studies (EWAS)...
May 18, 2017: Atherosclerosis
https://www.readbyqxmd.com/read/28574013/identifying-the-risk-of-producing-aneuploids-using-meiotic-recombination-genes-as-biomarkers-a-copy-number-variation-approach
#17
Raviraj V Suresh, Kusuma Lingaiah, Avinash M Veerappa, Nallur B Ramachandra
BACKGROUND & OBJECTIVES: Aneuploids are the most common chromosomal abnormality in liveborns and are usually the result of non-disjunction (NDJ) in meiosis. Copy number variations (CNVs) are large structural variations affecting the human genome. CNVs influence critical genes involved in causing NDJ by altering their copy number which affects the clinical outcome. In this study influence of CNVs on critical meiotic recombination was examined using new computational technologies to assess their role in causing aneuploidy...
January 2017: Indian Journal of Medical Research
https://www.readbyqxmd.com/read/28570644/comparison-of-the-adolescent-and-adult-mouse-prefrontal-cortex-proteome
#18
Abigail E Agoglia, Sarah E Holstein, Amanda T Small, Marina Spanos, Brainard M Burrus, Clyde W Hodge
Adolescence is a developmental period characterized by unique behavioral phenotypes (increased novelty seeking, risk taking, sociability and impulsivity) and increased risk for destructive behaviors, impaired decision making and psychiatric illness. Adaptive and maladaptive adolescent traits have been associated with development of the medial prefrontal cortex (mPFC), a brain region that mediates regulatory control of behavior. However, the molecular changes that underlie brain development and behavioral vulnerability have not been fully characterized...
2017: PloS One
https://www.readbyqxmd.com/read/28555042/the-cytotoxicity-of-the-ajoene-analogue-bispmb-in-whco1-oesophageal-cancer-cells-is-mediated-by-chop-gadd153
#19
Vuyolwethu Siyo, Georgia Schäfer, Roger Hunter, Andriy Grafov, Iryna Grafova, Martin Nieger, Arieh A Katz, M Iqbal Parker, Catherine H Kaschula
Garlic is a food and medicinal plant that has been used in folk medicine since ancient times for its beneficial health effects, which include protection against cancer. Crushed garlic cloves contain an array of small sulfur-rich compounds such as ajoene. Ajoene is able to interfere with biological processes and is cytotoxic to cancer cells in the low micromolar range. BisPMB is a synthetic ajoene analogue that has been shown in our laboratory to have superior cytotoxicity to ajoene. In the current study we have performed a DNA microarray analysis of bisPMB-treated WHCO1 oesophageal cancer cells to identify pathways and processes that are affected by bisPMB...
May 28, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28551182/identification-and-functional-analysis-of-bull-bos-taurus-cauda-epididymal-fluid-proteome
#20
B Westfalewicz, M A Dietrich, A Mostek, A Partyka, W Bielas, W Niżański, A Ciereszko
Despite recent advances in bull epididymal fluid proteome research, significant numbers of proteins secreted to epididymal lumen remain unidentified. The objective of this study was to expand the number of identified cauda epididymal fluid proteins in bulls and to contextualize them in a broader view of their mutual interactions and involvement in biological processes and pathways, to fully elucidate the ways in which epididymal fluid proteins are involved in storage and maturation of spermatozoa in epididymis...
May 24, 2017: Journal of Dairy Science
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