scholarly journals Malachite: A Gene Enrichment Meta-Analysis (GEM) Tool for ToppGene

2019 ◽  
Author(s):  
Gregory R. Gershkowitz ◽  
Zachary B. Abrams ◽  
Caitlin E. Coombes ◽  
Kevin R. Coombes
Keyword(s):  
Gene Expression ◽  
Meta Analysis ◽  
Nicotinamide Adenine Dinucleotide Phosphate ◽  
Gene Expression Omnibus ◽  
Data Sets ◽  
Multiple Gene ◽  
Gene Enrichment ◽  
Multiple Data ◽  
Multiple Data Sets ◽  
Approved Drugs

AbstractBackgroundResearchers commonly use online tools such as ToppGene to conduct enrichment analyses on gene expression data. This process does not easily allow multiple gene data sets to be analyzed and compared at once. ToppGene requires the user to manually enter gene symbols or other gene identifiers into a text box and to manually sift through forms with many adjustable parameters in order to obtain a downloadable text file of results. This process makes the analysis of multiple sets of genes tedious, time-consuming, and error prone. To address this problem, we developed Malachite, a Python package that enables researchers to perform gene enrichment analyses on multiple gene lists and concatenate the resulting enrichment statistics. In this way, Malachite enables meta-enrichment analyses across multiple data sets.ResultsTo illustrate its use, we applied Malachite to three data sets from the Gene Expression Omnibus comparing gene expression in the large airways of smokers and non-smokers. Biological processes enriched in all three data sets were related to xenobiotic stimulus; molecular functions typically involved nicotinamide adenine dinucleotide phosphate (NADP) activity.ConclusionMalachite enables researchers to automate gene enrichment metaanalyses using ToppGene. Malachite also enhances ToppGene’s gene set analysis of drug-gene relationships by further filtering for FDA approved drugs.

scholarly journals Horizontal meta-analysis identifies common deregulated genes across AML subgroups providing a robust prognostic signature

2020 ◽  
Vol 4 (20) ◽  
pp. 5322-5335
Author(s):  
Ali Nehme ◽  
Hassan Dakik ◽  
Frédéric Picou ◽  
Meyling Cheok ◽  
Claude Preudhomme ◽  
...  
Keyword(s):  
Gene Expression ◽  
Microarray Data ◽  
Meta Analysis ◽  
Prognostic Score ◽  
Gene Expression Omnibus ◽  
Response To Therapy ◽  
Data Sets ◽  
Dna Hypermethylation ◽  
Transcriptomic Data ◽  
Differential Gene

Abstract Advances in transcriptomics have improved our understanding of leukemic development and helped to enhance the stratification of patients. The tendency of transcriptomic studies to combine AML samples, regardless of cytogenetic abnormalities, could lead to bias in differential gene expression analysis because of the differential representation of AML subgroups. Hence, we performed a horizontal meta-analysis that integrated transcriptomic data on AML from multiple studies, to enrich the less frequent cytogenetic subgroups and to uncover common genes involved in the development of AML and response to therapy. A total of 28 Affymetrix microarray data sets containing 3940 AML samples were downloaded from the Gene Expression Omnibus database. After stringent quality control, transcriptomic data on 1534 samples from 11 data sets, covering 10 AML cytogenetically defined subgroups, were retained and merged with the data on 198 healthy bone marrow samples. Differentially expressed genes between each cytogenetic subgroup and normal samples were extracted, enabling the unbiased identification of 330 commonly deregulated genes (CODEGs), which showed enriched profiles of myeloid differentiation, leukemic stem cell status, and relapse. Most of these genes were downregulated, in accordance with DNA hypermethylation. CODEGs were then used to create a prognostic score based on the weighted sum of expression of 22 core genes (CODEG22). The score was validated with microarray data of 5 independent cohorts and by quantitative real time-polymerase chain reaction in a cohort of 142 samples. CODEG22-based stratification of patients, globally and into subpopulations of cytologically healthy and elderly individuals, may complement the European LeukemiaNet classification, for a more accurate prediction of AML outcomes.

scholarly journals Meta-analysis reveals pathway signature of Septic Shock

2016 ◽  
Author(s):  
Samanwoy Mukhopadhyay ◽  
Abhaydeep Pandey ◽  
Pravat K Thatoi ◽  
Bidyut K Das ◽  
Balachandran Ravindran ◽  
...  
Keyword(s):  
Gene Expression ◽  
Septic Shock ◽  
Human Subjects ◽  
Major Gene ◽  
Meta Analysis ◽  
Osteoclast Differentiation ◽  
Medical Problem ◽  
High Morbidity ◽  
Multiple Data ◽  
Multiple Data Sets

Septic shock is a major medical problem with high morbidity and mortality and incompletely understood biology. Availability of genome-wide expression data from different studies on septic shock empowers the quest for hitherto unidentified pathways by integration and meta-analysis of multiple data sets. Electronic search was performed on medical literature and gene expression databases. Selection of studies was based on the organism (human subjects), tissue of origin (circulating leukocytes) and the platform technology (gene expression microarray). Gene-level meta-analysis was conducted on the six selected studies to identify the genes consistently differentially expressed in septic shock. These genes were then subjected to pathway analysis. The identified up-regulated pathway hsa04380 (Osteoclast Differentiation) was validated in an independent cohort of patients. A simplified model was generated showing the major gene-modules dysregulated in SS.

The development of nurses’ foundational values

2021 ◽  
pp. 096973302110032
Author(s):  
Sastrawan Sastrawan ◽  
Jennifer Weller-Newton ◽  
Gabrielle Brand ◽  
Gulzar Malik
Keyword(s):  
Professional Training ◽  
Reference Points ◽  
Constructivist Grounded Theory ◽  
Professional Values ◽  
Data Sets ◽  
Value System ◽  
Institutional Values ◽  
Multiple Data ◽  
Human Ethics ◽  
Multiple Data Sets

Background: In the ever-changing and complex healthcare environment, nurses encounter challenging situations that may involve a clash between their personal and professional values resulting in a profound impact on their practice. Nevertheless, there is a dearth of literature on how nurses develop their personal–professional values. Aim: The aim of this study was to understand how nurses develop their foundational values as the base for their value system. Research design: A constructivist grounded theory methodology was employed to collect multiple data sets, including face-to-face focus group and individual interviews, along with anecdote and reflective stories. Participants and research context: Fifty-four nurses working across various nursing settings in Indonesia were recruited to participate. Ethical considerations: Ethics approval was obtained from the Monash University Human Ethics Committee, project approval number 1553. Findings: Foundational values acquisition was achieved through family upbringing, professional nurse education and organisational/institutional values reinforcement. These values are framed through three reference points: religious lens, humanity perspective and professionalism. This framing results in a unique combination of personal–professional values that comprise nurses’ values system. Values are transferred to other nurses either in a formal or informal way as part of one’s professional responsibility and customary social interaction via telling and sharing in person or through social media. Discussion: Values and ethics are inherently interweaved during nursing practice. Ethical and moral values are part of professional training, but other values are often buried in a hidden curriculum, and attained and activated through interactions during nurses’ training. Conclusion: Developing a value system is a complex undertaking that involves basic social processes of attaining, enacting and socialising values. These processes encompass several intertwined entities such as the sources of values, the pool of foundational values, value perspectives and framings, initial value structures, and methods of value transference.

scholarly journals Evaluation of daily precipitation statistics and monsoon onset/retreat over western Sahel in multiple data sets

2014 ◽  
Vol 45 (5-6) ◽  
pp. 1325-1354 ◽  
Author(s):  
Emilia Paula Diaconescu ◽  
Philippe Gachon ◽  
John Scinocca ◽  
René Laprise
Keyword(s):  
Daily Precipitation ◽  
Monsoon Onset ◽  
Data Sets ◽  
Multiple Data ◽  
Western Sahel ◽  
Multiple Data Sets

Can earning much lead to doing good? Firm performance implications for corporate social responsibility

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Siyu Hou ◽  
Zhaoyang Guo ◽  
Chuangneng Cai ◽  
Xiaobo Jiao
Keyword(s):  
Corporate Social Responsibility ◽  
Firm Performance ◽  
Social Responsibility ◽  
State Ownership ◽  
Data Sets ◽  
Content Type ◽  
Multiple Data ◽  
Instrumental Variable Regression ◽  
Multiple Data Sets ◽  
Corporate Social

Purpose The purpose of this study is to examine the influence of firm performance on corporate social responsibility (CSR) and its possible moderating effect. Despite the significance of CSR, there remains an extensive debate about how it is affected by firm performance. Design/methodology/approach The conceptual model is mainly built on goal-setting theory. Based on archival data from multiple data sets on 1,650 companies, collected from 2010 to 2017, the hypotheses are tested using the two-stage instrumental variable regression method. Findings There is an inverted U-shaped relationship between firm performance and CSR that first increases and then decreases. In addition, considering the boundary conditions, state ownership makes the inverted U-shaped curve steeper, while high executive wage concentration makes the inverted U-shaped curve flatter. Research limitations/implications This study harmonizes the traditional contradictory findings of the influence of firm performance on CSR, that is, it supports a positive, negative or neutral relationship between the two. Originality/value This research provides a necessary structure for the CSR literature. By delving deeply into the relationship between firm performance and CSR, it enables scholars to better address the critical management question of whether earning more will lead to doing good.

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