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  • Ray G. Butler

Data Exploration In Biomedical Research

By means of this “dynamic” article, we would like to share with you the most interesting and/or promising approaches to the use of EDA techniques we come across with in our daily surveillance of the matter.

Since we started up with Butler Scientifics, the number of scientific publications and clinical trials underlying the increasingly relevant role of Exploratory Data Analysis (EDA) in their studies has grown substantially.

For us this trend is both encouraging and challenging. It is encouraging as it means scientists are becoming more comfortable at relying on exploratory analysis, while it is challenging for the rising number of dimensions and new approaches that come to light every day, opening paths that need to be taken care of.

Jul 2019, Sports, Cannabis Use, PEACE Survey, Clustering, Exploratory Factor Analysis

"The Athlete PEACE Survey examined cannabis use patterns and subjective effects to cannabis in a community-based cohort of adult athletes. Cluster analysis was used to determine cannabis user phenotypes and exploratory factor analysis (EFA) was used to create subjective effects factors. Associations between cannabis user phenotype clusters and the subjective effects factors were explored using multivariate analysis. "

Jun 2019, Mendelian Diseases, Variant Combinations, ORVAL Study, Integrative Machine Learning

"This online platform integrates innovative machine learning methods for combinatorial variant pathogenicity prediction with visualization techniques, offering several interactive and exploratory tools, such as pathogenic gene and protein interaction networks, a ranking of pathogenic gene pairs, as well as visual mappings of the cellular location and pathway information."

Jun 2018, Psychology, Sleep Quality, Questionnaires, Exploratory Factor Analysis

"The objective was to shorten the Pittsburgh Quality Sleep Index (PSQI) for young adults. Nonparametric correlation analysis (Spearman's rho) was conducted between the global sleep scores of the shortened and original surveys."

(HIGH IMPACT) May 2018, Oncology, HER2-Negative Advanced Breast Cancer, Exploratory Biomarker Analysis

"Here we report updated efficacy and safety data, together with exploratory biomarker analyses, from the MONALEESA-2 study."

(HIGH IMPACT) Apr 2018, Oncology, Colorectal Cancer, Electronic Medical Records

"We conducted an exploratory post-hoc analysis of RAISE trial and a retrospective, observational analysis of electronic medical record (EMR) data to determine and verify the association of neutropaenia, baseline absolute neutrophil count (ANC) and survival."

Mar 2018, Cardiology, Hypertension, Correlational Analysis

"We explored the relationship of sample size, trial duration, baseline blood pressure, and number of treatment arms to placebo/drug response and efficacy outcome measures."

Feb 2018, Neuroscience, Dementia, Edinburgh Feeding Evaluation (EdFED), Exploratory Factor Analysis

"A version of EdFED culturally adapted to Spanish was obtained. An additional three-factor structure was tested using an exploratory factorial analysis performed with a subsample that was later verified by confirmatory factor analysis in the remaining sample."

Jan 2018, Hematology, Genetics, Activation-induced deaminase (AID), Machine Learning

"Integrative analysis of the molecular features of mutated genes coupled to machine learning has produced a powerful predictive tool for AID targets."

Dec 2017, Hematology, Mantle Cell Lymphoma, Subgroup Analysis

"Here we present the long-term follow-up data and results of preplanned subgroup exploratory analyses to evaluate the potential impact of demographic factors, baseline clinical characteristics and prior therapies on PFS."

Nov 2017, Chronic Pain, Adverse Events, Data Mining

"We used the US FDA's Adverse Events Reporting System (FAERS) database to conduct exploratory analysis on the demographics of those who reported painkiller-related AEs, examine the AEs most commonly associated with different types of painkillers, and identify potential safety signals."

Oct 2017, Neuroscience, Huntington's Disease, Linear Regression

"This exploratory study aimed to evaluate, for the first time, whether multidisciplinary rehabilitation can slow further deterioration of disease-related brain changes and related cognitive deficits in individuals with manifest Huntington's Disease."

Sept 2017, Oncology, Glioblastoma, Clinical Trial, Exploratory Efficacy

"The exploratory objective of this study was to evaluate expression of factors associated with tumor angiogenesis using a multiples cytokine assay among participants undergoing therapy with AMG 386 with response to therapy and development of resistance."

(HIGH IMPACT) Jul 2017, Neurology, Acute Stroke, Efficacy Analysis

"Our aim was to test for a treatment-by-ipsilateral atherosclerotic stenosis interaction in a subgroup analysis of patients in the Acute Stroke or Transient Ischaemic Attack Treated with Aspirin or Ticagrelor and Patient Outcomes (SOCRATES) trial."

(HIGH IMPACT) Jun 2017, Oncology, AKT1 Mutations, Predictive Biomarkers, Survival Analysis

"In an exploratory biomarker analysis, imbalance of the AKT1 E17K-mutant allele ... was associated with longer progression-free survival as was the presence of coincident PI3K pathway hotspot mutations.

This study provides the first clinical data that AKT1 E17K is a therapeutic target in human cancer."

(HIGH IMPACT) May 2017, Oncology, Non-Small-Cell Lung Cancer, Phase II Trial

"This article reports the results from the phase II of AURA project, a study that treats patients with advanced NSCLC who have already received at least one course of specific anti-cancer treatment but the tumour has started to re-grow following that treatment.

Patient-reported outcomes comprised an exploratory objective..."

(HIGH IMPACT) May 2017, Cardiology, Migraine, Ischemic Stroke, Multivariable Logistic Regression

"The objective of this study is to evaluate whether patients with migraine are at increased risk of perioperative ischemic stroke and whether this may lead to an increased hospital readmission rate.

Exploratory outcomes included post-discharge stroke and strata of neuroanatomical stroke location."

(HIGH IMPACT) May 2017, Oncology, Epidermal Growth Factor Receptor, Cox Regression

"We performed an individual patient data meta-analysis to examine the impact of first-generation epidermal growth factor receptor (EGFR tyrosine kinase inhibitor (TKI) therapy on overall survival (OS) in advanced non-small cell lung cancer (NSCLC)."

Apr 2017, Burns, Scarring, POSAS, Exploratory-Confirmatory Design

"Exploratory Factor Analysis was used initially to identify the number of factors within the tool, then Confirmatory Factor Analysis using structural equation modelling explored areas of misfit within each factor and whether the model provided a predictable structure to capture patient perception of scar severity."

(HIGH IMPACT) Mar 2017, Chemistry, Materials Genome Initiative, Machine Learning, Integrated Analysis

"We used information on 'dark' reactions collected from archived laboratory notebooks from our laboratory, and added physicochemical property descriptions using cheminformatics techniques.

We used the resulting data to train a machine-learning model to predict reaction success."

(HIGH IMPACT) Feb 2017, Oncology, Palliative Care, PCA, Exploratory Factor Analysis

"This is the largest quantitative study ever done looking at perceptions of palliative care provision among health professionals.

Principal components analysis, exploratory factor analysis, and logistic regression were performed to examine the factor structure and relationship to clinical practice."

Jan 2017, Cardiology, Pulmonary Artery Pressure, Comparison Study, Correlative Analysis

"A post hoc analysis of prospectively collected hemodynamic data was performed, examining correlations between Inferior Vena Cava Collapsibility Index (IVC-CI) and PAPs in a convenience sample of adult Surgical Intensive Care Unit patients."

Dec 2016, Cardiology, Ischemia, CHAMPION Trials, Exploratory Pooled Analysis

"In this exploratory pooled analysis of individual patient-level data from the 3 CHAMPION trials we compared ischemic and bleeding risks in patients assigned to Cangrelor with patients Clopidogrel.

Based on our PS-matched analysis, cangrelor may offer an alternative potent, parenteral strategy to GPIs with a favorable bleeding profile in PCI."

Nov 2016, Genetics, Stem Cells, Prediction

"We examined whether social environment affects expression of a stress-related gene expression profile.

A post hoc exploratory analysis suggests that low socioeconomic status is associated with increased expression of the CTRA gene profile (conserved transcriptional response to adversity), and CTRA gene expression is associated with adverse hematopoietic stem cell transplant clinical outcomes."

Oct 2016, Neurosciences, Schizophrenia, fMRI, Neural Correlates

"This study examined the extent to which the core neural system of mental state attribution is involved in mental state attribution.

An exploratory whole brain analysis suggests that while schizophrenia patients rely on the same neural network as controls do when attributing beliefs of others, patients did not show reduced activation in the key regions."

Aug 2016, Genetics, Ulcerative Colitis, Complex Data

"The aim of this project was to identify the genetic predictors of benign Ulcerative Colitis phenotype.

The rs11742570 variant on chromosome 5 was the one with the greatest association to benign disease although the association did not reach the predefined significant threshold."

Jul 2016, Orthostatic Tremor, fMRI, Network Connectivity

"In this exploratory study, we observed selective impairments of resting-state networks intrinsic functional connectivity in orthostatic tremor (OT) patients.

This and other future resting-state fMRI studies might provide a novel method to understand the pathophysiological mechanisms of motor and nonmotor features of OT."

Jun 2016, RNA Seq, Glimma, EdgeR, Linear Modelling, Empirical Bayes

"In this workflow article, we analyse RNA-sequencing data from the mouse mammary gland, demonstrating use of the popular edgeR package to import, organise, filter and normalise the data, followed by the limma package with its voom method, linear modelling and empirical Bayes moderation to assess differential expression and perform gene set testing."

May 2016, Virology, Cytomegalovirus, Metabolomics Multivariate Analysis, Network Mapping

"The aim of this study was to evaluate the metabolic profile in amniotic fluid samples obtained from HCMV-infected, and uninfected fetuses in order to elucidate changes in metabolic pathways during congenital HCMV infection and to recognize new potential diagnostic and/or prognostic biomarkers.

One of the key conclusions is that metabolomics may be a promising tool to improve the accuracy of an early diagnosis, and the management of HCMV pregnancy-related infections."

(HIGH IMPACT) Apr 2016, Oncology, Breast Cancer, Exploratory Biomarker Analysis

"The current analysis aimed to identify biomarkers to predict the clinical efficacy of everolimus treatment.

Although exploratory, this analysis suggests that patients with human epidermal growth factor receptor 2-positive advanced breast cancer having tumors with PIK3CA mutations, PTEN loss, or hyperactive PI3K pathway could derive PFS benefit from everolimus."

Mar 2016, Chemistry, Wastewater, Principal Component Analysis

"The study presents a novel approach for exploratory analysis of a comprehensive water chemistry dataset, incorporating principal components analysis (PCA) and partial least squares (PLS) regressions.

The methodologies presented in this study are applicable to a wide range of natural and engineered systems."

Feb 2016, Psychiatry/Psychology, Cannabis, Regression Models

"Researchers performed an observational study with exploratory analysis to investigate whether cannabis use is associated with increased risk of relapse (number of hospital admissions) and whether antipsychotic treatment failure (number of antipsychotics prescribed) may mediate this effect.

This is the largest known study (over 2000 participants) to investigate the association of cannabis use with clinical outcome in people with first episode psychosis."

Jan 2016, Health Care, Elderly, Multivariate Analysis

"No formal definition for the "complex elderly" exists; moreover, these older patients with high levels of multi-morbidity are not readily identified as such at point of hospitalisation. By using exploratory analysis authors identified multi-morbidity groups based on 20 target conditions whose hospital prevalence was ≥ 1%. "

Dec 2015, Oncology, Fission Yeast, Data Integration

"AnGeLi (Analysis of Gene Lists) is an intuitive, integrated web-tool for comprehensive and customized interrogation of gene lists from the fission yeast. AnGeLi searches for significant enrichments among multiple qualitative and quantitative information sources. The tool offers a rigorous yet flexible statistical analysis platform for rich insights into functional enrichments and biological context for query gene lists, thus providing a powerful exploratory tool"

Nov 2015, Health Care, Quality of Life, Confirmatory & Exploratory Analysis

"The study aim was to confirm the factorial structure of the short (14 item) version of the ChronIc Venous Insufficiency quality of life Questionnaire (CIVIQ-14) using the Vein Consult Program (VCP) results. The factorial structure of the questionnaire was evaluated using two methods: exploratory data analysis (EDA) to calculate the probabilities of items and dimensions remaining stable and to study the dimensionality of the scale using explained variance criteria, followed by confirmatory data analysis (CDA) to confirm the original three dimensional structure and investigate alternative models that may have arisen from the dimensionality analysis.."

Oct 2015, Pediatrics, Anti-Inflammatory, Descriptive EDA

"This study was aimed to determine the frequency of prescription of these drugs according to the best scientific evidence and use approved by regulatory agencies.The authors chose to perform an exploratory, descriptive study aiming to identify, record, and analyze the characteristics to generate a hypothesis about the criteria used in pediatric prescription of analgesic, antipyretic, and NSAIDs."

Sept 2015, Oncology, Colorectal Cancer, Correlation, Multivariate Analysis

"Tumoral heterogeneity is a major determinant of resistance in solid tumors. FDG-PET/CT can identify early during chemotherapy non-responsive lesions within the whole body tumor load. This prospective multicentric proof-of-concept study explores intra-individual metabolic response (mR) heterogeneity as a treatment efficacy biomarker in chemorefractory metastatic colorectal cancer (mCRC)."

Aug 2015, Obesity, Physical Disabilities, Correlation

"The purposes of this study were to assess the accuracy of clinical measures for predictingadiposity when compared with a criterion standard of body fat percentage measured by dual-energy X-ray absorptiometry and to determine the most appropriate cut points for classifying obesity for each measure in adolescents with physical disability. Clinical measures correlated with body fat as measured by dual-energy X-ray absorptiometry."

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