Microarray data analysis: from disarray to consolidation and consensus

Allison, David B.; Cui, Xiangqin; Page, Grier P.; Sabripour, Mahyar

doi:10.1038/nrg1749

Cited by 1,155 publications

(987 citation statements)

References 87 publications

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“…A typical next step involves statistical comparisons across groups of interest using either parametric or non-parametric analysis of variance. Unfortunately, there is no clear consensus as to which statistical test is most appropriate for a given data set, and it is particularly troubling that lists of 'differentially regulated genes', from the same data set, can substantially vary based on the statistical test [8,9]. Regardless of what statistical test one uses, it is imperative that the statistical test incorporates corrections for multiple comparisons to account for a substantially high risk of false positives.…”

Section: Technology Approaches and Limitationsmentioning

confidence: 99%

Clinical review: Sepsis and septic shock - the potential of gene arrays

Wong

2012

Critical Care

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Over the past decade several investigators have applied microarray technology and related bioinformatic approaches to clinical sepsis and septic shock, thus allowing for an assessment of how, or if, this branch of genomic medicine has meaningfully impacted the field of sepsis research. The ability to simultaneously and efficiently measure the steady-state mRNA abundance of thousands of transcripts from a given tissue source (that is, 'transcriptomics') has provided an unprecedented opportunity to gain a broader, genome-level 'picture' of complex and heterogeneous clinical syndromes such as sepsis. A trancriptomic approach to sepsis and septic shock is technically challenging on multiple levels, but nonetheless modest, tangible advances are being realized. These include a genome-level understanding of the complexity of sepsis and septic shock, identification of novel candidate pathways and targets for potential intervention, discovery of novel, candidate diagnostic and stratification biomarkers, and the ability to stratify patients into clinically relevant, expression-based subclasses. The challenges moving forward include robust validation studies, standardization of technical approaches, standardization and further development of analytical algorithms, and large-scale collaborations.

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Section: Technology Approaches and Limitationsmentioning

confidence: 99%

Clinical review: Sepsis and septic shock - the potential of gene arrays

Wong

2012

Critical Care

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“…34,35 False discovery rate q-values were calculated by multiplying the P-values by the number of tests performed and then dividing them by the rank order of each P-value. Rank order 1 was assigned to the smallest P-value.…”

Section: Statistical Analysesmentioning

confidence: 99%

Genetic variations in regulatory pathways of fatty acid and glucose metabolism are associated with obesity phenotypes: a population-based cohort study

et al. 2009

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Background: As nuclear receptors and transcription factors have an important regulatory function in adipocyte differentiation and fat storage, genetic variation in these key regulators and downstream pathways may be involved in the onset of obesity. Objective: To explore associations between single nucleotide polymorphisms (SNPs) in candidate genes from regulatory pathways that control fatty acid and glucose metabolism, and repeated measurements of body mass index (BMI) and waist circumference in a large Dutch study population. Methods: Data of 327 SNPs across 239 genes were analyzed for 3575 participants of the Doetinchem cohort, who were examined three times during 11 years, using the Illumina Golden Gate assay. Adjusted random coefficient models were used to analyze the relationship between SNPS and obesity phenotypes. False discovery rate q-values were calculated to account for multiple testing. Significance of the associations was defined as a q-value p0.20. Results: Two SNPs (in NR1H4 and SMARCA2 in women only) were significantly associated with both BMI and waist circumference. In addition, two SNPs (in SIRT1 and SCAP in women only) were associated with BMI alone. A functional SNP, in IL6, was strongly associated with waist. Conclusion: In this explorative study among participants of a large population-based cohort, five SNPs, mainly located in transcription mediator genes, were strongly associated with obesity phenotypes. The results from whole genome and candidate gene studies support the potential role of NR1H4, SIRT1, SMARCA2 and IL6 in obesity. Although replication of our findings and further research on the functionality of these SNPs and underlying mechanism is necessary, our data indirectly suggest a role of GATA transcription factors in weight control.

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“…With an integration method, the higher the ratio between intra-EC gene similarities and inter-EC gene similarities, the better the integration method is. Quantitatively, we utilize the logged fold change (LogFC) measure which has been widely used in the gene expression studies [31]. The LogFC score of EC ei is defined in Eq 7:…”

Section: Methodsmentioning

confidence: 99%

Towards integrative gene functional similarity measurement

2014

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BackgroundIn Gene Ontology, the "Molecular Function" (MF) categorization is a widely used knowledge framework for gene function comparison and prediction. Its structure and annotation provide a convenient way to compare gene functional similarities at the molecular level. The existing gene similarity measures, however, solely rely on one or few aspects of MF without utilizing all the rich information available including structure, annotation, common terms, lowest common parents.ResultsWe introduce a rank-based gene semantic similarity measure called InteGO by synergistically integrating the state-of-the-art gene-to-gene similarity measures. By integrating three GO based seed measures, InteGO significantly improves the performance by about two-fold in all the three species studied (yeast, Arabidopsis and human).ConclusionsInteGO is a systematic and novel method to study gene functional associations. The software and description are available at http://www.msu.edu/~jinchen/InteGO.

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Microarray data analysis: from disarray to consolidation and consensus

Cited by 1,155 publications

References 87 publications

Clinical review: Sepsis and septic shock - the potential of gene arrays

Clinical review: Sepsis and septic shock - the potential of gene arrays

Genetic variations in regulatory pathways of fatty acid and glucose metabolism are associated with obesity phenotypes: a population-based cohort study

Towards integrative gene functional similarity measurement

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