Dataset Information

GeneRank: using search engine technology for the analysis of microarray experiments.

ABSTRACT:

Background

Interpretation of simple microarray experiments is usually based on the fold-change of gene expression between a reference and a "treated" sample where the treatment can be of many types from drug exposure to genetic variation. Interpretation of the results usually combines lists of differentially expressed genes with previous knowledge about their biological function. Here we evaluate a method--based on the PageRank algorithm employed by the popular search engine Google--that tries to automate some of this procedure to generate prioritized gene lists by exploiting biological background information.

Results

GeneRank is an intuitive modification of PageRank that maintains many of its mathematical properties. It combines gene expression information with a network structure derived from gene annotations (gene ontologies) or expression profile correlations. Using both simulated and real data we find that the algorithm offers an improved ranking of genes compared to pure expression change rankings.

Conclusion

Our modification of the PageRank algorithm provides an alternative method of evaluating microarray experimental results which combines prior knowledge about the underlying network. GeneRank offers an improvement compared to assessing the importance of a gene based on its experimentally observed fold-change alone and may be used as a basis for further analytical developments.

SUBMITTER: Morrison JL

PROVIDER: S-EPMC1261158 | biostudies-literature | 2005 Sep

REPOSITORIES: biostudies-literature

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Publications

GeneRank: using search engine technology for the analysis of microarray experiments.

Morrison Julie L JL Breitling Rainer R Higham Desmond J DJ Gilbert David R DR

BMC bioinformatics 20050921

<h4>Background</h4>Interpretation of simple microarray experiments is usually based on the fold-change of gene expression between a reference and a "treated" sample where the treatment can be of many types from drug exposure to genetic variation. Interpretation of the results usually combines lists of differentially expressed genes with previous knowledge about their biological function. Here we evaluate a method--based on the PageRank algorithm employed by the popular search engine Google--that ...[more]

PMID: 16176585

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Project description:BackgroundTobacco smoking is an important public health issue and a core indicator of public health policy worldwide. However, global pandemics and natural disasters have prevented surveys from being conducted.ObjectiveThe purpose of this study was to predict smoking prevalence by prefecture and sex in Japan using Internet search trends.MethodsThis study used the infodemiology approach. The outcome variable was smoking prevalence by prefecture, obtained from national surveys. The predictor variables were the search volumes on Yahoo! Japan Search. We collected the search volumes for queries related to terms from the thesaurus of the Japanese medical article database Ichu-shi. Predictor variables were converted to per capita values and standardized as z scores. For smoking prevalence, the values for 2016 and 2019 were used, and for search volume, the values for the April 1 to March 31 fiscal year (FY) 1 year prior to the survey (ie, FY 2015 and FY 2018) were used. Partial correlation coefficients, adjusted for data year, were calculated between smoking prevalence and search volume, and a regression analysis using a generalized linear mixed model with random effects was conducted for each prefecture. Several models were tested, including a model that included all search queries, a variable reduction method, and one that excluded cigarette product names. The best model was selected with the Akaike information criterion corrected (AICC) for small sample size and the Bayesian information criterion (BIC). We compared the predicted and actual smoking prevalence in 2016 and 2019 based on the best model and predicted the smoking prevalence in 2022.ResultsThe partial correlation coefficients for men showed that 9 search queries had significant correlations with smoking prevalence, including cigarette (r=-0.417, P<.001), cigar in kanji (r=-0.412, P<.001), and cigar in katakana (r=-0.399, P<.001). For women, five search queries had significant correlations, including vape (r=0.335, P=.001), quitting smoking (r=0.288, P=.005), and cigar (r=0.286, P=.006). The models with all search queries were the best models for both AICC and BIC scores. Scatter plots of actual and estimated smoking prevalence in 2016 and 2019 confirmed a relatively high degree of agreement. The average estimated smoking prevalence in 2022 in the 47 prefectures for the total sample was 23.492% (95% CI 21.617%-25.367%), showing an increasing trend, with an average of 29.024% (95% CI 27.218%-30.830%) for men and 8.793% (95% CI 7.531%-10.054%) for women.ConclusionsThis study suggests that the search volume of tobacco-related queries in internet search engines can predict smoking prevalence by prefecture and sex in Japan. These findings will enable the development of low-cost, timely, and crisis-resistant health indicators that will enable the evaluation of health measures and contribute to improved public health.

Dataset Information

GeneRank: using search engine technology for the analysis of microarray experiments.

Background

Results

Conclusion

Publications

GeneRank: using search engine technology for the analysis of microarray experiments.

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