A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases <s> Challenges of Validation <s> The identification of genes involved in health and disease remains a challenge. We describe a bioinformatics approach, together with a freely accessible, interactive and flexible software termed Endeavour, to prioritize candidate genes underlying biological processes or diseases, based on their similarity to known genes involved in these phenomena. Unlike previous approaches, ours generates distinct prioritizations for multiple heterogeneous data sources, which are then integrated, or fused, into a global ranking using order statistics. In addition, it offers the flexibility of including additional data sources. Validation of our approach revealed it was able to efficiently prioritize 627 genes in disease data sets and 76 genes in biological pathway sets, identify candidates of 16 mono- or polygenic diseases, and discover regulatory genes of myeloid differentiation. Furthermore, the approach identified a novel gene involved in craniofacial development from a 2-Mb chromosomal region, deleted in some patients with DiGeorgelike birth defects. The approach described here offers an alternative integrative method for gene discovery. <s> BIB001 </s> A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases <s> Challenges of Validation <s> The identification of genes associated with hereditary disorders has contributed to improving medical care and to a better understanding of gene functions, interactions, and pathways. However, there are well over 1500 Mendelian disorders whose molecular basis remains unknown. At present, methods such as linkage analysis can identify the chromosomal region in which unknown disease genes are located, but the regions could contain up to hundreds of candidate genes. In this work, we present a method for prioritization of candidate genes by use of a global network distance measure, random walk analysis, for definition of similarities in protein-protein interaction networks. We tested our method on 110 disease-gene families with a total of 783 genes and achieved an area under the ROC curve of up to 98% on simulated linkage intervals of 100 genes surrounding the disease gene, significantly outperforming previous methods based on local distance measures. Our results not only provide an improved tool for positional-cloning projects but also add weight to the assumption that phenotypically similar diseases are associated with disturbances of subnetworks within the larger protein interactome that extend beyond the disease proteins themselves. <s> BIB002 </s> A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases <s> Challenges of Validation <s> Finding the most promising genes among large lists of candidate genes has been defined as the gene prioritization problem. It is a recurrent problem in genetics in which genetic conditions are reported to be associated with chromosomal regions. In the last decade, several different computational approaches have been developed to tackle this challenging task. In this study, we review 19 computational solutions for human gene prioritization that are freely accessible as web tools and illustrate their differences. We summarize the various biological problems to which they have been successfully applied. Ultimately, we describe several research directions that could increase the quality and applicability of the tools. In addition we developed a website (http://www.esat.kuleuven.be/gpp) containing detailed information about these and other tools, which is regularly updated. This review and the associated website constitute together a guide to help users select a gene prioritization strategy that suits best their needs. <s> BIB003 </s> A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases <s> Challenges of Validation <s> Various studies (such as genetic linkage or 'omics'-based approaches) generate large lists of candidate genes, of which only a minority may be biologically relevant for a phenotype or disease of interest. This Review discusses computational tools for gene prioritization, emphasizing key considerations for how biologists can incorporate these tools into their research, and it includes hands-on tutorials. <s> BIB004 </s> A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases <s> Challenges of Validation <s> Motivation: Gene prioritization aims at identifying the most promising candidate genes among a large pool of candidates—so as to maximize the yield and biological relevance of further downstream validation experiments and functional studies. During the past few years, several gene prioritization tools have been defined, and some of them have been implemented and made available through freely available web tools. In this study, we aim at comparing the predictive performance of eight publicly available prioritization tools on novel data. We have performed an analysis in which 42 recently reported disease-gene associations from literature are used to benchmark these tools before the underlying databases are updated. ::: ::: Results: Cross-validation on retrospective data provides performance estimate likely to be overoptimistic because some of the data sources are contaminated with knowledge from disease-gene association. Our approach mimics a novel discovery more closely and thus provides more realistic performance estimates. There are, however, marked differences, and tools that rely on more advanced data integration schemes appear more powerful. ::: ::: Contact: yves.moreau@esat.kuleuven.be ::: ::: Supplementary information: Supplementary data are available at Bioinformatics online. <s> BIB005 </s> A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases <s> Challenges of Validation <s> Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report the results from the first large-scale community-based critical assessment of protein function annotation (CAFA) experiment. Fifty-four methods representing the state of the art for protein function prediction were evaluated on a target set of 866 proteins from 11 organisms. Two findings stand out: (i) today's best protein function prediction algorithms substantially outperform widely used first-generation methods, with large gains on all types of targets; and (ii) although the top methods perform well enough to guide experiments, there is considerable need for improvement of currently available tools. <s> BIB006 </s> A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases <s> Challenges of Validation <s> Recent advances in genetics have spurred rapid progress towards the systematic identification of genes involved in complex diseases. Still, the detailed understanding of the molecular and physiological mechanisms through which these genes affect disease phenotypes remains a major challenge. Here, we identify the asthma disease module, i.e. the local neighborhood of the interactome whose perturbation is associated with asthma, and validate it for functional and pathophysiological relevance, using both computational and experimental approaches. We find that the asthma disease module is enriched with modest GWAS P-values against the background of random variation, and with differentially expressed genes from normal and asthmatic fibroblast cells treated with an asthma-specific drug. The asthma module also contains immune response mechanisms that are shared with other immune-related disease modules. Further, using diverse omics (genomics, gene-expression, drug response) data, we identify the GAB1 signaling pathway as an important novel modulator in asthma. The wiring diagram of the uncovered asthma module suggests a relatively close link between GAB1 and glucocorticoids (GCs), which we experimentally validate, observing an increase in the level of GAB1 after GC treatment in BEAS-2B bronchial epithelial cells. The siRNA knockdown of GAB1 in the BEAS-2B cell line resulted in a decrease in the NFkB level, suggesting a novel regulatory path of the pro-inflammatory factor NFkB by GAB1 in asthma. <s> BIB007 </s> A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases <s> Challenges of Validation <s> Motivation: Genome‐wide association studies have identified thousands of loci associated with human disease, but identifying the causal genes at these loci is often difficult. Several methods prioritize genes most likely to be disease causing through the integration of biological data, including protein‐protein interaction and phenotypic data. Data availability is not the same for all genes however, potentially influencing the performance of these methods. Results: We demonstrate that whilst disease genes tend to be associated with greater numbers of data, this may be at least partially a result of them being better studied. With this observation we develop PhenoRank, which prioritizes disease genes whilst avoiding being biased towards genes with more available data. Bias is avoided by comparing gene scores generated for the query disease against gene scores generated using simulated sets of phenotype terms, which ensures that differences in data availability do not affect the ranking of genes. We demonstrate that whilst existing prioritization methods are biased by data availability, PhenoRank is not similarly biased. Avoiding this bias allows PhenoRank to effectively prioritize genes with fewer available data and improves its overall performance. PhenoRank outperforms three available prioritization methods in cross‐validation (PhenoRank area under receiver operating characteristic curve [AUC]=0.89, DADA AUC = 0.87, EXOMISER AUC = 0.71, PRINCE AUC = 0.83, P < 2.2 × 10−16). Availability and implementation: PhenoRank is freely available for download at https://github.com/alexjcornish/PhenoRank. Supplementary information: Supplementary data are available at Bioinformatics online. <s> BIB008 </s> A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases <s> Challenges of Validation <s> Motivation Computational gene prioritization can aid in disease gene identification. Here, we propose pBRIT (prioritization using Bayesian Ridge regression and Information Theoretic model), a novel adaptive and scalable prioritization tool, integrating Pubmed abstracts, Gene Ontology, Sequence similarities, Mammalian and Human Phenotype Ontology, Pathway, Interactions, Disease Ontology, Gene Association database and Human Genome Epidemiology database, into the prediction model. We explore and address effects of sparsity and inter‐feature dependencies within annotation sources, and the impact of bias towards specific annotations. Results pBRIT models feature dependencies and sparsity by an Information‐Theoretic (data driven) approach and applies intermediate integration based data fusion. Following the hypothesis that genes underlying similar diseases will share functional and phenotype characteristics, it incorporates Bayesian Ridge regression to learn a linear mapping between functional and phenotype annotations. Genes are prioritized on phenotypic concordance to the training genes. We evaluated pBRIT against nine existing methods, and on over 2000 HPO‐gene associations retrieved after construction of pBRIT data sources. We achieve maximum AUC scores ranging from 0.92 to 0.96 against benchmark datasets and of 0.80 against the time‐stamped HPO entries, indicating good performance with high sensitivity and specificity. Our model shows stable performance with regard to changes in the underlying annotation data, is fast and scalable for implementation in routine pipelines. Availability and implementation http://biomina.be/apps/pbrit/; https://bitbucket.org/medgenua/pbrit. <s> BIB009
Many methods reduce gene prioritization problem to the problem of finding genes most similar to seed genes and thus the result may strongly depend on seed gene selection. Nevertheless, no universal rule on seed selection exists, and the choice of seeds is usually made subjectively. Expert decisions on optimal number of seed genes vary from several to dozens BIB003 , BIB004 , BIB005 or even over a hundred BIB007 . However, since seed genes must have a proven role in the disease, for monogenic and oligogenic disorders only one or few such genes exist. Consequently, for these diseases, the methods accepting disease terms and analyzing gene-disease associations bypassing seed genes, e.g. via phenotype similarities are more suitable. In turn, multifactorial disorders have many associations of various confidence and power, but by no means all are causal. Furthermore, none of the multifactorial disorders are fully explained, therefore gold standard datasets may be incomplete or contain false associations and therefore give uncertain performance estimates. Finally, if no evidence of association between a gene and a complex disease found, we still cannot be sure whether this gene is a true negative indeed, due to the incompleteness of current knowledge. At the same time with a lack of reliable ground truth, there are two issues related to the oversupply of biomedical knowledge and its rapid and non-uniform growth. The first problem also referred to as knowledge bias BIB001 , BIB002 is that well-characterized genes have a better chance to be ranked higher than unannotated ones, only because they have more connections with other biological entities. This effect can be at least partially eliminated by including large-scale experimental data  e.g. whole interactome, co-expression network or the results of GWAS. Cornish et al. BIB008 suggest an elegant way to reduce the effect of knowledge bias on gene ranking. They developed PhenoRank, which computes empirical p-values for each gene score, comparing scores obtained on the real disease with scores for the same genes, prioritized for simulated sets of phenotype terms. This improvement allowed PhenoRank outperforming three other gene prioritization tools BIB008 . Another problem concerning the reliability of benchmark results is a possible uncontrolled inclusion of testing associations into evidence sources, leading to overestimation of the actual performance of the tool. Tranchevent et al.  proposed to adopt the methodology BIB006 termed time-stamped benchmark, in order to reduce this "knowledge contamination". They saved novel gene-disease association predictions made at the beginning of 2013 and checked which of them were published during the next 2 years. Although in some works researchers apply time-stamped benchmark  , BIB009 , while reducing "knowledge contamination", it excludes from the validation cohort the most reliable and well-studied associations, which may also result in a biased performance estimate.