GeneTide--Terra Incognita Discovery Endeavor: a new transcriptome focused member of the GeneCards/GeneNote suite of databases

Shklar, Maxim; Strichman-Almashanu, Liora Z.; Shmueli, Orit; Shmoish, Michael; Lancet, Doron

doi:10.1093/nar/gki122

Cited by 12 publications

(9 citation statements)

References 14 publications

(15 reference statements)

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“… 35 KCTD2 expression is ubiquitous according to GeneNote. 36 However, the highest levels of expression are noted in the cerebral cortex and cerebellum.…”

Section: Discussionmentioning

confidence: 99%

ATP5H/KCTD2 locus is associated with Alzheimer's disease risk

et al. 2013

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To identify loci associated with Alzheimer disease, we conducted a three-stage analysis using existing genome-wide association studies (GWAS) and genotyping in a new sample. In Stage I, all suggestive single-nucleotide polymorphisms (at P<0.001) in a previously reported GWAS of seven independent studies (8082 Alzheimer's disease (AD) cases; 12 040 controls) were selected, and in Stage II these were examined in an in silico analysis within the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium GWAS (1367 cases and 12904 controls). Six novel signals reaching P<5 × 10−6 were genotyped in an independent Stage III sample (the Fundació ACE data set) of 2200 sporadic AD patients and 2301 controls. We identified a novel association with AD in the adenosine triphosphate (ATP) synthase, H+ transporting, mitochondrial F0 (ATP5H)/Potassium channel tetramerization domain-containing protein 2 (KCTD2) locus, which reached genome-wide significance in the combined discovery and genotyping sample (rs11870474, odds ratio (OR)=1.58, P=2.6 × 10−7 in discovery and OR=1.43, P=0.004 in Fundació ACE data set; combined OR=1.53, P=4.7 × 10−9). This ATP5H/KCTD2 locus has an important function in mitochondrial energy production and neuronal hyperpolarization during cellular stress conditions, such as hypoxia or glucose deprivation.

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“… 35 KCTD2 expression is ubiquitous according to GeneNote. 36 However, the highest levels of expression are noted in the cerebral cortex and cerebellum.…”

Section: Discussionmentioning

confidence: 99%

ATP5H/KCTD2 locus is associated with Alzheimer's disease risk

et al. 2013

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“…Furthermore, we checked whether our method could predict novel susceptibility genes that have been identified only recently. We found 63 genes (Additional file 1 : Table S1) suggested as disease genes and 28 genes reported to cause obesity or fatty liver annotated by DAVID [ 47 ] and GeneCards [ 48 ]. Taking genes LEP and NPY as examples, gene LEP was ranked 4th and gene NPY 6th in our prediction.…”

Section: Resultsmentioning

confidence: 99%

Integrating human omics data to prioritize candidate genes

Chen

Jiang

2013

BMC Med Genomics

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BackgroundThe identification of genes involved in human complex diseases remains a great challenge in computational systems biology. Although methods have been developed to use disease phenotypic similarities with a protein-protein interaction network for the prioritization of candidate genes, other valuable omics data sources have been largely overlooked in these methods.MethodsWith this understanding, we proposed a method called BRIDGE to prioritize candidate genes by integrating disease phenotypic similarities with such omics data as protein-protein interactions, gene sequence similarities, gene expression patterns, gene ontology annotations, and gene pathway memberships. BRIDGE utilizes a multiple regression model with lasso penalty to automatically weight different data sources and is capable of discovering genes associated with diseases whose genetic bases are completely unknown.ResultsWe conducted large-scale cross-validation experiments and demonstrated that more than 60% known disease genes can be ranked top one by BRIDGE in simulated linkage intervals, suggesting the superior performance of this method. We further performed two comprehensive case studies by applying BRIDGE to predict novel genes and transcriptional networks involved in obesity and type II diabetes.ConclusionThe proposed method provides an effective and scalable way for integrating multi omics data to infer disease genes. Further applications of BRIDGE will be benefit to providing novel disease genes and underlying mechanisms of human diseases.

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“…When TissueInfo is used to process a collection of known or predicted transcripts from a genome project, the tissue expression profiles of the transcript are unambiguously linked to all the annotations maintained by the genome database about these transcripts. Linking EST clusters to genomic information is possible, but requires non-trivial data integration ( 46 ). The TissueInfo web site offers tissue expression profiles calculated from Ensembl cDNAs that can be used directly for gene discovery.…”

Section: Discussionmentioning

confidence: 99%

Beyond tissueInfo: functional prediction using tissue expression profile similarity searches

Aguilar

Skrabanek

Gross

et al. 2008

Nucleic Acids Research

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We present and validate tissue expression profile similarity searches (TEPSS), a computational approach to identify transcripts that share similar tissue expression profiles to one or more transcripts in a group of interest. We evaluated TEPSS for its ability to discriminate between pairs of transcripts coding for interacting proteins and non-interacting pairs. We found that ordering protein–protein pairs by TEPSS score produces sets significantly enriched in reported pairs of interacting proteins [interacting versus non-interacting pairs, Odds-ratio (OR) = 157.57, 95% confidence interval (CI) (36.81–375.51) at 1% coverage, employing a large dataset of about 50 000 human protein interactions]. When used with multiple transcripts as input, we find that TEPSS can predict non-obvious members of the cytosolic ribosome. We used TEPSS to predict S-nitrosylation (SNO) protein targets from a set of brain proteins that undergo SNO upon exposure to physiological levels of S-nitrosoglutathione in vitro. While some of the top TEPSS predictions have been validated independently, several of the strongest SNO TEPSS predictions await experimental validation. Our data indicate that TEPSS is an effective and flexible approach to functional prediction. Since the approach does not use sequence similarity, we expect that TEPSS will be useful for various gene discovery applications. TEPSS programs and data are distributed at http://icb.med.cornell.edu/crt/tepss/index.xml.

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GeneTide--Terra Incognita Discovery Endeavor: a new transcriptome focused member of the GeneCards/GeneNote suite of databases

Cited by 12 publications

References 14 publications

ATP5H/KCTD2 locus is associated with Alzheimer's disease risk

ATP5H/KCTD2 locus is associated with Alzheimer's disease risk

Integrating human omics data to prioritize candidate genes

Beyond tissueInfo: functional prediction using tissue expression profile similarity searches

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