JavaStat: a Java/R-based statistical computing environment

Harner, E. James; Luo, Dajie; Tan, Jun

doi:10.1007/s00180-008-0131-y

Cited by 7 publications

(4 citation statements)

References 1 publication

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“…Associations were deemed significant at BH<0.20 [50] , [51] . Linear regression was done using the javastat package [52] in Java. False Discovery Rate analysis was done using the multtest package [53] in the R statistical environment [54] .…”

Section: Methodsmentioning

confidence: 99%

Post-GWAS Functional Characterization of Susceptibility Variants for Chronic Lymphocytic Leukemia

et al. 2012

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Recent genome-wide association studies (GWAS) have identified several gene variants associated with sporadic chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL). Many of these CLL/SLL susceptibility loci are located in non-coding or intergenic regions, posing a significant challenge to determine their potential functional relevance. Here, we review the literature of all CLL/SLL GWAS and validation studies, and apply eQTL analysis to identify putatively functional SNPs that affect gene expression that may be causal in the pathogenesis of CLL/SLL. We tested 12 independent risk loci for their potential to alter gene expression through cis-acting mechanisms, using publicly available gene expression profiles with matching genotype information. Sixteen SNPs were identified that are linked to differential expression of SP140, a putative tumor suppressor gene previously associated with CLL/SLL. Three additional SNPs were associated with differential expression of DACT3 and GNG8, which are involved in the WNT/β-catenin- and G protein-coupled receptor signaling pathways, respectively, that have been previously implicated in CLL/SLL pathogenesis. Using in silico functional prediction tools, we found that 14 of the 19 significant eQTL SNPs lie in multiple putative regulatory elements, several of which have prior implications in CLL/SLL or other hematological malignancies. Although experimental validation is needed, our study shows that the use of existing GWAS data in combination with eQTL analysis and in silico methods represents a useful starting point to screen for putatively causal SNPs that may be involved in the etiology of CLL/SLL.

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Section: Methodsmentioning

confidence: 99%

Post-GWAS Functional Characterization of Susceptibility Variants for Chronic Lymphocytic Leukemia

et al. 2012

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“…Maternal lineages of the PL were identified by comparison with the female haplotypes and expressed as proportions, with 95% confidence intervals (calculated using javastat , Harner et al . ). The observed contribution amongst females was tested using a chi‐square test against a Poisson distribution with expected probabilities estimated from the observed data using the formula (Zar )…”

Section: Primer Sequences For All Primers Trialled For Use In Penaeusmentioning

confidence: 97%

A tool for tracking genetic contributions of wild Penaeus (Melicertus) plebejus broodstock to hatchery populations

2014

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Stock enhancement, restocking and sea ranching are being increasingly applied in both fisheries and conservation. The contribution of hatchery stock to fishery harvest and the maintenance of the genetic structure of stocked populations are both important considerations when releasing captive-bred organisms into natural systems. Use of wild-caught broodstock generally overcomes some of the genetic problems associated with domesticated hatchery populations, but there is still a need to ensure that a sufficient proportion of the natural population contribute to production of the stocked cohort to realise the genetic benefits of using wild-caught broodstock. Releases of Penaeus (Melicertus) plebejus are under investigation as a means of increasing prawn production in recruitment-limited areas. We used the highly variable mitochondrial control region (mtCR) to assign post-larvae to maternal lineages in the hatchery and also to investigate the reproductive performance of female broodstock in terms of contribution to the production of the cohorts of post-larvae in the hatchery. Our data showed that mtCR can be a useful tool for tracking lineages and provided genetic evidence that unequal contribution and underproducing females can occur even in wild-caught broodstock. This work therefore highlights the importance of monitoring the genetic composition of pre-release hatchery stocks.

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“…From an implementation perspective, the building temperature predictor was modelled using the R language and was interfaced to the Java implementation through JRI [51]. During the initialization, the R engine loads two data files that contain the two models, MP5ON and MP5OFF.…”

Section: Model Description and Trainingmentioning

confidence: 99%

Demand response algorithms for smart-grid ready residential buildings using machine learning models

2019

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JavaStat: a Java/R-based statistical computing environment

Abstract: R, Java, JavaStat, RMI, JRI,

Cited by 7 publications

References 1 publication

Post-GWAS Functional Characterization of Susceptibility Variants for Chronic Lymphocytic Leukemia

Post-GWAS Functional Characterization of Susceptibility Variants for Chronic Lymphocytic Leukemia

A tool for tracking genetic contributions of wild Penaeus (Melicertus) plebejus broodstock to hatchery populations

Demand response algorithms for smart-grid ready residential buildings using machine learning models

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