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Anaissi A.,Intelligent Systems Technology, Inc. | Kennedy P.J.,Intelligent Systems Technology, Inc. | Goyal M.,Intelligent Systems Technology, Inc. | Catchpoole D.R.,Childrens Cancer Research Unit
BMC Bioinformatics | Year: 2013

Background: The wealth of gene expression values being generated by high throughput microarray technologies leads to complex high dimensional datasets. Moreover, many cohorts have the problem of imbalanced classes where the number of patients belonging to each class is not the same. With this kind of dataset, biologists need to identify a small number of informative genes that can be used as biomarkers for a disease.Results: This paper introduces a Balanced Iterative Random Forest (BIRF) algorithm to select the most relevant genes for a disease from imbalanced high-throughput gene expression microarray data. Balanced iterative random forest is applied on four cancer microarray datasets: a childhood leukaemia dataset, which represents the main target of this paper, collected from The Children's Hospital at Westmead, NCI 60, a Colon dataset and a Lung cancer dataset. The results obtained by BIRF are compared to those of Support Vector Machine-Recursive Feature Elimination (SVM-RFE), Multi-class SVM-RFE (MSVM-RFE), Random Forest (RF) and Naive Bayes (NB) classifiers. The results of the BIRF approach outperform these state-of-the-art methods, especially in the case of imbalanced datasets. Experiments on the childhood leukaemia dataset show that a 7% ∼ 12% better accuracy is achieved by BIRF over MSVM-RFE with the ability to predict patients in the minor class. The informative biomarkers selected by the BIRF algorithm were validated by repeating training experiments three times to see whether they are globally informative, or just selected by chance. The results show that 64% of the top genes consistently appear in the three lists, and the top 20 genes remain near the top in the other three lists.Conclusion: The designed BIRF algorithm is an appropriate choice to select genes from imbalanced high-throughput gene expression microarray data. BIRF outperforms the state-of-the-art methods, especially the ability to handle the class-imbalanced data. Moreover, the analysis of the selected genes also provides a way to distinguish between the predictive genes and those that only appear to be predictive. © 2013 Anaissi et al.; licensee BioMed Central Ltd.


De Bock C.E.,University of New South Wales | De Bock C.E.,Queensland Institute of Medical Research | Lin Z.,University of New South Wales | Mekkawy A.H.,University of New South Wales | And 3 more authors.
International Journal of Oncology | Year: 2010

The urokinase-type plasminogen activator receptor (uPAR) has diverse biological functions including roles in proteolysis, cell adhesion and cellular signaling. We identified a heat shock protein MRJ (DNAJB6) as a novel uPAR-interacting protein in a yeast two-hybrid screen and confirmed the interaction and co-localization by GST-pull down assays, and co-immunoprecipitation in cells transfected with MRJ. Endogenous interaction between uPAR and MRJ was also detected in breast cancer MDA-MB-231 cells. Deletion mapping demonstrated that the C-terminal region of MRJ is required to mediate its interaction with uPAR. To understand the biological function of the uPAR-MRJ complex, we determined whether MRJ regulated uPAR mediated adhesion to vitronectin in human embryonic kidney (HEK) 293 cells stably transfected with uPAR. After transfection with full length MRJ, there was a 50% increase in cell adhesion compared to the mock transfected control (p<0.01). This increase in adhesion is dependent on the uPAR/full length MRJ interaction as cells transfected with the mutant construct containing only N-terminal region or C-terminal region of MRJ had no increase in cell adhesion. The observed increase in adhesion to vitronectin by MRJ was also blocked by an anti-uPAR domain I antibody suggesting that the induced adhesion is at least in part contributed by uPAR on the cell surface. These data provide a novel mechanism by which uPAR plays a role in cell adhesion to vitronectin.


Andersson A.K.,St Jude Childrens Research Hospital | Andersson A.K.,Lund University | Ma J.,St Jude Childrens Research Hospital | Wang J.,St Jude Childrens Research Hospital | And 47 more authors.
Nature Genetics | Year: 2015

Infant acute lymphoblastic leukemia (ALL) with MLL rearrangements (MLL-R) represents a distinct leukemia with a poor prognosis. To define its mutational landscape, we performed whole-genome, exome, RNA and targeted DNA sequencing on 65 infants (47 MLL-R and 18 non-MLL-R cases) and 20 older children (MLL-R cases) with leukemia. Our data show that infant MLL-R ALL has one of the lowest frequencies of somatic mutations of any sequenced cancer, with the predominant leukemic clone carrying a mean of 1.3 non-silent mutations. Despite this paucity of mutations, we detected activating mutations in kinase-PI3K-RAS signaling pathway components in 47% of cases. Surprisingly, these mutations were often subclonal and were frequently lost at relapse. In contrast to infant cases, MLL-R leukemia in older children had more somatic mutations (mean of 6.5 mutations/case versus 1.3 mutations/case, P = 7.15 × 10-5) and had frequent mutations (45%) in epigenetic regulators, a category of genes that, with the exception of MLL, was rarely mutated in infant MLL-R ALL. © 2015 Nature America, Inc. All rights reserved.


Swarbrick A.,Garvan Institute of Medical Research | Swarbrick A.,University of New South Wales | Woods S.L.,University of California at San Francisco | Woods S.L.,Queensland Institute of Medical Research | And 25 more authors.
Nature Medicine | Year: 2010

A drawback of electrical stimulation for muscle control is that large, fatigable motor units are preferentially recruited before smaller motor units by the lowest-intensity electrical cuff stimulation. This phenomenon limits therapeutic applications because it is precisely the opposite of the normal physiological (orderly) recruitment pattern; therefore, a mechanism to achieve orderly recruitment has been a long-sought goal in physiology, medicine and engineering. Here we demonstrate a technology for reliable orderly recruitment in vivo. We find that under optical control with microbial opsins, recruitment of motor units proceeds in the physiological recruitment sequence, as indicated by multiple independent measures of motor unit recruitment including conduction latency, contraction and relaxation times, stimulation threshold and fatigue. As a result, we observed enhanced performance and reduced fatigue in vivo. These findings point to an unanticipated new modality of neural control with broad implications for nervous system and neuromuscular physiology, disease research and therapeutic innovation. © 2010 Nature America, Inc. All rights reserved.


Messenger S.W.,University of Wisconsin - Madison | Thomas D.D.H.,University of Wisconsin - Madison | Falkowski M.A.,University of Wisconsin - Madison | Byrne J.A.,Childrens Cancer Research Unit | And 2 more authors.
American Journal of Physiology - Gastrointestinal and Liver Physiology | Year: 2013

Zymogen granule (ZG) formation in acinar cells involves zymogen cargo sorting from trans-Golgi into immature secretory granules (ISGs). ISG maturation progresses by removal of lysosomal membrane and select content proteins, which enter endosomal intermediates prior to their apical exocytosis. Constitutive and stimulated secretion through this mechanism is termed the constitutive-like and minor-regulated pathways, respectively. However, the molecular components that control membrane trafficking within these endosomal compartments are largely unknown. We show that tumor protein D52 is highly expressed in endosomal compartments following pancreatic acinar cell stimulation and regulates apical exocytosis of an apically directed endolysosomal compartment. Secretion from the endolysosomal compartment was detected by cell-surface antigen labeling of lysosomeassociated membrane protein LAMP1, which is absent from ZGs, and had incomplete overlap with surface labeling of synaptotagmin 1, a marker of ZG exocytosis. Although culturing (16-18 h) of isolated acinar cells is accompanied by a loss of secretory responsiveness, the levels of SNARE proteins necessary for ZG exocytosis were preserved. However, levels of endolysosomal proteins D52, EEA1, Rab5, and LAMP1 markedly decreased with culture. When D52 levels were restored by adenoviral delivery, the levels of these regulatory proteins and secretion of both LAMP1 (endolysosomal) and amylase was strongly enhanced. These secretory effects were absent in alanine and aspartate substitutions of serine 136, the major D52 phosphorylation site, and were inhibited by brefeldin A, which does not directly affect the ZG compartment. Our results indicate that D52 directly regulates apical endolysosomal secretion and are consistent with previous studies, suggesting that this pathway indirectly regulates ZG secretion of digestive enzymes. © 2013 the American Physiological Society.

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