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Abstract Motivation Detecting cancer gene expression and transcriptome changes with mRNA-sequencing (RNA-Seq) or array-based data are important for understanding the molecular mechanisms underlying carcinogenesis and cellular events during cancer progression. In previous studies, the differentially expressed genes were detected across patients in one cancer type. These studies ignored the role of mRNA expression changes in driving tumorigenic mechanisms that are either universal or specific in different tumor types. To address the problem, we introduce two network-based multi-task learning frameworks, NetML and NetSML, to discover common differentially expressed genes shared across different cancer types as well as differentially expressed genes specific to each cancer type. The proposed frameworks consider the common latent gene co-expression modules and gene-sample biclusters underlying the multiple cancer datasets to learn the knowledge crossing different tumor types. Results Large-scale experiments on simulations and real cancer high-throughput datasets validate that the proposed network-based multi-task learning frameworks perform better sample classification compared with the models without the knowledge sharing across different cancer types. The common and cancer specific molecular signatures detected by multi-task learning frameworks on TCGA ovarian cancer, breast cancer, and prostate cancer datasets are correlated with the known marker genes and enriched in cancer relevant KEGG pathwaysmore »and Gene Ontology terms. Availability and Implementation Source code is available at: https://github.com/compbiolabucf/NetML Supplementary information Supplementary data are available at Bioinformatics« less

Bacterial fruit blotch (BFB) caused byAcidovorax citrulliis one of the most important bacterial diseases of cucurbits worldwide. However, the mechanisms associated withA. citrullipathogenicity and genetics of host resistance have not been extensively investigated. We idenitfiedNicotiana benthamianaandNicotiana tabacumas surrogate hosts for studyingA. citrullipathogenicity and non‐host resistance triggered by type III secreted (T3S) effectors. TwoA. citrullistrains, M6 and AAC00‐1, that represent the two major groups amongstA. citrullipopulations, induced disease symptoms onN. benthamiana, but triggered a hypersensitive response (HR) onN. tabacumplants. Transient expression of 19 T3S effectors fromA. citrulliinN. benthamianaleaves revealed that three effectors, Aave_1548, Aave_2708, and Aave_2166, trigger water‐soaking‐like cell death inN. benthamiana.Aave_1548knockout mutants of M6 and AAC00‐1 displayed reduced virulence onN. benthamianaand melon (Cucumis meloL.). Transient expression of Aave_1548 and Aave_2166 effectors triggered a non‐host HR inN. tabacum, which was dependent on the functionality of the immune signalling component,NtSGT1. Hence, employingNicotianaspecies as surrogate hosts for studyingA. citrullipathogenicity may help characterize the function ofA. citrulliT3S effectors and facilitate the development of new strategies for BFB management.