title: Identification of interconnected markers for T-cell acute lymphoblastic leukemia.
abstract: T-cell acute lymphoblastic leukemia (T-ALL) is a complex disease, resulting from proliferation of differentially arrested immature T cells. The molecular mechanisms and the genes involved in the generation of T-ALL remain largely undefined. In this study, we propose a set of genes to differentiate individuals with T-ALL from the nonleukemia/healthy ones and genes that are not differential themselves but interconnected with highly differentially expressed ones. We provide new suggestions for pathways involved in the cause of T-ALL and show that network-based classification techniques produce fewer genes with more meaningful and successful results than expression-based approaches. We have identified 19 significant subnetworks, containing 102 genes. The classification/prediction accuracies of subnetworks are considerably high, as high as 98%. Subnetworks contain 6 nondifferentially expressed genes, which could potentially participate in pathogenesis of T-ALL. Although these genes are not differential, they may serve as biomarkers if their loss/gain of function contributes to generation of T-ALL via SNPs. We conclude that transcription factors, zinc-ion-binding proteins, and tyrosine kinases are the important protein families to trigger T-ALL. These potential disease-causing genes in our subnetworks may serve as biomarkers, alternative to the traditional ones used for the diagnosis of T-ALL, and help understand the pathogenesis of the disease.
authors: Center for Computational Biology and Bioinformatics and College of Engineering, Koç University, Rumelifeneri Yolu, Sariyer, 34450 Istanbul, Turkey.
authors: Emine Guven
authors: EG
authors: Maiorov
authors: Ozlem
authors: O
authors: Keskin
authors: Ozden Hatirnaz
authors: OH
authors: Ng
authors: Ugur
authors: U
authors: Ozbek
authors: Attila
authors: A
authors: Gursoy
mesh_terms: D014408:Biomarkers, Tumor / Q000096:biosynthesis / Q000235:genetics; D004268:DNA-Binding Proteins / Q000378:metabolism*; D015973:Gene Expression Regulation, Leukemic; D006801:Humans; D046228:Microarray Analysis; D020641:Polymorphism, Single Nucleotide; D054218:Precursor T-Cell Lymphoblastic Leukemia-Lymphoma / Q000235:genetics* / Q000473:pathology; D060066:Protein Interaction Maps; D014158:Transcription, Genetic
chemical_list: D014408:Biomarkers, Tumor; D004268:DNA-Binding Proteins
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