title: kMEn: Analyzing noisy and bidirectional transcriptional pathway responses in single subjects.
abstract: Understanding dynamic, patient-level transcriptomic response to therapy is an important step forward for precision medicine. However, conventional transcriptome analysis aims to discover cohort-level change, lacking the capacity to unveil patient-specific response to therapy. To address this gap, we previously developed two N-of-1-pathways methods, Wilcoxon and Mahalanobis distance, to detect unidirectionally responsive transcripts within a pathway using a pair of samples from a single subject. Yet, these methods cannot recognize bidirectionally (up and down) responsive pathways. Further, our previous approaches have not been assessed in presence of background noise and are not designed to identify differentially expressed mRNAs between two samples of a patient taken in different contexts (e.g. cancer vs non cancer), which we termed responsive transcripts (RTs).
  
  
  
  We propose a new N-of-1-pathways method, k-Means Enrichment (kMEn), that detects bidirectionally responsive pathways, despite background noise, using a pair of transcriptomes from a single patient. kMEn identifies transcripts responsive to the stimulus through k-means clustering and then tests for an over-representation of the responsive genes within each pathway. The pathways identified by kMEn are mechanistically interpretable pathways significantly responding to a stimulus.
  
  
  
  In ∼9000 simulations varying six parameters, superior performance of kMEn over previous single-subject methods is evident by: (i) improved precision-recall at various levels of bidirectional response and (ii) lower rates of false positives (1-specificity) when more than 10% of genes in the genome are differentially expressed (background noise). In a clinical proof-of-concept, personal treatment-specific pathways identified by kMEn correlate with therapeutic response (p-value<0.01).
  
  
  
  Through improved single-subject transcriptome dynamics of bidirectionally-regulated signals, kMEn provides a novel approach to identify mechanism-level biomarkers.
authors.affiliation: Center for Biomedical Informatics and Biostatistics, The University of Arizona, Tucson, AZ 85721, USA; Bio5 Institute, The University of Arizona, Tucson, AZ 85721, USA; Department of Medicine, The University of Arizona, Tucson, AZ 85721, USA; Graduate Interdisciplinary Program in Statistics, The University of Arizona, Tucson, AZ 85721, USA.
authors.forename: Qike
authors.initials: Q
authors.lastname: Li
authors.affiliation: Center for Biomedical Informatics and Biostatistics, The University of Arizona, Tucson, AZ 85721, USA; Bio5 Institute, The University of Arizona, Tucson, AZ 85721, USA; Department of Medicine, The University of Arizona, Tucson, AZ 85721, USA; Graduate Interdisciplinary Program in Statistics, The University of Arizona, Tucson, AZ 85721, USA.
authors.forename: A Grant
authors.initials: AG
authors.lastname: Schissler
authors.affiliation: Center for Biomedical Informatics and Biostatistics, The University of Arizona, Tucson, AZ 85721, USA; Bio5 Institute, The University of Arizona, Tucson, AZ 85721, USA; Department of Medicine, The University of Arizona, Tucson, AZ 85721, USA.
authors.forename: Vincent
authors.initials: V
authors.lastname: Gardeux
authors.affiliation: Center for Biomedical Informatics and Biostatistics, The University of Arizona, Tucson, AZ 85721, USA; Bio5 Institute, The University of Arizona, Tucson, AZ 85721, USA; Department of Medicine, The University of Arizona, Tucson, AZ 85721, USA.
authors.forename: Joanne
authors.initials: J
authors.lastname: Berghout
authors.affiliation: Center for Biomedical Informatics and Biostatistics, The University of Arizona, Tucson, AZ 85721, USA; Bio5 Institute, The University of Arizona, Tucson, AZ 85721, USA; Department of Medicine, The University of Arizona, Tucson, AZ 85721, USA.
authors.forename: Ikbel
authors.initials: I
authors.lastname: Achour
authors.affiliation: Center for Biomedical Informatics and Biostatistics, The University of Arizona, Tucson, AZ 85721, USA; Bio5 Institute, The University of Arizona, Tucson, AZ 85721, USA; Department of Medicine, The University of Arizona, Tucson, AZ 85721, USA.
authors.forename: Colleen
authors.initials: C
authors.lastname: Kenost
authors.affiliation: Center for Biomedical Informatics and Biostatistics, The University of Arizona, Tucson, AZ 85721, USA; Bio5 Institute, The University of Arizona, Tucson, AZ 85721, USA; Department of Medicine, The University of Arizona, Tucson, AZ 85721, USA. Electronic address: haiquan@email.arizona.edu.
authors.forename: Haiquan
authors.initials: H
authors.lastname: Li
authors.affiliation: Graduate Interdisciplinary Program in Statistics, The University of Arizona, Tucson, AZ 85721, USA; Department of Mathematics, The University of Arizona, Tucson, AZ 85721, USA. Electronic address: hzhang@math.arizona.edu.
authors.forename: Hao Helen
authors.initials: HH
authors.lastname: Zhang
authors.affiliation: Center for Biomedical Informatics and Biostatistics, The University of Arizona, Tucson, AZ 85721, USA; Bio5 Institute, The University of Arizona, Tucson, AZ 85721, USA; Department of Medicine, The University of Arizona, Tucson, AZ 85721, USA; Graduate Interdisciplinary Program in Statistics, The University of Arizona, Tucson, AZ 85721, USA; University of Arizona Cancer Center, The University of Arizona, Tucson, AZ 85721, USA; Institute for Genomics and Systems Biology, The University of Chicago, IL 60637, USA. Electronic address: yves@email.arizona.edu.
authors.forename: Yves A
authors.initials: YA
authors.lastname: Lussier
mesh_terms: D016000:Cluster Analysis; D003627:Data Interpretation, Statistical; D020869:Gene Expression Profiling; D006801:Humans; D057285:Precision Medicine; D012333:RNA, Messenger; D059467:Transcriptome
chemical_list: D012333:RNA, Messenger
keywords: HIV treatment response; N-of-1-pathways; Pathway analysis; Precision medicine; Single subject analysis; k-means clustering