‘Gene shaving’ as a method for identifying distinct sets of genes with similar expression patterns

Background: Large gene expression studies, such as those conducted using DNA arrays, often provide millions of different pieces of data. To address the problem of analyzing such data, we describe a statistical method, which we have called ‘gene shaving’. The method identifies subsets of genes with coherent expression patterns and large variation across conditions. Gene shaving differs from hierarchical clustering and other widely used methods for analyzing gene expression studies in that genes may belong to more than one cluster, and the clustering may be supervised by an outcome measure. The technique can be ‘unsupervised’, that is, the genes and samples are treated as unlabeled, or partially or fully supervised by using known properties of the genes or samples to assist in finding meaningful groupings. Results: We illustrate the use of the gene shaving method to analyze gene expression measurements made on samples from patients with diffuse large B-cell lymphoma. The method identifies a small cluster of genes whose expression is highly predictive of survival. Conclusions: The gene shaving method is a potentially useful tool for exploration of gene expression data and identification of interesting clusters of genes worth further investigation.

Psychological and Support Characteristics of Parents of Child Sexual Abuse Victims: Relationship with Child Functioning and Treatment

Child sexual abuse continues to be a prevalent and complex problem in today’s society as it poses serious and pervasive mental health risks to child victims and their non-offending parents. The main objectives of this study were (a) to elucidate the psychological symptoms and support needs of parents of child sexual abuse victims as they present to group treatment, (b) to examine changes in psychological symptoms and support needs and their relationship with child functioning over the course of a parallel group treatment, and (c) to examine the impact of these factors on completion of group treatment. Participants included 104 sexually abused youth and their non-offending parent presenting to Project SAFE Group Intervention, a 12-session cognitive-behavioral group treatment for sexually abused children and their non-offending parents. This project had a unique advantage of utilizing a variety of demographic, parent-, and child-report measures, allowing for a more comprehensive examination of change in symptomatology and needs over the course of treatment. Several significant findings were noted, including the identification of four clusters of youth at pre-treatment, which were maintained at post-treatment; elevations on the CTQ Sexual Abuse scale; parents of youth sexually abused by a non-family member had significantly higher PSI-Restriction of Role subscale scores; parental expectations of a negative impact on their child were worse for older children; several parent characteristics predicted client treatment retention (e.g., older parents, lower SCL-90-R GSI scores); and an early age of onset of abuse also increased treatment retention. Future directions, recommendations, and limitations were discussed.