MethSurv: a web tool to perform multivariable survival analysis using DNA methylation data.

Aim: To develop a web tool for survival analysis based on CpG methylation patterns.

Materials & Methods: We utilized methylome data from 'The Cancer Genome Atlas' and used the Cox proportional-hazards model to develop an interactive web interface for survival analysis.

Results: MethSurv enables survival analysis for a CpG located in or around the proximity of a query gene.

Mutation analysis and copy number alterations of in non-small-cell lung cancer exhibiting over-expression.

KIF23 was recently suggested to be a potential molecular target for the treatment of lung cancer. This proposal is based on elevated expression of in several tumors affecting breast, lung, brain, and liver, and also on the presence of mutations in melanoma and colorectal cancer. Recently, we identified a mutation in the gene causing a rare hereditary form of dyserythropoietic anemia (CDA III) with predisposition to blood cancer.

Correction: Methylation Markers of Early-Stage Non-Small Cell Lung Cancer.

[This corrects the article DOI: 10.1371/journal.pone.

seqlm: an MDL based method for identifying differentially methylated regions in high density methylation array data.

Motivation: One of the main goals of large scale methylation studies is to detect differentially methylated loci. One way is to approach this problem sitewise, i.e.

Genetic and epigenetic regulation of gene expression in fetal and adult human livers.

Background: The liver plays a central role in the maintenance of homeostasis and health in general. However, there is substantial inter-individual variation in hepatic gene expression, and although numerous genetic factors have been identified, less is known about the epigenetic factors.

Results: By analyzing the methylomes and transcriptomes of 14 fetal and 181 adult livers, we identified 657 differentially methylated genes with adult-specific expression, these genes were enriched for transcription factor binding sites of HNF1A and HNF4A.

DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns.

Background: DNA epigenetic modifications, such as methylation, are important regulators of tissue differentiation, contributing to processes of both development and cancer. Profiling the tissue-specific DNA methylome patterns will provide novel insights into normal and pathogenic mechanisms, as well as help in future epigenetic therapies. In this study, 17 somatic tissues from four autopsied humans were subjected to functional genome analysis using the Illumina Infinium HumanMethylation450 BeadChip, covering 486 428 CpG sites.

Methylation markers of early-stage non-small cell lung cancer.

Background: Despite of intense research in early cancer detection, there is a lack of biomarkers for the reliable detection of malignant tumors, including non-small cell lung cancer (NSCLC). DNA methylation changes are common and relatively stable in various types of cancers, and may be used as diagnostic or prognostic biomarkers.

Methods: We performed DNA methylation profiling of samples from 48 patients with stage I NSCLC and 18 matching cancer-free lung samples using microarrays that cover the promoter regions of more than 14,500 genes.