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Jobs marked as "running". A monitor URL is assigned to each

by Wilbert Seely (2020-08-16)


Jobs marked as "running". A monitor URL is assigned to each job, which allows users to check the status of their jobs. The user has an option to provide an e-mail address for notification when the job is running and a link to results. This option is particularly useful if multiple large databases are selected (e.g. GO and MeSH).Cross-experiment visualization via clustering in LRpathLRpath results from multiple experiments may be integrated in order to interactively view and explore the enrichment profiles across experiments. It provides a user-friendly method for (+)-Dihydrexidine filtering, merging, and clustering LRpath results using several options. The input for this part of the application is the set of URLs from previous LRpath analyses to be clustered. The user has the ability to choose the values to be used to cluster, the type of distance matrix method, the type of linkage method for hierarchical clustering, and which biological concepts to include. The output is a set of files to input directly into PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/27221208 the widely-used and freelyavailable TreeView software [47,48]. Here, users can view the hierarchical clustering with each row corresponding to a concept, and each column corresponding to an experiment.Reanalysis of publicly available CpG methylation data in cancersFor this study, we selected ten tumor versus normal CpG methylation studies profiled on the Illumina HumanMethylation27 BeadChip, four studies from Gene Expression Obmibus (GEO) and six studies from The Cancer Genome Atlas (TCGA) database based on available sample size (N > 40) and PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28493825 the availability of normal adjacent methylation profiling status (at least three normal samples). To represent a wide spectrum of cancers, all studies, with the exception of lung cancer, which is classified into adenocarcinoma and squamous cell carcinoma, were from unique sites: breast, colon [49], brain [50], myeloma [51], kidney, ovarian [52], prostate [53], and stomach. From 27,543 CpG sites, those sites withKim et al. BMC Genomics 2012, 13:526 http://www.biomedcentral.com/1471-2164/13/Page 14 ofmissing beta score in any one study were filtered out, and 23,050 sites remained for further downstream analysis. Our analyses included 6 paired and 4 non-paired studies, and using LIMMA package in R software, the differential methylation between tumor and adjacent normal samples was examined using beta scores according to experimental design (paired or non-paired). Resulting p-values were adjusted for multiple-comparison using the false discovery rate (FDR) method.Additional filesAdditional file 1: Table S1. Significance of overlap in the specific differentially methylated genes in significant GO terms between pairs of studies using Fisher's exact test (p-value<0.05 is indicated with red text) GO term - Immune Response GO term - Epidermis Development GO term ?Neurogenesis. Additional file 2: Figure S1. Waterfall plots showing the methylation change in significant genes between normal and tumor samples involved in neurogenesis and epidermis development (GO terms). Positive values indicate hypermethylation in cancer, while negative values indicate hypomethylation in cancer. A. Neurogenesis. B. Epidermis Development. Figure S2. Change in average percent methylation of HOX gene family, PAX gene family, and WT1 involved in Transcription Factor Activity. Figure S3. Unsupervised clustering of probes involved in Sequence-specific Transcription Factor Activity. Figure S4. The status of PRC2 targets and CpG islands for those p.