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Subhankar Chakraborty, M.D., Ph.D. NEBRASKA’S HEALTH SCIENCE CENTER A partner with Nebraska Health System May 8, 2017 Editor-in-Chief Annals of Gastroenterology Dear Editor Thank you for considering our manuscript entitled “In Silico Analysis Identifies Genes Common between Five Primary Gastrointestinal Cancer Sites with Potential Therapeutic Implications” for review. We thank the reviewers for their insightful comments and suggestions. We have revised the manuscript and hope the changes made will be acceptable to the reviewers. We have included a point by point answer to the comments from the reviewers. I look forward to hearing from you soon. Reviewer comments with rebuttal Reviewer A: This is a very interesting and detailed manuscript that merits publication in your journal. The only thing that according to my opinion needs to be greatly elaborated is the clinical relevance of this manuscripts findings. This is something that should be added in the manuscript before its publication. Response: We thank the reviewer for his positive comments. We have added a discussion about the clinical implications of the study in the revised manuscript. Reviewer B: The current study is an interesting investigation in public databases with microarrays data regarding the genetic profile of the most common GI cancer. Despite the high numbers of samples and genes analyzed the studies presented several weaknesses which should be addressed before the manuscript is considering suitable for publication • The main point is that the study is looking like fishing expedition, No rational is providing for the selection of specific tumors, tools, database, genes. Response: We thank the reviewer for his comments. We beg to differ from the reviewer and we provide specific examples to hopefully answer his/her concern. These are directly derived from the manuscript. Rationale: "While there are numerous studies that have investigated the global gene expression in various GI cancers compared to normal GI tissue, there are differences in the results from study to study. Thus, analysis of results from multiple studies provides the opportunity to get a more accurate picture of differential gene expression in cancer tissues. The gastrointestinal tract is embryologically derived from the endoderm with the esophagus and stomach derived from the foregut, duodenum from the foregut and midgut, liver from the ventral mesentery, pancreas from the septum transversum, transverse and ascending colon from the midgut and the transverse colon and rectum from the hindgut. If we could identify a Department of Internal Medicine, 982055 Nebraska Medical Center, University of Nebraska Medical Center. Omaha, NE 68198-2055. Phone: (978)-810-5992, E-mail: [email protected] set of genes that are common between cancers arising from multiple GI sites, this would help identify pathways and in turn targets for therapy of GI malignancies" Why we chose Oncomine: "The Oncomine database allows us to compare gene expression across multiple studies to identify the genes that are differentially over or under expressed in majority of the studies." • Related with this there is no data regarding the biological function of the genes up-or downregulated in each cancer type, not even for a general description of them (i.e. transcription factor, oncogene, growth factor, invasion etc). Response: We thank the reviewer for his suggestion. We agree that we have not provided a description of the function of every up or downregulated gene. There are 5,000 genes that were included in initial analysis and it would be difficult with space constraints to describe the function of each gene. There are several online tools that are available to look up the function of a particular gene. • The tile includes the ambitious term “potential therapeutic implications” but in the body of the manuscript no data provided. The author should delete this from the title or discuss in details this issue in the discussion section Response: We appreciate the reviewer's comments. We have added further discussion about the clinical applications of this article in the revised manuscript. We have also revised the title to read "In Silico Analysis Identifies Genes Common between Five Primary Gastrointestinal Cancer Sites with Potential Clinical Applications". We feel the study has wide applications including diagnosis, therapy and prognosis of GI cancers. If you have any questions, please contact me at (978) 810 5992. Thank you for your consideration. Looking forward to hearing from you soon. Sincerely, Subhankar Chakraborty, M.D., Ph.D. Dept. of Internal Medicine, University of Nebraska Medical Omaha. Nebraska Center. Department of Internal Medicine, 982055 Nebraska Medical Center, University of Nebraska Medical Center. Omaha, NE 68198-2055. Phone: (978)-810-5992, E-mail: [email protected]