{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T02:52:56Z","timestamp":1760151176233,"version":"build-2065373602"},"reference-count":38,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2022,2,21]],"date-time":"2022-02-21T00:00:00Z","timestamp":1645401600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Purdue University Fort Wayne, Startup Fund","award":["NA"],"award-info":[{"award-number":["NA"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>The goal of this research is to computationally identify candidate modifiers for retinitis pigmentosa (RP), a group of rare genetic disorders that trigger the cellular degeneration of retinal tissue. RP being subject to phenotypic variation complicates diagnosis and treatment of the disease. In a previous study, modifiers of RP were identified by an association between genetic variation in the DNA sequence and variation in eye size in a well-characterized Drosophila model of RP. This study will instead focus on RNA expression data to identify candidate modifier genes whose expression is correlated with phenotypic variation in eye size. The proposed approach uses the K-Means algorithm to cluster 171 Drosophila strains based on their expression profiles for 18,140 genes in adult females. This algorithm is designed to investigate the correlation between Drosophila eye size and genetic expression and gather suspect genes from clusters with abnormally large or small eyes. The clustering algorithm was implemented using the R scripting language and successfully identified 10 suspected candidate modifiers for RP. This analysis was followed by a validation study that tested seven candidate modifiers and found that the loss of five of them significantly altered the degeneration phenotype and thus can be labeled as a bona fide modifier of disease.<\/jats:p>","DOI":"10.3390\/genes13020386","type":"journal-article","created":{"date-parts":[[2022,2,21]],"date-time":"2022-02-21T20:24:21Z","timestamp":1645475061000},"page":"386","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Cluster-Based Analysis of Retinitis Pigmentosa Modifiers Using Drosophila Eye Size and Gene Expression Data"],"prefix":"10.3390","volume":"13","author":[{"given":"James","family":"Amstutz","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, Purdue University Fort Wayne, Fort Wayne, IN 46805, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2054-7869","authenticated-orcid":false,"given":"Amal","family":"Khalifa","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Purdue University Fort Wayne, Fort Wayne, IN 46805, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rebecca","family":"Palu","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Purdue University Fort Wayne, Fort Wayne, IN 46805, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4562-3290","authenticated-orcid":false,"given":"Kaushara","family":"Jahan","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Purdue University Fort Wayne, Fort Wayne, IN 46805, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,2,21]]},"reference":[{"key":"ref_1","unstructured":"(2021, April 13). Retinitis Pigmentosa, Available online: https:\/\/www.nei.nih.gov\/learn-about-eye-health\/eye-conditions-and-diseases\/retinitis-pigmentosa#:~:text=Retinitis%20pigmentosa%20(RP)%20is%20a,of%20side%20(peripheral)%20vision."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1795","DOI":"10.1016\/S0140-6736(06)69740-7","article-title":"Retinitis Pigmentosa","volume":"368","author":"Hartong","year":"2006","journal-title":"Lancet"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Tsang, S., and Sharma, T. (2019). Atlas on Inherited Retinal Diseases, Springer.","DOI":"10.1007\/978-3-319-95046-4"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S1877-1173(09)88001-0","article-title":"Chapter 1 Rhodopsin-Mediated Retinitis Pigmentosa","volume":"Volume 88","author":"Malanson","year":"2009","journal-title":"Progress in Molecular Biology and Translational Science"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1093\/hmg\/ddv502","article-title":"Candidate Genetic Modifiers of Retinitis Pigmentosa Identified by Exploiting Natural Variation in Drosophila","volume":"25","author":"Chow","year":"2016","journal-title":"Hum. Mol. Genet."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1038\/nature10811","article-title":"The Drosophila Melanogaster Genetic Reference Panel","volume":"482","author":"Mackay","year":"2012","journal-title":"Nature"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1038\/sj.emboj.7601477","article-title":"Unfolded Protein Response in a Drosophila Model for Retinal Degeneration","volume":"26","author":"Ryoo","year":"2007","journal-title":"EMBO J."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"913","DOI":"10.1534\/genetics.119.303004","article-title":"Decoupling of Apoptosis from Activation of the ER Stress Response by the Drosophila Metallopeptidase Superdeath","volume":"214","author":"Palu","year":"2020","journal-title":"Genetics"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Palu, R.A.S., and Chow, C.Y. (2018). Baldspot\/ELOVL6 Is a Conserved Modifier of Disease and the ER Stress Response. PLoS Genet., 14.","DOI":"10.1371\/journal.pgen.1007557"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"E6010","DOI":"10.1073\/pnas.1519159112","article-title":"Genetic Basis of Transcriptome Diversity in Drosophila Melanogaster","volume":"112","author":"Huang","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Chen, L., and Wong, G. (2019). Transcriptome Informatics. Encyclopedia of Bioinformatics and Computational Biology, Elsevier.","DOI":"10.1016\/B978-0-12-809633-8.20204-5"},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Soneson, C., and Delorenzi, M. (2013). A Comparison of Methods for Differential Expression Analysis of RNA-Seq Data. BMC Bioinform., 14.","DOI":"10.1186\/1471-2105-14-91"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Wang, T., Li, B., Nelson, C.E., and Nabavi, S. (2019). Comparative Analysis of Differential Gene Expression Analysis Tools for Single-Cell RNA Sequencing Data. BMC Bioinform., 20.","DOI":"10.1186\/s12859-019-2599-6"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1186\/s13059-015-0604-6","article-title":"DGEclust: Differential Expression Analysis of Clustered Count Data","volume":"16","author":"Vavoulis","year":"2015","journal-title":"Genome Biol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1370","DOI":"10.1109\/TKDE.2004.68","article-title":"Cluster Analysis for Gene Expression Data: A Survey","volume":"16","author":"Jiang","year":"2004","journal-title":"IEEE Trans. Knowl. Data Eng."},{"key":"ref_16","first-page":"100","article-title":"Algorithm AS 136: A K-Means Clustering Algorithm","volume":"28","author":"Hartigan","year":"1979","journal-title":"J. R. Stat. Soc. Ser. C Appl. Stat."},{"key":"ref_17","unstructured":"Parsian, M. (2015). Data Algorithms, O\u2019Reilly Media, Inc.. [1st ed.]."},{"key":"ref_18","unstructured":"(2021, April 12). k-Means Clustering Algorithm. Available online: https:\/\/sites.google.com\/site\/dataclusteringalgorithms\/k-means-clustering-algorithm."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/0377-0427(87)90125-7","article-title":"Silhouettes: A Graphical Aid to the Interpretation and Validation of Cluster Analysis","volume":"20","author":"Rousseeuw","year":"1987","journal-title":"J. Comput. Appl. Math."},{"key":"ref_20","unstructured":"Moore, D.S., and McCabe, G.P. (2003). Introduction to the Practice of Statistics, W.H. Freeman and Co.. [4th ed.]."},{"key":"ref_21","unstructured":"Boslaugh, S., and Watters, P.A. (2008). Statistics in a Nutshell, O\u2019Reilly."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"292","DOI":"10.5951\/MT.102.4.0292","article-title":"The Evolution of Pearson\u2019s Correlation Coefficient","volume":"102","author":"Kader","year":"2008","journal-title":"Math. Teach."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/j.anbehav.2015.01.010","article-title":"Effective Use of Spearman\u2019s and Kendall\u2019s Correlation Coefficients for Association between Two Measured Traits","volume":"102","author":"Puth","year":"2015","journal-title":"Anim. Behav."},{"key":"ref_24","unstructured":"R Core Team (2020). R: The R Project for Statistical Computing, R Foundation for Statistical Computing."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Wickham, H. (2016). Ggplot2: Elegant Graphics for Data Analysis, Springer.","DOI":"10.1007\/978-3-319-24277-4_9"},{"key":"ref_26","unstructured":"Kassambara, A., and Mundt, F. (2022, February 15). Factoextra: Extract and Visualize the Results of Multivariate Data Analyses; CRAN. Available online: https:\/\/scirp.org\/reference\/referencespapers.aspx?referenceid=3067217."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"a003640","DOI":"10.1101\/cshperspect.a003640","article-title":"In Vivo RNAi: Today and Tomorrow","volume":"2","author":"Perrimon","year":"2010","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"ref_28","unstructured":"FlyBase Curators (2020, October 05). Assigning Gene Ontology (GO) Terms by Sequence Similarity in FlyBase. Available online: https:\/\/flybase.org\/reports\/FBrf0202953.html."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"480","DOI":"10.1021\/bi048016f","article-title":"Microsomal Glutathione S -Transferase 1 in the Retinal Pigment Epithelium: Protection against Oxidative Stress and a Potential Role in Aging","volume":"44","author":"Maeda","year":"2005","journal-title":"Biochemistry"},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Liu, H.J., Tan, Y.R., Li, M.L., Liu, C., Xiang, Y., and Qin, X.Q. (2011). Cloning of a Novel Protein Interacting with BRS-3 and Its Effects in Wound Repair of Bronchial Epithelial Cells. PLoS ONE, 6.","DOI":"10.1371\/journal.pone.0023072"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"7705","DOI":"10.1523\/JNEUROSCI.21-19-07705.2001","article-title":"Soluble Guanylate Cyclase Is Required during Development for Visual System Function in Drosophila","volume":"21","author":"Gibbs","year":"2001","journal-title":"J. Neurosci."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"969","DOI":"10.1038\/embor.2008.183","article-title":"Function and Regulation of Protein Neddylation","volume":"9","author":"Rabut","year":"2008","journal-title":"EMBO Rep."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"3460","DOI":"10.1016\/j.bbamcr.2013.06.028","article-title":"ER Stress-Induced Cell Death Mechanisms","volume":"1833","author":"Sano","year":"2013","journal-title":"Biochim. Biophys. Acta BBA-Mol. Cell Res."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"17043","DOI":"10.1073\/pnas.0905566106","article-title":"Suppression of Retinal Degeneration in Drosophila by Stimulation of ER-Associated Degradation","volume":"106","author":"Kang","year":"2009","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"454","DOI":"10.1016\/j.bbrc.2006.05.161","article-title":"A Novel 21-KDa Cytochrome c-Releasing Factor Is Generated upon Treatment of Human Leukemia U937 Cells with Geranylgeraniol","volume":"346","author":"Masuda","year":"2006","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1093\/bib\/bbr042","article-title":"Phylogenetic-Based Propagation of Functional Annotations within the Gene Ontology Consortium","volume":"12","author":"Gaudet","year":"2011","journal-title":"Brief. Bioinform."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"2403","DOI":"10.1101\/gad.1011402","article-title":"Distinct Protein Degradation Mechanisms Mediated by Cul1 and Cul3 Controlling Ci Stability in Drosophila Eye Development","volume":"16","author":"Ou","year":"2002","journal-title":"Genes Dev."},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Kapil, S., Chawla, M., and Ansari, M.D. (2016, January 22\u201324). On K-Means Data Clustering Algorithm with Genetic Algorithm. Proceedings of the 2016 Fourth International Conference on Parallel, Distributed and Grid Computing (PDGC), Waknaghat, India.","DOI":"10.1109\/PDGC.2016.7913145"}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/13\/2\/386\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T22:23:42Z","timestamp":1760135022000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/13\/2\/386"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,2,21]]},"references-count":38,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2022,2]]}},"alternative-id":["genes13020386"],"URL":"https:\/\/doi.org\/10.3390\/genes13020386","relation":{},"ISSN":["2073-4425"],"issn-type":[{"type":"electronic","value":"2073-4425"}],"subject":[],"published":{"date-parts":[[2022,2,21]]}}}