{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T16:11:27Z","timestamp":1790093487907,"version":"4.0.1"},"reference-count":37,"publisher":"Bioscientifica","issue":"9","license":[{"start":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T00:00:00Z","timestamp":1788393600000},"content-version":"vor","delay-in-days":2,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["journals.bioscientifica.com"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2026,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Pheochromocytomas and paragangliomas (PPGLs) are rare neuroendocrine tumors with unique biological behavior and remarkably high heritability, yet dedicated bioinformatics resources for these diagnoses remain limited. Existing cancer multi-omics platforms are pan-cancer in scope, often lacking the disease-specific annotations, granularity, and cross-database harmonization required for meaningful stratification and hypothesis generation. Here, we introduce PPGLomics, an interactive Web-based platform designed for comprehensive PPGL transcriptomics analysis. PPGLomics v1.0 integrates two major datasets, the TCGA-PCPG cohort (n = 160) spanning multiple molecular subtypes and the A5 Consortium SDHB cohort (n = 91) with detailed clinicopathological and molecular annotations. The platform provides basic and clinical scientists, as well as a broad range of healthcare professionals, with tools for differential expression analysis, correlation analysis, survival analysis, and visualization, including boxplots, heatmaps, volcano plots, and Kaplan\u2013Meier survival plots, enabling exploration of gene expression patterns across PPGL subtypes without requiring bioinformatics expertise. PPGLomics v1.0 is freely available at https:\/\/alkaissilab.shinyapps.io\/PPGLomics.<\/jats:p>","DOI":"10.1530\/erc-26-0140","type":"journal-article","created":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T14:38:39Z","timestamp":1788446319000},"update-policy":"https:\/\/doi.org\/10.1530\/crossmarkpolicy-8","source":"Crossref","is-referenced-by-count":0,"title":["PPGLomics: an interactive platform for pheochromocytoma and paraganglioma transcriptomics"],"prefix":"10.1530","volume":"33","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0861-9348","authenticated-orcid":true,"given":"Hussam","family":"Alkaissi","sequence":"first","affiliation":[{"name":"1 Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catherine M","family":"Gordon","sequence":"additional","affiliation":[{"name":"1 Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3541-3767","authenticated-orcid":true,"given":"Karel","family":"Pacak","sequence":"additional","affiliation":[{"name":"1 Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA"},{"name":"Center of Adrenal Endocrine Tumors, AKESO 2 , ,","place":["Prague 5, Czech Republic"]},{"name":"Faculty of Medicine, Palacky University 3 , ,","place":["Olomouc, Czech Republic"]},{"name":"Faculty of Medicine, 5th Department of Medicine, Comenius University 4 , ,","place":["Bratislava, Slovakia"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"416","published-online":{"date-parts":[[2026,9,3]]},"reference":[{"key":"2026092211445757700_bib1","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1038\/35057062","article-title":"Initial sequencing and analysis of the human genome","volume":"409","author":"Lander","year":"2001","journal-title":"Nature"},{"key":"2026092211445757700_bib2","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1038\/s41576-022-00551-z","article-title":"Navigating bottlenecks and trade-offs in genomic data analysis","volume":"24","author":"Berger","year":"2023","journal-title":"Nat Rev Genet"},{"key":"2026092211445757700_bib3","doi-asserted-by":"crossref","first-page":"2063","DOI":"10.1056\/NEJMc2512825","article-title":"Toward same-day genome sequencing in the critical care setting","volume":"393","author":"Wojcik","year":"2025","journal-title":"N Engl J Med"},{"key":"2026092211445757700_bib4","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1038\/ng.2764","article-title":"The cancer genome Atlas pan-cancer analysis project","volume":"45","author":"Weinstein","year":"2013","journal-title":"Nat Genet"},{"key":"2026092211445757700_bib5","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1158\/2159-8290.CD-12-0095","article-title":"The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data","volume":"2","author":"Cerami","year":"2012","journal-title":"Cancer Discov"},{"key":"2026092211445757700_bib6","doi-asserted-by":"crossref","first-page":"W556","DOI":"10.1093\/nar\/gkz430","article-title":"GEPIA2: an enhanced web server for large-scale expression profiling and interactive analysis","volume":"47","author":"Tang","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2026092211445757700_bib7","doi-asserted-by":"crossref","first-page":"649","DOI":"10.1016\/j.neo.2017.05.002","article-title":"UALCAN: a portal for facilitating tumor subgroup gene expression and survival analyses","volume":"19","author":"Chandrashekar","year":"2017","journal-title":"Neoplasia"},{"key":"2026092211445757700_bib8","doi-asserted-by":"crossref","first-page":"D1334","DOI":"10.1093\/nar\/gkab970","article-title":"OncoDB: an interactive online database for analysis of gene expression and viral infection in cancer","volume":"50","author":"Tang","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2026092211445757700_bib9","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1038\/s41587-020-0546-8","article-title":"Visualizing and interpreting cancer genomics data via the Xena platform","volume":"38","author":"Goldman","year":"2020","journal-title":"Nat Biotechnol"},{"key":"2026092211445757700_bib10","doi-asserted-by":"crossref","first-page":"2052","DOI":"10.1097\/CM9.0000000000003254","article-title":"Bioinformatics tools and resources for cancer and application","volume":"137","author":"Huang","year":"2024","journal-title":"Chin Med J Engl"},{"key":"2026092211445757700_bib11","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1530\/ERC-21-0359","article-title":"Head\/neck paragangliomas: focus on tumor location, mutational status and plasma methoxytyramine","volume":"29","author":"Richter","year":"2022","journal-title":"Endocr Relat Cancer"},{"key":"2026092211445757700_bib12","doi-asserted-by":"crossref","first-page":"3296","DOI":"10.1210\/jc.2017-00992","article-title":"Malignant pheochromocytoma and paraganglioma: 272 patients over 55 years","volume":"102","author":"Hamidi","year":"2017","journal-title":"J Clin Endocrinol Metab"},{"key":"2026092211445757700_bib13","doi-asserted-by":"crossref","first-page":"2946","DOI":"10.1210\/clinem\/dgaf259","article-title":"Approach to the patient with metastatic pheochromocytoma and paraganglioma","volume":"110","author":"Alkaissi","year":"2025","journal-title":"J Clin Endocrinol Metab"},{"key":"2026092211445757700_bib14","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1007\/s12022-022-09704-6","article-title":"Overview of the 2022 WHO classification of paragangliomas and pheochromocytomas","volume":"33","author":"Mete","year":"2022","journal-title":"Endocr Pathol"},{"key":"2026092211445757700_bib15","doi-asserted-by":"crossref","first-page":"1253","DOI":"10.1016\/j.eprac.2022.09.003","article-title":"New biology of pheochromocytoma and paraganglioma","volume":"28","author":"Pacak","year":"2022","journal-title":"Endocr Pract"},{"key":"2026092211445757700_bib16","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1016\/j.ccell.2017.01.001","article-title":"Comprehensive molecular characterization of pheochromocytoma and paraganglioma","volume":"31","author":"Fishbein","year":"2017","journal-title":"Cancer Cell"},{"key":"2026092211445757700_bib17","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1038\/nrc3648","article-title":"Pheochromocytoma and paraganglioma pathogenesis: learning from genetic heterogeneity","volume":"14","author":"Dahia","year":"2014","journal-title":"Nat Rev Cancer"},{"key":"2026092211445757700_bib18","doi-asserted-by":"crossref","DOI":"10.1530\/JME-22-0167","article-title":"Genetic bases of pheochromocytoma and paraganglioma","volume":"70","author":"Cascon","year":"2023","journal-title":"J Mol Endocrinol"},{"key":"2026092211445757700_bib19","doi-asserted-by":"crossref","first-page":"2632","DOI":"10.1038\/s41467-025-57595-y","article-title":"Multi-omic analysis of SDHB-deficient pheochromocytomas and paragangliomas identifies metastasis and treatment-related molecular profiles","volume":"16","author":"Flynn","year":"2025","journal-title":"Nat Commun"},{"key":"2026092211445757700_bib20","doi-asserted-by":"crossref","first-page":"2382","DOI":"10.1210\/me.2010-0256","article-title":"Research resource: transcriptional profiling reveals different pseudohypoxic signatures in SDHB and VHL-related pheochromocytomas","volume":"24","author":"Lopez-Jimenez","year":"2010","journal-title":"Mol Endocrinol"},{"key":"2026092211445757700_bib21","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1038\/ng.533","article-title":"Germline mutations in TMEM127 confer susceptibility to pheochromocytoma","volume":"42","author":"Qin","year":"2010","journal-title":"Nat Genet"},{"key":"2026092211445757700_bib22","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1371\/journal.pgen.0010008","article-title":"A HIF1alpha regulatory loop links hypoxia and mitochondrial signals in pheochromocytomas","volume":"1","author":"Dahia","year":"2005","journal-title":"PLoS Genet"},{"key":"2026092211445757700_bib23","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1593\/neo.122132","article-title":"Genotype and tumor locus determine expression profile of pseudohypoxic pheochromocytomas and paragangliomas","volume":"15","author":"Shankavaram","year":"2013","journal-title":"Neoplasia"},{"key":"2026092211445757700_bib24","doi-asserted-by":"crossref","first-page":"2054","DOI":"10.1002\/ijc.28868","article-title":"Opposing effects of HIF1alpha and HIF2alpha on chromaffin cell phenotypic features and tumor cell proliferation: insights from MYC-associated factor X","volume":"135","author":"Qin","year":"2014","journal-title":"Int J Cancer"},{"key":"2026092211445757700_bib25","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1210\/jc.2017-01314","article-title":"Expression of contactin 4 is associated with malignant behavior in pheochromocytomas and paragangliomas","volume":"103","author":"Evenepoel","year":"2018","journal-title":"J Clin Endocrinol Metab"},{"key":"2026092211445757700_bib26","doi-asserted-by":"crossref","first-page":"3974","DOI":"10.1093\/hmg\/ddr324","article-title":"Integrative genomic analysis reveals somatic mutations in pheochromocytoma and paraganglioma","volume":"20","author":"Burnichon","year":"2011","journal-title":"Hum Mol Genet"},{"key":"2026092211445757700_bib27","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1002\/path.6348","article-title":"The evolutionary history of metastatic pancreatic neuroendocrine tumours reveals a therapy driven route to high-grade transformation","volume":"264","author":"Backman","year":"2024","journal-title":"J Pathol"},{"key":"2026092211445757700_bib28","doi-asserted-by":"crossref","DOI":"10.1016\/j.bbadis.2022.166382","article-title":"PIMREG expression level predicts glioblastoma patient survival and affects temozolomide resistance and DNA damage response","volume":"1868","author":"Serafim","year":"2022","journal-title":"Biochim Biophys Acta Mol Basis Dis"},{"key":"2026092211445757700_bib29","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1016\/j.ebiom.2019.04.001","article-title":"Overexpression of PIMREG promotes breast cancer aggressiveness via constitutive activation of NF-kappaB signaling","volume":"43","author":"Jiang","year":"2019","journal-title":"EBioMedicine"},{"key":"2026092211445757700_bib30","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1016\/j.tibs.2010.08.004","article-title":"BUB1 and BUBR1: multifaceted kinases of the cell cycle","volume":"36","author":"Bolanos-Garcia","year":"2011","journal-title":"Trends Biochem Sci"},{"key":"2026092211445757700_bib31","doi-asserted-by":"crossref","first-page":"973","DOI":"10.1152\/physrev.00025.2010","article-title":"Physiological relevance of cell cycle kinases","volume":"91","author":"Malumbres","year":"2011","journal-title":"Physiol Rev"},{"key":"2026092211445757700_bib32","doi-asserted-by":"crossref","first-page":"4461","DOI":"10.1038\/s41598-024-55080-y","article-title":"Expression of the checkpoint kinase BUB1 is a predictor of response to cancer therapies","volume":"14","author":"Ciciro","year":"2024","journal-title":"Sci Rep"},{"key":"2026092211445757700_bib33","doi-asserted-by":"crossref","first-page":"2826","DOI":"10.1016\/j.apsb.2023.03.013","article-title":"Emerging roles of Aurora-A kinase in cancer therapy resistance","volume":"13","author":"Zheng","year":"2023","journal-title":"Acta Pharm Sin B"},{"key":"2026092211445757700_bib34","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-026-49408-z","article-title":"BUB1 as a candidate non-oncogene addiction vulnerability in metastatic phaeochromocytoma\/paraganglioma","volume":"16","author":"Ahmadi","year":"2026","journal-title":"Sci Rep"},{"key":"2026092211445757700_bib35","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.13722","article-title":"The cell proliferation antigen Ki-67 organises heterochromatin","volume":"5","author":"Sobecki","year":"2016","journal-title":"eLife"},{"key":"2026092211445757700_bib36","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1038\/nature18610","article-title":"Ki-67 acts as a biological surfactant to disperse mitotic chromosomes","volume":"535","author":"Cuylen","year":"2016","journal-title":"Nature"},{"key":"2026092211445757700_bib37","doi-asserted-by":"crossref","first-page":"6281","DOI":"10.18632\/oncotarget.7057","article-title":"Ki-67 is required for maintenance of cancer stem cells but not cell proliferation","volume":"7","author":"Cidado","year":"2016","journal-title":"Oncotarget"}],"container-title":["Endocrine-Related Cancer"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.bioscientifica.com\/erc\/article-pdf\/doi\/10.1530\/ERC-26-0140\/524879\/erc-26-0140.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/journals.bioscientifica.com\/erc\/article-pdf\/doi\/10.1530\/ERC-26-0140\/524879\/erc-26-0140.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T15:45:08Z","timestamp":1790091908000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.bioscientifica.com\/erc\/article\/33\/9\/e260140\/78148\/PPGLomics-an-interactive-platform-for"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,1]]},"references-count":37,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2026,9,1]]}},"URL":"https:\/\/doi.org\/10.1530\/erc-26-0140","relation":{},"ISSN":["1351-0088","1479-6821"],"issn-type":[{"value":"1351-0088","type":"print"},{"value":"1479-6821","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,1]]},"article-number":"e260140"}}