{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,7]],"date-time":"2024-09-07T00:36:22Z","timestamp":1725669382395},"reference-count":42,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2024,4,1]],"date-time":"2024-04-01T00:00:00Z","timestamp":1711929600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2024,4,1]],"date-time":"2024-04-01T00:00:00Z","timestamp":1711929600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2024,4,1]],"date-time":"2024-04-01T00:00:00Z","timestamp":1711929600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2024,4,1]],"date-time":"2024-04-01T00:00:00Z","timestamp":1711929600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2024,4,1]],"date-time":"2024-04-01T00:00:00Z","timestamp":1711929600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2024,4,1]],"date-time":"2024-04-01T00:00:00Z","timestamp":1711929600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003395","name":"Shanghai Municipal Education Commission","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003395","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Computational Biology and Chemistry"],"published-print":{"date-parts":[[2024,4]]},"DOI":"10.1016\/j.compbiolchem.2024.108025","type":"journal-article","created":{"date-parts":[[2024,2,6]],"date-time":"2024-02-06T01:20:44Z","timestamp":1707182444000},"page":"108025","update-policy":"http:\/\/dx.doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":1,"special_numbering":"C","title":["Cytokine expression patterns: A single-cell RNA sequencing and machine learning based roadmap for cancer classification"],"prefix":"10.1016","volume":"109","author":[{"ORCID":"http:\/\/orcid.org\/0000-0002-4104-3790","authenticated-orcid":false,"given":"Zhixiang","family":"Ren","sequence":"first","affiliation":[]},{"given":"Yiming","family":"Ren","sequence":"additional","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0001-6130-6968","authenticated-orcid":false,"given":"Pengfei","family":"Liu","sequence":"additional","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0002-9009-3786","authenticated-orcid":false,"given":"Huan","family":"Xu","sequence":"additional","affiliation":[]}],"member":"78","reference":[{"key":"10.1016\/j.compbiolchem.2024.108025_bib1","first-page":"86","article-title":"Cytokine production by tumor bioptate at different pathological prognostic stages in breast cancer","volume":"volume 497","author":"AIAutenshlyus","year":"2021"},{"key":"10.1016\/j.compbiolchem.2024.108025_bib2","first-page":"14","article-title":"Machine learning for neuroimaging with scikit-learn","volume":"8","author":"Alexandre Abraham","year":"2014","journal-title":"Front. Neuroinform."},{"key":"10.1016\/j.compbiolchem.2024.108025_bib3","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1016\/j.ctrv.2017.08.004","article-title":"Interleukin-8 in cancer pathogenesis, treatment and follow-up","volume":"60","author":"Alfaro","year":"2017","journal-title":"Cancer Treat. Rev."},{"key":"10.1016\/j.compbiolchem.2024.108025_bib4","doi-asserted-by":"crossref","unstructured":"Amodio, Matthew, Van Dijk,, David, Srinivasan, Krishnan, Chen, William S., Mohsen, Hussein, Moon, Kevin R., Campbell, Allison, Zhao, Yujiao, Wang, Xiaomei, Venkataswamy, Manjunathaet al. Exploring 2019.single-cell data with deep multitasking neural networks Nature methods, 16(11):1139\u20131145..","DOI":"10.1038\/s41592-019-0576-7"},{"issue":"2","key":"10.1016\/j.compbiolchem.2024.108025_bib5","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1038\/s41590-018-0276-y","article-title":"Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage","volume":"20","author":"Aran","year":"2019","journal-title":"Nat. Immunol."},{"issue":"D1","key":"10.1016\/j.compbiolchem.2024.108025_bib6","doi-asserted-by":"crossref","first-page":"D711","DOI":"10.1093\/nar\/gky964","article-title":"Arrayexpress update\u2013 from bulk to single-cell expression data","volume":"47","author":"Athar","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.compbiolchem.2024.108025_bib7","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/j.cbpa.2020.02.005","article-title":"Advances in theranostic biomarkers for tumor immunotherapy","volume":"56","author":"Bellesoeur","year":"2020","journal-title":"Curr. Opin. Chem. Biol."},{"issue":"1","key":"10.1016\/j.compbiolchem.2024.108025_bib8","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-018-34242-9","article-title":"Radiogenomics profiling for glioblastoma- related immune cells reveals cd49d expression correlation with mri parameters and prognosis","volume":"8","author":"Cho","year":"2018","journal-title":"Sci. Rep."},{"issue":"9","key":"10.1016\/j.compbiolchem.2024.108025_bib9","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0272302","article-title":"Tmexplorer: a tumour microenvironment single-cell rnaseq database and search tool","volume":"17","author":"Christensen","year":"2022","journal-title":"Plos One"},{"key":"10.1016\/j.compbiolchem.2024.108025_bib10","doi-asserted-by":"crossref","unstructured":"Diakos, Connie I., Charles, Kellie A., McMillan, Donald C., Clarke, Stephen J.Cancer-related inflammation and treatment effec- tiveness. , :\u2013, 2014.and The Lancet Oncology1511e493e503..","DOI":"10.1016\/S1470-2045(14)70263-3"},{"issue":"S1","key":"10.1016\/j.compbiolchem.2024.108025_bib11","doi-asserted-by":"crossref","first-page":"S34","DOI":"10.1002\/eji.200737772","article-title":"Historical insights into cytokines.","volume":"37","author":"Dinarello","year":"2007","journal-title":"Eur. J. Immunol."},{"issue":"1","key":"10.1016\/j.compbiolchem.2024.108025_bib12","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1186\/s13045-021-01103-4","article-title":"Spatial architecture of the immune microenvironment orchestrates tumor immunity and therapeutic re- sponse","volume":"14","author":"Fu","year":"2021","journal-title":"J. Hematol. Oncol."},{"issue":"10","key":"10.1016\/j.compbiolchem.2024.108025_bib13","doi-asserted-by":"crossref","first-page":"1014","DOI":"10.1038\/ni.2703","article-title":"Innate and adaptive immune cells in the tumor microenvironment","volume":"14","author":"Gajewski","year":"2013","journal-title":"Nat. Immunol."},{"issue":"13","key":"10.1016\/j.compbiolchem.2024.108025_bib14","doi-asserted-by":"crossref","first-page":"3573","DOI":"10.1016\/j.cell.2021.04.048","article-title":"Integrated analysis of multimodal single-cell data","volume":"184","author":"Hao","year":"2021","journal-title":"Cell"},{"key":"10.1016\/j.compbiolchem.2024.108025_bib15","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1016\/j.pharmthera.2017.02.025","article-title":"Interleukin 32, inflammation and cancer","volume":"174","author":"Hong","year":"2017","journal-title":"Pharmacol. Ther."},{"issue":"D1","key":"10.1016\/j.compbiolchem.2024.108025_bib16","first-page":"D77","article-title":"Expression atlas update: from tissues to single cells","volume":"48","author":"Irene Papatheodorou","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.compbiolchem.2024.108025_bib17","doi-asserted-by":"crossref","unstructured":"Jan Dohmen, Artem Baranovskii, Jonathan Ronen, Bora Uyar, Franke, Ve- dran, Altuna Akalin. Identifying tumor cells at the single-2022., and cell level using machine learning Genome Biology, 23(1):123..","DOI":"10.1186\/s13059-022-02683-1"},{"key":"10.1016\/j.compbiolchem.2024.108025_bib18","unstructured":"Jian Hu,, Xiangjie, Li, Kyle Coleman, Amelia Schroeder, Nan Ma, David, J., Irwin, Edward, Lee, B., Russell, T., Shinohara, Mingyao Li. Spagcn: Integrating gene expression, spatial location and histology. 2021.to identify spatial domains and spatially variable genes by graph convolutional networkNature methods181113421351.."},{"issue":"D1","key":"10.1016\/j.compbiolchem.2024.108025_bib19","doi-asserted-by":"crossref","first-page":"D1147","DOI":"10.1093\/nar\/gkab905","article-title":"Cancerscem: a database of single-cell expression map across various human cancers","volume":"50","author":"Jingyao Zeng","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.compbiolchem.2024.108025_bib20","doi-asserted-by":"crossref","unstructured":"Kanehisa, Minoru, Furumichi, Miho, Sato, Yoko, Kawashima, Masayuki, Ishiguro-Watanabe, Mari\u00a0Kegg for taxonomy-based analysis of pathways and genomes., 51(D1):D587\u2013D592,2023., and Nucleic acids research..","DOI":"10.1093\/nar\/gkac963"},{"issue":"5","key":"10.1016\/j.compbiolchem.2024.108025_bib21","doi-asserted-by":"crossref","first-page":"1360","DOI":"10.1093\/bioinformatics\/btz772","article-title":"Cancer classification of single-cell gene expression data by neural network","volume":"36","author":"Kim","year":"2020","journal-title":"Bioinformatics"},{"issue":"7-8","key":"10.1016\/j.compbiolchem.2024.108025_bib22","doi-asserted-by":"crossref","first-page":"2000144","DOI":"10.1002\/pmic.202000144","article-title":"Global analysis of lysine acetylome reveals the potential role of ccl18 in non- small cell lung cancer","volume":"21","author":"Kong","year":"2021","journal-title":"Proteomics"},{"issue":"13","key":"10.1016\/j.compbiolchem.2024.108025_bib23","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2020.108566","article-title":"Aging- associated alterations in mammary epithelia and stroma revealed by single-cell rna sequencing","volume":"33","author":"Li","year":"2020","journal-title":"Cell Rep."},{"key":"10.1016\/j.compbiolchem.2024.108025_bib24","doi-asserted-by":"crossref","DOI":"10.1016\/j.intimp.2020.106939","article-title":"Effects of immune cells and cytokines on inflammation and immunosuppression in the tumor microenvironment","volume":"88","author":"Li","year":"2020","journal-title":"Int. Immunopharmacol."},{"issue":"6","key":"10.1016\/j.compbiolchem.2024.108025_bib25","doi-asserted-by":"crossref","first-page":"e218","DOI":"10.1016\/S1470-2045(12)70582-X","article-title":"Cytokine patterns in patients with cancer: a systematic review","volume":"14","author":"Lippitz","year":"2013","journal-title":"Lancet Oncol."},{"issue":"1","key":"10.1016\/j.compbiolchem.2024.108025_bib26","doi-asserted-by":"crossref","DOI":"10.1136\/jitc-2020-001895","article-title":"Blocking il-17a\u00a0enhances tumor response to anti-pd\u22121 immunotherapy in microsatel- lite stable colorectal cancer","volume":"9","author":"Liu","year":"2021","journal-title":"J. Immunother. Cancer"},{"key":"10.1016\/j.compbiolchem.2024.108025_bib27","article-title":"A step-by- step workflow for low-level analysis of single-cell rna-seq data with bioconductor","volume":"5","author":"Lun","year":"2016","journal-title":"F1000Research"},{"issue":"1","key":"10.1016\/j.compbiolchem.2024.108025_bib28","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2164-14-632","article-title":"An expression atlas of human primary cells: inference of gene function from coexpression networks","volume":"14","author":"Mabbott","year":"2013","journal-title":"BMC Genom."},{"issue":"2","key":"10.1016\/j.compbiolchem.2024.108025_bib29","doi-asserted-by":"crossref","DOI":"10.1016\/j.ygeno.2022.01.001","article-title":"Panclassif: improving pan cancer classification of single cell rna-seq gene expression data using machine learning","volume":"114","author":"Mahin","year":"2022","journal-title":"Genomics"},{"key":"10.1016\/j.compbiolchem.2024.108025_bib30","first-page":"236","article-title":"Unravel- ing the crosstalk between melanoma and immune cells in the tumor microenvironment","volume":"volume 59","author":"Marzagalli","year":"2019"},{"key":"10.1016\/j.compbiolchem.2024.108025_bib31","doi-asserted-by":"crossref","first-page":"671","DOI":"10.3389\/fgene.2019.00671","article-title":"Pan- cancer and single-cell modeling of genomic alterations through gene expression","volume":"10","author":"Mercatelli","year":"2019","journal-title":"Front. Genet."},{"key":"10.1016\/j.compbiolchem.2024.108025_bib32","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1007\/978-3-030-36667-4_3","article-title":"Ccl4 signaling in the tumor microenvironment.","author":"Mukaida","year":"2020","journal-title":"Tumor Microenviron.: Role Chemokines\u2013Part A"},{"issue":"1","key":"10.1016\/j.compbiolchem.2024.108025_bib33","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1038\/s41416-018-0328-y","article-title":"Cytokines in clinical cancer immunotherapy","volume":"120","author":"Pedro Berraondo","year":"2019","journal-title":"Br. J. Cancer"},{"issue":"24","key":"10.1016\/j.compbiolchem.2024.108025_bib34","doi-asserted-by":"crossref","first-page":"11906","DOI":"10.1073\/pnas.1818488116","article-title":"Single-cell rna sequencing unveils the shared and the distinct cytotoxic hallmarks of human tcrv\u03b41 and tcrv\u03b42 Y\u03b4 t lymphocytes","volume":"116","author":"Pizzolato","year":"2019","journal-title":"Proc. Natl. Acad. Sci."},{"issue":"4","key":"10.1016\/j.compbiolchem.2024.108025_bib35","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1038\/s41593-020-00789-y","article-title":"Single-cell profiling of myeloid cells in glioblastoma across species and disease stage reveals macrophage competition and specialization","volume":"24","author":"Pombo Antunes","year":"2021","journal-title":"Nat. Neurosci."},{"issue":"4","key":"10.1016\/j.compbiolchem.2024.108025_bib36","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1038\/s41571-021-00588-9","article-title":"Harnessing cytokines and chemokines for cancer therapy","volume":"19","author":"Propper","year":"2022","journal-title":"Nat. Rev. Clin. Oncol."},{"key":"10.1016\/j.compbiolchem.2024.108025_bib37","doi-asserted-by":"crossref","unstructured":"Yafang Qian, Peng Ding, Jie Xu, Xiaohu Nie, and Bin Lu. Ccl2 activates akt signaling to promote glycolysis and chemoresistance in glioma cells. Cell Biology International, 46(5):819\u2013828, 2022.","DOI":"10.1002\/cbin.11778"},{"key":"10.1016\/j.compbiolchem.2024.108025_bib38","doi-asserted-by":"crossref","unstructured":"Farhad Seif, Zahra Torki, Hamidreza Zalpoor, Mehran Habibi, , Majid Pornour. Breast cancer tumor microenvironment affects treg\/il17-producing treg\/th17 cell axis: Molecular and therapeutic perspectives. Molecular Therapy Oncolytics, 28:132, 2023.","DOI":"10.1016\/j.omto.2023.01.001"},{"key":"10.1016\/j.compbiolchem.2024.108025_bib39","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1007\/978-1-0716-1307-8_19","article-title":"Single-cell rna sequencing analysis: a step-by-step overview","author":"Slovin","year":"2021","journal-title":"RNA Bioinforma."},{"key":"10.1016\/j.compbiolchem.2024.108025_bib40","doi-asserted-by":"crossref","unstructured":"Dongqing Sun, Jin Wang, Ya Han, Xin Dong, Jun Ge, Rongbin Zheng, Xiaoying Shi, Binbin Wang, Ziyi Li, Pengfei Ren, et al. Tisch: a comprehensive web resource enabling interactive single- cell transcriptome visualization of tumor microenvironment. Nucleic acids research, 49(D1):D1420\u2013D1430, 2021.","DOI":"10.1093\/nar\/gkaa1020"},{"issue":"D1","key":"10.1016\/j.compbiolchem.2024.108025_bib41","doi-asserted-by":"crossref","first-page":"D991","DOI":"10.1093\/nar\/gks1193","article-title":"Ncbi geo: archive for functional genomics data sets\u2014update","volume":"41","author":"Tanya Barrett","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.compbiolchem.2024.108025_bib42","doi-asserted-by":"crossref","unstructured":"Juexin Wang, Anjun Ma,Yuzhou Chang, Jianting Gong, Yuexu Jiang, Ren Qi, Cankun Wang, Hongjun Fu, Qin Ma, and Dong Xu. scgnn is a novel graph neural network framework for single-cell rna-seq analyses. Nature communications, 12(1):1882, 2021.","DOI":"10.1038\/s41467-021-22197-x"}],"container-title":["Computational Biology and Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1476927124000136?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1476927124000136?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2024,3,20]],"date-time":"2024-03-20T11:34:38Z","timestamp":1710934478000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1476927124000136"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,4]]},"references-count":42,"alternative-id":["S1476927124000136"],"URL":"https:\/\/doi.org\/10.1016\/j.compbiolchem.2024.108025","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.06.01.542694","asserted-by":"object"}]},"ISSN":["1476-9271"],"issn-type":[{"type":"print","value":"1476-9271"}],"subject":[],"published":{"date-parts":[[2024,4]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Cytokine expression patterns: A single-cell RNA sequencing and machine learning based roadmap for cancer classification","name":"articletitle","label":"Article Title"},{"value":"Computational Biology and Chemistry","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.compbiolchem.2024.108025","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2024 Elsevier Ltd. All rights reserved.","name":"copyright","label":"Copyright"}],"article-number":"108025"}}