{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,27]],"date-time":"2025-03-27T19:54:26Z","timestamp":1743105266905,"version":"3.40.3"},"publisher-location":"Cham","reference-count":37,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783031062193"},{"type":"electronic","value":"9783031062209"}],"license":[{"start":{"date-parts":[[2022,1,1]],"date-time":"2022-01-01T00:00:00Z","timestamp":1640995200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2022,1,1]],"date-time":"2022-01-01T00:00:00Z","timestamp":1640995200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022]]},"DOI":"10.1007\/978-3-031-06220-9_18","type":"book-chapter","created":{"date-parts":[[2022,5,14]],"date-time":"2022-05-14T12:10:26Z","timestamp":1652530226000},"page":"311-339","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Deciphering the\u00a0Tissue-Specific Regulatory Role of\u00a0Intronless Genes Across Cancers"],"prefix":"10.1007","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6338-7930","authenticated-orcid":false,"given":"Katia","family":"Avi\u00f1a-Padilla","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3800-2434","authenticated-orcid":false,"given":"Jos\u00e9 Antonio","family":"Ram\u00edrez-Rafael","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7358-6637","authenticated-orcid":false,"given":"Octavio","family":"Zambada-Moreno","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1737-196X","authenticated-orcid":false,"given":"Gabriel Emilio","family":"Herrera-Oropeza","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9363-4106","authenticated-orcid":false,"given":"Guillermo","family":"Romero","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8934-9919","authenticated-orcid":false,"given":"Ishaan","family":"Gupta","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1878-1223","authenticated-orcid":false,"given":"Maribel","family":"Hern\u00e1ndez-Rosales","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2022,5,15]]},"reference":[{"key":"18_CR1","doi-asserted-by":"publisher","unstructured":"Ademuwagun, I., et al.: Contributors. In: Forero, D.A., Patrinos, G.P. (eds.) Genome Plasticity in Health and Disease, pp. xi\u2013xiv. Translational and Applied Genomics, Academic Press (2020). https:\/\/doi.org\/10.1016\/B978-0-12-817819-5.01002-0. https:\/\/www.sciencedirect.com\/science\/article\/pii\/B9780128178195010020","DOI":"10.1016\/B978-0-12-817819-5.01002-0"},{"key":"18_CR2","doi-asserted-by":"publisher","unstructured":"Amigo, J.D., et al.: The reprimo gene family: a novel gene lineage in gastric cancer with tumor suppressive properties. Int. J. Mol. Sci. 19(7), 1862 (2018). https:\/\/doi.org\/10.3390\/ijms19071862. https:\/\/www.mdpi.com\/1422-0067\/19\/7\/1862","DOI":"10.3390\/ijms19071862"},{"key":"18_CR3","unstructured":"An, G., et al.: Cloning and characterization of UROC28, a novel gene overexpressed in prostate, breast, and bladder cancers1. Cancer Res. 60(24), 7014\u20137020 (2000)"},{"key":"18_CR4","doi-asserted-by":"publisher","unstructured":"Avi\u00f1a-Padilla, K., et al.: Evolutionary perspective and expression analysis of intronless genes highlight the conservation of their regulatory role. Front. Genet. 12, 1101 (2021). https:\/\/doi.org\/10.3389\/fgene.2021.654256. https:\/\/www.frontiersin.org\/article\/10.3389\/fgene.2021.654256","DOI":"10.3389\/fgene.2021.654256"},{"key":"18_CR5","doi-asserted-by":"publisher","unstructured":"Bujko, M., Kober, P., Mikula, M., Ligaj, M., Ostrowski, J., Siedlecki, J.: Expression changes of cell-cell adhesion-related genes in colorectal tumors. Oncol. Lett. 9, 2463\u20132470 (2015). https:\/\/doi.org\/10.3892\/ol.2015.3107. https:\/\/doi.org\/10.3109\/10428194.2010.514968. pMID 20919851","DOI":"10.3892\/ol.2015.3107"},{"key":"18_CR6","doi-asserted-by":"publisher","unstructured":"Chen, K., Bao, Z., hua Gong, W., Tang, P.C., Yoshimura, T., Wang, J.M.: Regulation of inflammation by members of the formyl-peptide receptor family. J. Autoimmun. 85, 64\u201377 (2017). https:\/\/doi.org\/10.1016\/j.jaut.2017.06.012. https:\/\/pubmed.ncbi.nlm.nih.gov\/28689639\/","DOI":"10.1016\/j.jaut.2017.06.012"},{"key":"18_CR7","doi-asserted-by":"publisher","unstructured":"Colaprico, A., et al.: TCGAbiolinks: an R\/Bioconductor package for integrative analysis of TCGA data. Nucleic Acids Res. 44(8), e71\u2013e71 (2015). https:\/\/doi.org\/10.1093\/nar\/gkv1507","DOI":"10.1093\/nar\/gkv1507"},{"issue":"2","key":"18_CR8","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1007\/s00428-020-02750-7","volume":"477","author":"GA Croci","year":"2020","unstructured":"Croci, G.A., et al.: Reproducibility of histologic prognostic parameters for mantle cell lymphoma: cytology, Ki67, p53 and SOX11. Virchows Arch. 477(2), 259\u2013267 (2020). https:\/\/doi.org\/10.1007\/s00428-020-02750-7","journal-title":"Virchows Arch."},{"key":"18_CR9","doi-asserted-by":"publisher","unstructured":"Dai, E., Zhu, Z., Wahed, S., Qu, Z., Storkus, W., Guo, Z.S.: Epigenetic modulation of antitumor immunity for improved cancer immunotherapy. Mol. Cancer 20, 141\u2013152 (2021). https:\/\/doi.org\/10.1186\/s12943-021-01464-x. https:\/\/link.springer.com\/article\/10.1007\/s10555-020-09944-0","DOI":"10.1186\/s12943-021-01464-x"},{"key":"18_CR10","doi-asserted-by":"publisher","first-page":"472","DOI":"10.1101\/gad.1267105","volume":"19","author":"J Dai","year":"2005","unstructured":"Dai, J., Sultan, S., Taylor, S.S., Higgins, J.M.: The kinase haspin is required for mitotic histone H3 Thr 3 phosphorylation and normal metaphase chromosome alignment. Genes Dev. 19, 472\u2013488 (2005). https:\/\/doi.org\/10.1101\/gad.1267105","journal-title":"Genes Dev."},{"key":"18_CR11","doi-asserted-by":"publisher","unstructured":"Denny, J.C., et al.: Variants near foxe1 are associated with hypothyroidism and other thyroid conditions: using electronic medical records for genome- and phenome-wide studies. Am. J. Hum. Genet. 89(4), 529\u2013542 (2011). https:\/\/doi.org\/10.1016\/j.ajhg.2011.09.008. https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0002929711003983","DOI":"10.1016\/j.ajhg.2011.09.008"},{"key":"18_CR12","doi-asserted-by":"publisher","unstructured":"Goh, K.I., Cusick, M.E., Valle, D., Childs, B., Vidal, M., Barab\u00e1si, A.L.: The human disease network. Proc. Natl. Acad. Sci. 104(21), 8685\u20138690 (2007). https:\/\/doi.org\/10.1073\/pnas.0701361104. https:\/\/www.pnas.org\/doi\/abs\/10.1073\/pnas.0701361104","DOI":"10.1073\/pnas.0701361104"},{"key":"18_CR13","doi-asserted-by":"publisher","unstructured":"Grzybowska, E.A.: Human intronless genes: functional groups, associated diseases, evolution, and mrna processing in absence of splicing. Biochem. Biophys. Res. Commun. 424(1), 1\u20136 (2012). https:\/\/doi.org\/10.1016\/j.bbrc.2012.06.092. https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0006291X12011874","DOI":"10.1016\/j.bbrc.2012.06.092"},{"key":"18_CR14","doi-asserted-by":"crossref","unstructured":"Hagberg, A., Swart, P., Chult, D.: Exploring network structure, dynamics, and function using networkx, pp. 11\u201315 (2008)","DOI":"10.25080\/TCWV9851"},{"key":"18_CR15","doi-asserted-by":"publisher","unstructured":"Herrera-Oropeza, G.E., Angulo-Rojo, C., G\u00e1stelum-L\u00f3pez, S.A., Varela-Echavarr\u00eda, A., Hern\u00e1ndez-Rosales, M., Avi\u00f1a-Padilla, K.: Glioblastoma multiforme: a multi-omics analysis of driver genes and tumour heterogeneity. Interface Focus 11(4), 20200072 (2021). https:\/\/doi.org\/10.1098\/rsfs.2020.0072. https:\/\/royalsocietypublishing.org\/doi\/abs\/10.1098\/rsfs.2020.0072","DOI":"10.1098\/rsfs.2020.0072"},{"issue":"S2","key":"18_CR16","doi-asserted-by":"publisher","first-page":"8685","DOI":"10.1186\/s12918-018-0537-2","volume":"12","author":"SH Huang","year":"2018","unstructured":"Huang, S.H., Lo, Y.S., Luo, Y.C., Tseng, Y.Y., Yang, J.M.: A homologous mapping method for three-dimensional reconstruction of protein networks reveals disease-associated mutations. BMC Syst. Biol. 12(S2), 8685\u20138690 (2018)","journal-title":"BMC Syst. Biol."},{"key":"18_CR17","doi-asserted-by":"publisher","unstructured":"Hung, M.S., et al.: Functional polymorphism of the ck2$$\\alpha $$ intronless gene plays oncogenic roles in lung cancer. PLoS ONE 5(7), 1\u201310 (2010). https:\/\/doi.org\/10.1371\/journal.pone.0011418","DOI":"10.1371\/journal.pone.0011418"},{"key":"18_CR18","doi-asserted-by":"crossref","unstructured":"Inamdar, A.A., et al.: Mantle cell lymphoma in the era of precision medicine-diagnosis, biomarkers and therapeutic agents. Oncotarget 7(30), 48692\u201348731 (2016). https:\/\/doi.org\/10.18632\/oncotarget.8961. https:\/\/www.oncotarget.com\/article\/8961\/","DOI":"10.18632\/oncotarget.8961"},{"key":"18_CR19","doi-asserted-by":"publisher","unstructured":"Jao, T.M., et al.: PCDH10 exerts tumor-suppressor functions through modulation of EGFR\/AKT axis in colorectal cancer. Cancer Lett. 499, 290\u2013300 (2021). https:\/\/doi.org\/10.1016\/j.canlet.2020.11.017. https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0304383520306108","DOI":"10.1016\/j.canlet.2020.11.017"},{"key":"18_CR20","doi-asserted-by":"publisher","unstructured":"Krzywinski, M., et al.: Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639\u20131645 (2009). https:\/\/doi.org\/10.1101\/gr.092759.109. https:\/\/genome.cshlp.org\/content\/19\/9\/1639","DOI":"10.1101\/gr.092759.109"},{"key":"18_CR21","doi-asserted-by":"publisher","unstructured":"Lachmann, A., Giorgi, F.M., Lopez, G., Califano, A.: ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information. Bioinformatics 32(14), 2233\u20132235 (2016). https:\/\/doi.org\/10.1093\/bioinformatics\/btw216","DOI":"10.1093\/bioinformatics\/btw216"},{"key":"18_CR22","doi-asserted-by":"publisher","unstructured":"Le, Y., Murphy, P.M., Wang, J.M.: Formyl-peptide receptors revisited. Trends Immunol. 23(11), 541\u2013548 (2002). https:\/\/doi.org\/10.1016\/S1471-4906(02)02316-5. https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1471490602023165","DOI":"10.1016\/S1471-4906(02)02316-5"},{"key":"18_CR23","doi-asserted-by":"publisher","unstructured":"Liang, W., et al.: The contribution of chemoattractant GPCRs, formylpeptide receptors, to inflammation and cancer. Front. Endocrinol. 11, 17 (2020). https:\/\/doi.org\/10.3389\/fendo.2020.00017. https:\/\/www.readcube.com\/articles\/10.3389\/fendo.2020.00017","DOI":"10.3389\/fendo.2020.00017"},{"key":"18_CR24","doi-asserted-by":"publisher","unstructured":"Liu, X.Y., et al.: Methylation of SOX1 and vim promoters in serum as potential biomarkers for hepatocellular carcinoma. Neoplasma 64, 745\u2013753 (2017). https:\/\/doi.org\/10.4149\/neo_2017_513","DOI":"10.4149\/neo_2017_513"},{"key":"18_CR25","unstructured":"Marcel, R., Lucas, S., Sean, D., Levi, W.: TCGAutils: TCGA utility functions for data management (2021). https:\/\/bioconductor.org\/packages\/release\/bioc\/html\/TCGAutils.html. R package version 1.14.4"},{"key":"18_CR26","doi-asserted-by":"publisher","unstructured":"Martin, A.M., Kulski, J.K., Witt, C., Pontarotti, P., Christiansen, F.T.: Leukocyte Ig-like receptor complex (LRC) in mice and men. Trends Immunol. 23(2), 81\u201388 (2002). https:\/\/doi.org\/10.1016\/S1471-4906(01)02155-X. https:\/\/www.sciencedirect.com\/science\/article\/pii\/S147149060102155X","DOI":"10.1016\/S1471-4906(01)02155-X"},{"key":"18_CR27","doi-asserted-by":"publisher","unstructured":"Ohki, R., et al.: Reprimo, a new candidate mediator of the P53-mediated cell cycle arrest at the G2 phase*. J. Biol. Chem. 275(30), 22627\u201322630 (2000). https:\/\/doi.org\/10.1074\/jbc.C000235200. https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0021925819661077","DOI":"10.1074\/jbc.C000235200"},{"key":"18_CR28","doi-asserted-by":"publisher","unstructured":"Pan, J., et al.: Lineage-specific epigenomic and genomic activation of oncogene HNF4A promotes gastrointestinal adenocarcinomas. Cancer Res. 80(13), 2722\u20132736 (2020). https:\/\/doi.org\/10.1158\/0008-5472.CAN-20-0390","DOI":"10.1158\/0008-5472.CAN-20-0390"},{"key":"18_CR29","unstructured":"Pedregosa, F., et al.: Scikit-learn: machine learning in python. J. Mach. Learn. Res. 12, 2825\u20132830 (2012). https:\/\/www.jmlr.org\/papers\/volume12\/pedregosa11a\/pedregosa11a.pdf"},{"issue":"3","key":"18_CR30","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1007\/s00428-015-1840-6","volume":"468","author":"B Sander","year":"2015","unstructured":"Sander, B., et al.: Mantle cell lymphoma\u2014a spectrum from indolent to aggressive disease. Virchows Arch. 468(3), 245\u2013257 (2015). https:\/\/doi.org\/10.1007\/s00428-015-1840-6","journal-title":"Virchows Arch."},{"key":"18_CR31","doi-asserted-by":"publisher","unstructured":"Sander, B.: Mantle cell lymphoma: recent insights into pathogenesis, clinical variability, and new diagnostic markers. Semin. Diagn. Pathol. 28(3), 245\u2013255 (2011). https:\/\/doi.org\/10.1053\/j.semdp.2011.02.010. https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0740257011000153. Seminars on Lymphomas, Part II","DOI":"10.1053\/j.semdp.2011.02.010"},{"key":"18_CR32","doi-asserted-by":"publisher","unstructured":"Szklarczyk, D., et al.: The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene\/measurement sets. Nucleic Acids Res. 49(D1), D605\u2013D612 (2020). https:\/\/doi.org\/10.1093\/nar\/gkaa1074","DOI":"10.1093\/nar\/gkaa1074"},{"key":"18_CR33","doi-asserted-by":"publisher","unstructured":"Verhaegen, M.E., et al.: Merkel cell polyomavirus small T antigen initiates merkel cell carcinoma-like tumor development in mice. Cancer Res. 77(12), 3151\u20133157 (2017). https:\/\/doi.org\/10.1158\/0008-5472.CAN-17-0035","DOI":"10.1158\/0008-5472.CAN-17-0035"},{"key":"18_CR34","doi-asserted-by":"publisher","unstructured":"Wang, F., et al.: Histone H3 Thr-3 phosphorylation by haspin positions aurora b at centromeres in mitosis. Science 330(6001), 231\u2013235 (2010). https:\/\/doi.org\/10.1126\/science.1189435. https:\/\/www.science.org\/doi\/abs\/10.1126\/science.1189435","DOI":"10.1126\/science.1189435"},{"key":"18_CR35","unstructured":"Wang, Y.Y., et al.: Expression of SOX11 mRNA in mantle cell lymphoma and its clinical significance. Zhonghua xue ye xue za zhi = Zhonghua xueyexue zazhi 33(7), 556\u2013560 (2012). http:\/\/europepmc.org\/abstract\/MED\/22967417"},{"key":"18_CR36","doi-asserted-by":"publisher","unstructured":"Xu, W., Li, J.Y.: SOX11 expression in mantle cell lymphoma. Leuk. Lymphoma 51(11), 1962\u20131967 (2010). https:\/\/doi.org\/10.3109\/10428194.2010.514968. pMID 20919851","DOI":"10.3109\/10428194.2010.514968"},{"key":"18_CR37","doi-asserted-by":"publisher","unstructured":"Yao, Z., et al.: The role of tumor suppressor gene SOX11 in prostate cancer. Tumour Biol. 8(36), 6133\u20136138 (2015). https:\/\/doi.org\/10.1007\/s13277-015-3296-3. http:\/\/europepmc.org\/abstract\/MED\/22967417","DOI":"10.1007\/s13277-015-3296-3"}],"container-title":["Lecture Notes in Computer Science","Comparative Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-031-06220-9_18","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,9,24]],"date-time":"2024-09-24T20:05:50Z","timestamp":1727208350000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-3-031-06220-9_18"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022]]},"ISBN":["9783031062193","9783031062209"],"references-count":37,"URL":"https:\/\/doi.org\/10.1007\/978-3-031-06220-9_18","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2022]]},"assertion":[{"value":"15 May 2022","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"RECOMB-CG","order":1,"name":"conference_acronym","label":"Conference Acronym","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"RECOMB International Workshop on Comparative Genomics","order":2,"name":"conference_name","label":"Conference Name","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"La Jolla, CA","order":3,"name":"conference_city","label":"Conference City","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"USA","order":4,"name":"conference_country","label":"Conference Country","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2022","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"20 May 2022","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"21 May 2022","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"19","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"rcg2022","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"https:\/\/recombcg2022.usask.ca\/","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Single-blind","order":1,"name":"type","label":"Type","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"EasyChair","order":2,"name":"conference_management_system","label":"Conference Management System","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"28","order":3,"name":"number_of_submissions_sent_for_review","label":"Number of Submissions Sent for Review","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"18","order":4,"name":"number_of_full_papers_accepted","label":"Number of Full Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"0","order":5,"name":"number_of_short_papers_accepted","label":"Number of Short Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"64% - The value is computed by the equation \"Number of Full Papers Accepted \/ Number of Submissions Sent for Review * 100\" and then rounded to a whole number.","order":6,"name":"acceptance_rate_of_full_papers","label":"Acceptance Rate of Full Papers","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"4","order":7,"name":"average_number_of_reviews_per_paper","label":"Average Number of Reviews per Paper","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"2","order":8,"name":"average_number_of_papers_per_reviewer","label":"Average Number of Papers per Reviewer","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"No","order":9,"name":"external_reviewers_involved","label":"External Reviewers Involved","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}}]}}