{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T22:40:00Z","timestamp":1785796800004,"version":"3.56.0"},"reference-count":37,"publisher":"Springer Science and Business Media LLC","issue":"S7","license":[{"start":{"date-parts":[[2018,12,1]],"date-time":"2018-12-01T00:00:00Z","timestamp":1543622400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2018,12]]},"DOI":"10.1186\/s12918-018-0639-x","type":"journal-article","created":{"date-parts":[[2018,12,14]],"date-time":"2018-12-14T09:21:43Z","timestamp":1544779303000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":29,"title":["Co-expression of long non-coding RNAs and autism risk genes in the developing human brain"],"prefix":"10.1186","volume":"12","author":[{"given":"Steven B.","family":"Cogill","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anand K.","family":"Srivastava","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mary Qu","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liangjiang","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2018,12,14]]},"reference":[{"key":"639_CR1","doi-asserted-by":"publisher","first-page":"159","DOI":"10.1016\/j.canlet.2013.06.013","volume":"339","author":"X Shi","year":"2013","unstructured":"Shi X, et al. Long non-coding RNAs: a new frontier in the study of human diseases. Cancer Lett. 2013;339:159\u201366.","journal-title":"Cancer Lett"},{"key":"639_CR2","doi-asserted-by":"publisher","first-page":"689","DOI":"10.1126\/science.1192002","volume":"329","author":"M Tsai","year":"2010","unstructured":"Tsai M, et al. Long noncoding RNA as modular scaffold of histone modification complexes. Science. 2010;329:689\u201393.","journal-title":"Science"},{"key":"639_CR3","doi-asserted-by":"publisher","DOI":"10.4161\/cib.27610","volume":"6","author":"S Wang","year":"2013","unstructured":"Wang S, Tran E. Unexpected functions of lncRNAs in gene regulation. Commun Integr Biol. 2013;6:e27610.","journal-title":"Commun Integr Biol"},{"key":"639_CR4","doi-asserted-by":"publisher","first-page":"1760","DOI":"10.1101\/gr.135350.111","volume":"22","author":"J Harrow","year":"2012","unstructured":"Harrow J, et al. GENCODE: the reference human genome annotation for the ENCODE project. Genome Res. 2012;22:1760\u201374.","journal-title":"Genome Res"},{"key":"639_CR5","doi-asserted-by":"publisher","first-page":"1775","DOI":"10.1101\/gr.132159.111","volume":"22","author":"T Derrien","year":"2012","unstructured":"Derrien T, et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 2012;22:1775\u201389.","journal-title":"Genome Res"},{"key":"639_CR6","first-page":"49","volume":"13","author":"S Cogill","year":"2014","unstructured":"Cogill S, Wang L. Co-expression network analysis of human lncRNAs and cancer genes. Cancer Inform. 2014;13:49\u201359.","journal-title":"Cancer Inform"},{"key":"639_CR7","doi-asserted-by":"publisher","first-page":"635","DOI":"10.1038\/nature12943","volume":"505","author":"A Necsulea","year":"2014","unstructured":"Necsulea A, et al. The evolution of lncRNA repertoires and expression patterns in tetrapods. Nature. 2014;505:635\u201340.","journal-title":"Nature"},{"key":"639_CR8","volume-title":"Diagnostic and statistical manual of mental disorders (5th ed., text rev.)","author":"American Psychiatric Association","year":"2012","unstructured":"American Psychiatric Association. Diagnostic and statistical manual of mental disorders (5th ed., text rev.). Washington, DC: Author; 2012."},{"key":"639_CR9","doi-asserted-by":"publisher","first-page":"907","DOI":"10.1001\/archpediatrics.2009.98","volume":"163","author":"R Rosenberg","year":"2009","unstructured":"Rosenberg R, et al. Characteristics and concordance of autism spectrum disorders among 277 twin pairs. Arch Pediatr Adolesc Med. 2009;163:907\u201314.","journal-title":"Arch Pediatr Adolesc Med"},{"key":"639_CR10","doi-asserted-by":"crossref","first-page":"e488","DOI":"10.1542\/peds.2010-2825","volume":"128","author":"S Ozonoff","year":"2011","unstructured":"Ozonoff S, et al. Recurrence risk for autism spectrum disorders: a baby siblings research consortium study. Pediatrics. 2011;128:e488\u201395.","journal-title":"Pediatrics"},{"key":"639_CR11","doi-asserted-by":"publisher","first-page":"244","DOI":"10.1016\/j.bbrc.2014.08.108","volume":"452","author":"X Liu","year":"2014","unstructured":"Liu X, Takumi T. Genomic and genetic aspects of autism spectrum disorder. Biochem Biophys Res Commun. 2014;452:244\u201353.","journal-title":"Biochem Biophys Res Commun"},{"key":"639_CR12","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1007\/s12031-012-9880-8","volume":"49","author":"M Ziats","year":"2013","unstructured":"Ziats M, Rennert O. Aberrant expression of long noncoding RNAs in autistic brain. J Mol Neurosci. 2013;49:589\u201393.","journal-title":"J Mol Neurosci"},{"key":"639_CR13","doi-asserted-by":"publisher","first-page":"1008","DOI":"10.1016\/j.cell.2013.10.031","volume":"155","author":"N Parikshak","year":"2013","unstructured":"Parikshak N, et al. Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism. Cell. 2013;155:1008\u201321.","journal-title":"Cell"},{"key":"639_CR14","doi-asserted-by":"publisher","first-page":"904","DOI":"10.1016\/j.molcel.2011.08.018","volume":"43","author":"K Wang","year":"2011","unstructured":"Wang K, Chang H. Molecular mechanisms of long noncoding RNAs. Mol Cell. 2011;43:904\u201314.","journal-title":"Mol Cell"},{"key":"639_CR15","doi-asserted-by":"publisher","first-page":"82","DOI":"10.1002\/aur.1427","volume":"8","author":"N Lange","year":"2015","unstructured":"Lange N, et al. Longitudinal volumetric brain changes in autism spectrum disorder ages 6-35 years. Autism Res. 2015;8:82\u201393.","journal-title":"Autism Res"},{"key":"639_CR16","doi-asserted-by":"publisher","first-page":"391","DOI":"10.1038\/nature11405","volume":"489","author":"M Hawrylycz","year":"2012","unstructured":"Hawrylycz M, et al. An anatomically comprehensive atlas of the adult human brain transcriptome. Nature. 2012;489:391\u20139.","journal-title":"Nature"},{"key":"639_CR17","first-page":"2825","volume":"12","author":"F Pedregosa","year":"2011","unstructured":"Pedregosa F, et al. Scikit-learn: machine learning in Python. J Mach Learn Res. 2011;12:2825\u201330.","journal-title":"J Mach Learn Res"},{"key":"639_CR18","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1186\/1471-2105-10-193","volume":"10","author":"D Tritchler","year":"2009","unstructured":"Tritchler D, et al. Filtering genes for cluster and network analysis. BMC Bioinformatics. 2009;10:193.","journal-title":"BMC Bioinformatics"},{"key":"639_CR19","doi-asserted-by":"publisher","first-page":"8283","DOI":"10.1038\/srep08283","volume":"5","author":"K Sakata","year":"2015","unstructured":"Sakata K, et al. System-wide analysis of the transcriptional network of human myelomonocytic leukemia cells predicts attractor structure and phorbol-ester-induced differentiation and dedifferentiation transitions. Sci Rep. 2015;5:8283.","journal-title":"Sci Rep"},{"key":"639_CR20","doi-asserted-by":"publisher","first-page":"D832","DOI":"10.1093\/nar\/gkn835","volume":"37","author":"S Basu","year":"2009","unstructured":"Basu S, et al. AutDB: a gene reference resource for autism research. Nucleic Acids Res. 2009;37:D832\u20136.","journal-title":"Nucleic Acids Res"},{"key":"639_CR21","doi-asserted-by":"publisher","first-page":"D1016","DOI":"10.1093\/nar\/gkr1145","volume":"40","author":"L Xu","year":"2012","unstructured":"Xu L, et al. AutismKB: an evidence-based knowledgebase of autism genetics. Nucleic Acids Res. 2012;40:D1016\u201322.","journal-title":"Nucleic Acids Res"},{"key":"639_CR22","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1038\/nature13772","volume":"515","author":"S De Rubeis","year":"2014","unstructured":"De Rubeis S, et al. Synaptic, transcriptional and chromatin genes disrupted in autism. Nature. 2014;515:209\u201315.","journal-title":"Nature"},{"key":"639_CR23","doi-asserted-by":"publisher","first-page":"719","DOI":"10.1093\/bioinformatics\/btm563","volume":"24","author":"P Langfelder","year":"2008","unstructured":"Langfelder P, et al. Defining clusters from a hierarchical cluster tree: the dynamic tree cut package for R. Bioinformatics. 2008;24:719\u201320.","journal-title":"Bioinformatics"},{"key":"639_CR24","unstructured":"Warnes, G. et al. gplots: Various R Programming Tools for Plotting Data. R package version 2.17.0. 2015. http:\/\/CRAN.R-project.org\/package=gplots . Accessed 17 Aug 2015."},{"key":"639_CR25","unstructured":"R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. 2014. https:\/\/www.r-project.org\/ . Accessed 6 Oct 2014."},{"key":"639_CR26","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1038\/nprot.2008.211","volume":"4","author":"W Huang da","year":"2009","unstructured":"Huang da W, et al. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4:44\u201357.","journal-title":"Nat Protoc"},{"key":"639_CR27","doi-asserted-by":"publisher","first-page":"2498","DOI":"10.1101\/gr.1239303","volume":"13","author":"P Shannon","year":"2003","unstructured":"Shannon P, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13:2498\u2013504.","journal-title":"Genome Res"},{"key":"639_CR28","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0102079","volume":"9","author":"K Oliver","year":"2014","unstructured":"Oliver K, et al. Harnessing gene expression networks to prioritize candidate epileptic encephalopathy genes. PLoS One. 2014;9:e102079.","journal-title":"PLoS One"},{"key":"639_CR29","doi-asserted-by":"publisher","first-page":"847","DOI":"10.1016\/j.biopsych.2010.10.029","volume":"69","author":"A Di Martino","year":"2011","unstructured":"Di Martino A, et al. Aberrant striatal functional connectivity in children with autism. Biol Psychiatry. 2011;69:847\u201356.","journal-title":"Biol Psychiatry"},{"key":"639_CR30","doi-asserted-by":"publisher","first-page":"894","DOI":"10.3389\/fnhum.2013.00894","volume":"7","author":"T Zalla","year":"2013","unstructured":"Zalla T, Sperduti M. The amygdala and the relevance detection theory of autism: an evolutionary perspective. Front Hum Neurosci. 2013;7:894.","journal-title":"Front Hum Neurosci"},{"key":"639_CR31","doi-asserted-by":"publisher","first-page":"48R","DOI":"10.1203\/PDR.0b013e3182130c54","volume":"69","author":"E Marco","year":"2011","unstructured":"Marco E, et al. Sensory processing in autism: a review of neurophysiologic findings. Pediatr Res. 2011;69:48R\u201354R.","journal-title":"Pediatr Res"},{"key":"639_CR32","doi-asserted-by":"publisher","first-page":"4756","DOI":"10.1091\/mbc.e12-03-0214","volume":"23","author":"J Wellburn","year":"2012","unstructured":"Wellburn J, Cheeseman I. The microtubule-binding protein Cep170 promotes the targeting of the kinesin-13 depolymerase Kif2b to the mitotic spindle. Mol Biol Cell. 2012;23:4756\u201395.","journal-title":"Mol Biol Cell"},{"key":"639_CR33","doi-asserted-by":"publisher","first-page":"541","DOI":"10.1016\/j.cell.2013.06.051","volume":"154","author":"J Black","year":"2013","unstructured":"Black J, et al. KDM4A lysine demethylase induces site-specific copy gain and rereplication of regions amplified in tumors. Cell. 2013;154:541\u201355.","journal-title":"Cell"},{"key":"639_CR34","doi-asserted-by":"publisher","first-page":"R104","DOI":"10.1186\/gb-2013-14-9-r104","volume":"14","author":"O Marin-Bejar","year":"2013","unstructured":"Marin-Bejar O, et al. Pint lincRNA connects the p53 pathway with epigenetic silencing by the polycomb repressive complex 2. Genome Biol. 2013;14:R104.","journal-title":"Genome Biol"},{"key":"639_CR35","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1016\/j.brainresbull.2013.06.001","volume":"97","author":"P Wu","year":"2013","unstructured":"Wu P, et al. Roles of long noncoding RNAs in brain development, functional diversification and neurodegenerative diseases. Brain Res Bull. 2013;97:69\u201380.","journal-title":"Brain Res Bull"},{"key":"639_CR36","doi-asserted-by":"publisher","first-page":"2997","DOI":"10.1182\/blood-2003-08-2768","volume":"103","author":"A Okamura","year":"2004","unstructured":"Okamura A, et al. Involvement of casein kinase iepsilon in cytokine-induced granulocytic differentiation. Blood. 2004;103:2997\u20133004.","journal-title":"Blood"},{"key":"639_CR37","doi-asserted-by":"publisher","first-page":"18594","DOI":"10.1074\/jbc.M910204199","volume":"275","author":"K Angata","year":"2000","unstructured":"Angata K, et al. Differential biosynthesis of polysialic acid on neural cell adhesion molecule (NCAM) and oligosaccharide acceptors by three distinct alpha 2,8- sialyltransferases, ST8Sia IV (PST), ST8Sia II (STX), and ST8Sia III. J Biol Chem. 2000;275:18594\u2013601.","journal-title":"J Biol Chem"}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12918-018-0639-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12918-018-0639-x\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12918-018-0639-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,9,8]],"date-time":"2022-09-08T08:32:56Z","timestamp":1662625976000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/s12918-018-0639-x"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,12]]},"references-count":37,"journal-issue":{"issue":"S7","published-print":{"date-parts":[[2018,12]]}},"alternative-id":["639"],"URL":"https:\/\/doi.org\/10.1186\/s12918-018-0639-x","relation":{},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,12]]},"assertion":[{"value":"14 December 2018","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Publisher\u2019s Note"}}],"article-number":"91"}}