{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,7,9]],"date-time":"2024-07-09T14:55:51Z","timestamp":1720536951320},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"9","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,5,1]]},"abstract":"Abstract<\/jats:title>\n Summary: High-throughput genome-wide studies of alternatively spliced mRNA transcripts have become increasingly important in clinical research. Consequently, easy-to-use software tools are required to process data from these studies, for example, using exon and junction arrays. Here, we introduce JETTA, an integrated software package for the calculation of gene expression indices as well as the identification and visualization of alternative splicing events. We demonstrate the software using data of human liver and muscle samples hybridized on an exon\u2013junction array.<\/jats:p>\n Availability: JETTA and its demonstrations are freely available at http:\/\/igenomed.stanford.edu\/~junhee\/JETTA\/index.html<\/jats:p>\n Contacts: \u00a0wxiao1@partners.org<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts134","type":"journal-article","created":{"date-parts":[[2012,3,22]],"date-time":"2012-03-22T16:22:17Z","timestamp":1332433337000},"page":"1274-1275","source":"Crossref","is-referenced-by-count":16,"title":["JETTA: junction and exon toolkits for transcriptome analysis"],"prefix":"10.1093","volume":"28","author":[{"given":"Junhee","family":"Seok","sequence":"first","affiliation":[{"name":"1 Stanford Genome Technology Center, 855 California Street, Palo Alto, CA 94304, 2Department of Statistics, Stanford University, 390 Serra Mall, Stanford, CA 94305 and 3Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA"},{"name":"1 Stanford Genome Technology Center, 855 California Street, Palo Alto, CA 94304, 2Department of Statistics, Stanford University, 390 Serra Mall, Stanford, CA 94305 and 3Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA"}]},{"given":"Weihong","family":"Xu","sequence":"additional","affiliation":[{"name":"1 Stanford Genome Technology Center, 855 California Street, Palo Alto, CA 94304, 2Department of Statistics, Stanford University, 390 Serra Mall, Stanford, CA 94305 and 3Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA"}]},{"given":"Hong","family":"Gao","sequence":"additional","affiliation":[{"name":"1 Stanford Genome Technology Center, 855 California Street, Palo Alto, CA 94304, 2Department of Statistics, Stanford University, 390 Serra Mall, Stanford, CA 94305 and 3Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA"}]},{"given":"Ronald W.","family":"Davis","sequence":"additional","affiliation":[{"name":"1 Stanford Genome Technology Center, 855 California Street, Palo Alto, CA 94304, 2Department of Statistics, Stanford University, 390 Serra Mall, Stanford, CA 94305 and 3Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA"}]},{"given":"Wenzhong","family":"Xiao","sequence":"additional","affiliation":[{"name":"1 Stanford Genome Technology Center, 855 California Street, Palo Alto, CA 94304, 2Department of Statistics, Stanford University, 390 Serra Mall, Stanford, CA 94305 and 3Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA"},{"name":"1 Stanford Genome Technology Center, 855 California Street, Palo Alto, CA 94304, 2Department of Statistics, Stanford University, 390 Serra Mall, Stanford, CA 94305 and 3Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA"}]}],"member":"286","published-online":{"date-parts":[[2012,3,19]]},"reference":[{"key":"2023012512231600600_B1","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1126\/science.1069415","article-title":"Genomewide analysis of mRNA processing in yeast using splicing-specific microarrays","volume":"296","author":"Clark","year":"2002","journal-title":"Science"},{"key":"2023012512231600600_B2","doi-asserted-by":"crossref","first-page":"R64","DOI":"10.1186\/gb-2007-8-4-r64","article-title":"Discovery of tissue-specific exons using comprehensive human exon microarrays","volume":"8","author":"Clark","year":"2007","journal-title":"Genome Biol."},{"key":"2023012512231600600_B3","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1093\/biostatistics\/4.2.249","article-title":"Exploration, normalization, and summaries of high density oligonucleotide array probe level data","volume":"4","author":"Irizarry","year":"2003","journal-title":"Biostatistics"},{"key":"2023012512231600600_B4","doi-asserted-by":"crossref","first-page":"1293","DOI":"10.1038\/nbt.1505","article-title":"An integrated software system for analyzing ChIP-chip and ChIP-seq data","volume":"26","author":"Ji","year":"2008","journal-title":"Nat. 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