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Comparative analysis of the transcriptome across distant species | |
Gerstein, Mark B.; Rozowsky, Joel; Yan, Koon-Kiu; Wang, Daifeng; Cheng, Chao; Brown, James B.; Davis, Carrie A.; Hillier, LaDeana; Sisu, Cristina; Li, Jingyi Jessica; Pei, Baikang; Harmanci, Arif O.; Duff, Michael O.; Djebali, Sarah; Alexander, Roger P.; Alver, Burak H.; Auerbach, Raymond; Bell, Kimberly; Bickel, Peter J.; Boeck, Max E.; Boley, Nathan P.; Booth, Benjamin W.; Cherbas, Lucy; Cherbas, Peter; Di, Chao; Dobins, Alex; Drenkows, Jorg; Ewing, Brent; Fang, Gang; Fastucas, Megan; Feingold, Elise A.; Frankish, Adam; Gao, Guanjun ![]() | |
2014 | |
发表期刊 | NATURE (IF:50.5[JCR-2023],54.4[5-Year]) |
ISSN | 0028-0836 |
EISSN | 1476-4687 |
卷号 | 512期号:7515页码:445-448 |
发表状态 | 已发表 |
DOI | 10.1038/nature13424 |
摘要 | The transcriptome is the readout of the genome. Identifying common features in it across distant species can reveal fundamental principles. To this end, the ENCODE and modENCODE consortia have generated large amounts of matched RNA-sequencing data for human, worm and fly. Uniform processing and comprehensive annotation of these data allow comparison across metazoan phyla, extending beyond earlier within-phylum transcriptome comparisons and revealing ancient, conserved features(1-6). Specifically, we discover co-expression modules shared across animals, many of which are enriched in developmental genes. Moreover, we use expression patterns to align the stages in worm and fly development and find a novel pairing between worm embryo and fly pupae, in addition to the embryo-to-embryo and larvae-to-larvae pairings. Furthermore, we find that the extent of non-canonical, non-coding transcription is similar in each organism, per base pair. Finally, we find in all three organisms that the gene-expression levels, both coding and non-coding, can be quantitatively predicted from chromatin features at the promoter using a 'universal model' based on a single set of organism-independent parameters. |
URL | 查看原文 |
收录类别 | SCI |
语种 | 英语 |
WOS研究方向 | Science & Technology - Other Topics |
WOS类目 | Multidisciplinary Sciences |
WOS记录号 | WOS:000340840600037 |
WOS关键词 | GENE-EXPRESSION ; LANDSCAPE ; EVOLUTION ; TISSUES ; GENOME ; CELLS |
原始文献类型 | Article |
引用统计 | 正在获取...
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文献类型 | 期刊论文 |
条目标识符 | https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/120390 |
专题 | 个人在本单位外知识产出 |
通讯作者 | Gerstein, Mark B.; McWhirter, Rebecca; Brenner, Steven E.; Graveley, Brenton R.; Ceniker, Susan E.; Gingeras, Thomas R. |
作者单位 | 1.Yale Univ, Program Computat Biol & Bioinformat, New Haven, CT 06520 USA 2.Yale Univ, Dept Mol Biophys & Biochem, New Haven, CT 06520 USA 3.Yale Univ, Dept Comp Sci, New Haven, CT 06511 USA 4.Geisel Sch Med Dartmouth, Dept Genet, Hanover, NH 03755 USA 5.Geisel Sch Med Dartmouth, Inst Quantitat Biomed Sci, Norris Cotton Canc Ctr, Lebanon, NH 03766 USA 6.Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Dept Genome Dynam, Berkeley, CA 94720 USA 7.Univ Calif Berkeley, Dept Stat, Berkeley, CA 94720 USA 8.Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA 9.Dept Genome Sci, Seattle, WA 98195 USA 10.Univ Washington, Sch Med, Seattle, WA 98195 USA 11.Univ Calif Los Angeles, Dept Stat, Los Angeles, CA 90095 USA 12.Univ Calif Los Angeles, Dept Human Genet, Los Angeles, CA 90095 USA 13.Univ Connecticut, Ctr Hlth, Inst Syst Genom, Dept Genet & Dev Biol, Farmington, CT 06030 USA 14.Ctr Genom Regulat, Barcelona 08003, Catalonia, Spain 15.Univ Pompeu Fabra, Dept Ciencies Expt Salut, Barcelona 08003, Catalonia, Spain 16.Harvard Univ, Sch Med, Ctr Biomed Informat, Boston, MA 02115 USA 17.Univ Calif Berkeley, Dept Stat, Berkeley, CA 94720 USA 18.Indiana Univ, Dept Biol, Bloomington, IN 47405 USA 19.Indiana Univ, Ctr Genom & Bioinformat, Bloomington, IN 47405 USA 20.Tsinghua Univ, Sch Life Sci, MOE Key Lab Bioinformat, Beijing 100084, Peoples R China 21.NHGRI, NIH, Bethesda, MD 20892 USA 22.Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England 23.Univ Lausanne, Ctr Integrat Genom, CH-1015 Lausanne, Switzerland 24.Swiss Inst Bioinformat, CH-1015 Lausanne, Switzerland 25.Kings Coll London, London WC2R 2LS, England 26.Yale Univ, Sch Med, Dept Genet, New Haven, CT 06520 USA 27.Yale Univ, Dept Mol Cellular & Dev Biol, New Haven, CT 06520 USA 28.Sloan Kettering Inst, New York, NY 10065 USA 29.Carnegie Mellon Univ, Dept Biol Sci, Pittsburgh, PA 15213 USA 30.Vanderbilt Univ, Dept Cell & Dev Biol, Nashville, TN 37232 USA 31.Univ Calif Irvine, Irvine, CA 92697 USA 32.Univ Calif Irvine, Ctr Complex Biol Syst, Irvine, CA 92697 USA 33.NIDDK, Sect Dev Genom, Lab Cellular & Dev Biol, NIH, Bethesda, MD 20892 USA 34.Harvard Univ, Sch Med, Dept Genet, Boston, MA 02115 USA 35.Harvard Univ, Sch Med, Drosophila RNAi Screening Ctr, Boston, MA 02115 USA 36.Harvard Univ, Sch Med, Howard Hughes Med Inst, Boston, MA 02115 USA 37.European Bioinformat Inst, Hinxton CB10 1SD, England 38.Univ Pompeu Fabra, Ctr Genom Regulat, Bioinformat & Genom Programme, Barcelona 08003, Catalonia, Spain 39.Univ Vienna, Theoret Biochem Grp TBI, Inst Theoret Chem, A-1090 Vienna, Austria 40.Chinese Acad Sci, Shanghai Inst Biol Sci, CAS MPG Partner Inst Computat Biol, Key Lab Computat Biol, Shanghai 200031, Peoples R China 41.Chinese Univ Hong Kong, Hong Kong Bioinformat Ctr, Shatin, Hong Kong, Peoples R China 42.Chinese Univ Hong Kong, CUHK BGI Innovat Inst Trans Omics 5, Shatin, Hong Kong, Peoples R China 43.Univ Calif Berkeley, Dept Mol & Cell Biol, Berkeley, CA 94720 USA 44.Univ Calif Berkeley, Dept Plant & Microbial Biol, Berkeley, CA 94720 USA |
推荐引用方式 GB/T 7714 | Gerstein, Mark B.,Rozowsky, Joel,Yan, Koon-Kiu,et al. Comparative analysis of the transcriptome across distant species[J]. NATURE,2014,512(7515):445-448. |
APA | Gerstein, Mark B..,Rozowsky, Joel.,Yan, Koon-Kiu.,Wang, Daifeng.,Cheng, Chao.,...&Waterston, Robert.(2014).Comparative analysis of the transcriptome across distant species.NATURE,512(7515),445-448. |
MLA | Gerstein, Mark B.,et al."Comparative analysis of the transcriptome across distant species".NATURE 512.7515(2014):445-448. |
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