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; Good, Peter J.; Guigo, Roderic; Hammonds, Ann; Harrow, Jen; Hoskins, Roger A.; Howald, Cedric; Hu, Long; Huang, Haiyan; Hubbard, Tim J. P.; Huynh, Chau; Jhas, Sonali; Kasper, Dionna; Kato, Masaomi; Kaufman, Thomas C.; Kitchen, Robert R.; Ladewig, Erik; Lagarde, Julien; Lai, Eric; Leng, Ling; Lu, Zhi; MacCoss, Michael; May, Gemma; McWhirter, Rebecca; Merrihew, Gennifer; Miller, David M.; Mortazavi, Ali; Murad, Rabi; Oliver, Brian; Olson, Sara; Park, Peter J.; Pazin, Michael J.; Perrimon, Norbert; Pervouchine, Dmitri; Reinke, Valerie; Reymond, Alexandre; Robinson, Garrett; Samsonova, Anastasia; Saunders, Gary I.; Schlesingers, Felix; Sethi, Anurag; Slack, Frank J.; Spencer, William C.; Stoiber, Marcus H.; Strasbourger, Pnina; Tanzer, Andrea; Thompson, Owen A.; Wan, Kenneth H.; Wang, Guilin; Wang, Huaien; Watkins, Kathie L.; Wen, Jiayu; Wen, Kejia; Xue, Chenghai; Yang, Li; Yip, Kevin; Zaleskis, Chris; Zhang, Yan; Zheng, Henry; Brenner, Steven E.; Graveley, Brenton R.; Ceniker, Susan E.; Gingeras, Thomas R.; Waterston, Robert
2014
发表期刊NATURE (IF:50.5[JCR-2023],54.4[5-Year])
ISSN0028-0836
EISSN1476-4687
卷号512期号:7515页码:445-448
发表状态已发表
DOI10.1038/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.

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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
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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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