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基因组中的暗物质研究的知识发现

已有 3986 次阅读 2010-12-31 09:03 |个人分类:知识发现|系统分类:论文交流| 基因组, 暗物质, 知识发现

http://www.sciencenet.cn/m/user_content.aspx?id=398234  王承志的博客

揭示基因组中的暗物质(CNS摘要翻译)
揭示基因组中的暗物质

 动物胚胎成功地从将它们基因组的二维编码转变成为可以面对自然选择挑战的多维有机体。在三维的身体之外,动物基因组还含有额外的维度:细胞协调形成组织,组织聚集成有功能的器官,然后器官形成了身体的系统,这样个体对生命的各种挑战和生存条件起适当的反应。食物中的毒素被解毒,病原体被杀死,寄生虫被清除,以及捕食者被逃避都这些精巧的反应都在基因组中编码了。目前还无法像胚胎那样有效地转换而从基因组来计算出一个有机体,但是本期的两篇文章,来自Gerstein 等和modENCODE委员会,将这个目标带离我们更近了。


Science. 2010 Dec 22. [Epub ahead of print]
Revealing the Dark Matter of the Genome.
Blaxter M.
Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, UK.
Abstract
Animal embryos successfully transform the two-dimensional code of their genome into multidimensional organisms that are ready to meet the challenge of natural selection. In addition to the three dimensions of the body, animal genomes inform additional dimensions: of cells coordinating to form tissues, tissues functioning together as organs, and organs shaping the body's systems; and of individuals responding appropriately to the varied challenges of life and surviving to breed. Poisons in food are detoxified, pathogens are killed, parasites are eliminated, and predators avoided through the deft employment of responses encoded in the genome. It is not currently possible to compute an organism from its genome, performing the transformation so efficiently executed by embryos, but two articles in this issue, by Gerstein et al. and the modENCODE Consortium, bring this goal closer.

http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/edit_b.cgi?refresh=T&ID=13570

Start A-Literature C-Literature B-list Filter Literature
  A-query: Dark Matter and Genome
C-query: organism and genome
The B-list contains title words and phrases (terms) that appeared in both the A and the C literature. 2 articles appeared in both literatures and were not included in the process of computing the B-list but can be viewed here. The results of this search are saved under id # 13570 and can be accessed from the start page after you leave this session. There are 191 terms on the current B-list (96 are predicted to be relevant), which is shown ranked according to predicted relevance. The list can be further trimmed down using the filters listed in the left margin.

To assess whether there appears to be a biologically significant relationship between the AB and BC literatures for specific B-terms, please select one or more B-terms and then click the button to view the corresponding AB and BC literatures. Use Ctrl to select multiple B-terms.

job id # 13570 started Thu Dec 30 20:38:33 2010
Max_citations: 50000
Stoplist: /var/www/html/arrowsmith_uic/data/stopwords_pubmed
Ngram_max: 3
13570 Search ARROWSMITH A
A_query_raw: Dark Matter and GenomeThu Dec 30 20:38:56 2010

A query = Dark Matter and Genome started Thu Dec 30 20:38:56 2010
A query resulted in 25 titles
13570 Search ARROWSMITH C
C_query_raw: organism and genome Thu Dec 30 20:41:19 2010

C: organism and genome 9686

A: pubmed_query_A 25

AC: ( Dark Matter and Genome ) AND ( organism and genome ) 2

C query = organism and genome started Thu Dec 30 20:41:20 2010
C query resulted in 9686 titles
A AND C query resulted in 2 titles
191 B-terms ready on Thu Dec 30 20:42:10 2010

B-list on Thu Dec 30 20:46:25 2010
1 rna world
2 vertebrate genome
3 transgene
4 proteome
5 genome wide
6 satellite dna
7 transcriptome
8 dna array
9 noncoding
10 intergenic
11 functional genomic
12 tiling array
13 complex trait
14 adaptive evolution
15 drosophila bithorax
16 ribosomal rna
17 analysis genome
18 microarray
19 noncoding rna
20 genome wide association
21 ribosomal
22 bithorax
23 beta amyloid
24 deep sea
25 genomic strategy
26 array data
27 drosophila
28 gene environment
29 evolutionary
30 genome tiling array
31 neurodegenerative
32 translation
33 environment interaction
34 transcription
35 homology
36 reveal novel
37 genomic
38 wide association study
39 vent
40 genome
41 regulated protein
42 bithorax complex
43 non coding
44 tiling array data
45 data reveal novel
46 rna
47 moss
48 amyloid precursor protein
49 genetic heterogeneity
50 wilson disease
51 pathway genome
52 silencing
53 vertebrate
54 association study
55 annotating
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58 transcript
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60 element
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62 evolutionary genomic
63 protein kinase
64 key developmental regulator
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67 tiling
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76 evolution
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78 gene environment interaction
79 mammalian
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81 dna
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86 study genetic
87 developmental
88 adaptive
89 ribosomal rna a
90 comparative analysis
91 deep
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93 coding
94 novel
95 nuclear
96 organization

http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/show_sentences.cgi

Start A-Literature C-Literature B-list Filter Literature

AB literature

 

B-term

 

BC literature

 

Dark Matter and Genome transgene organism and genome
1: Neurodegenerative changes associated with beta-amyloid deposition in the brains of mice carrying mutant amyloid precursor protein and mutant presenilin-1 transgenes. 2001
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1: Geographic and molecular variation in a natural plant transgene. 2010
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2: Distinct RNA-dependent RNA polymerases are required for RNAi triggered by double-stranded RNA versus truncated transgenes in Paramecium tetraurelia. 2010
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3: The Q system: a repressible binary system for transgene expression, lineage tracing, and mosaic analysis. 2010
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4: Recombination technologies for enhanced transgene stability in bioengineered insects. 2010
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5: Effect of transgene introduction and recloning on efficiency of porcine transgenic cloned embryo production in vitro. 2009
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6: Generation of Chlamydomonas strains that efficiently express nuclear transgenes. 2009
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7: Transgene expression of enhanced green fluorescent protein in cloned rabbits generated from in vitro-transfected adult fibroblasts. 2009
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8: Strategies to facilitate transgene expression in Chlamydomonas reinhardtii. 2009
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9: Transgene expression of green fluorescent protein and germ line transmission in cloned pigs derived from in vitro transfected adult fibroblasts. 2008
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10: A new transgene reporter for in vivo magnetic resonance imaging. 2005
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11: Activity of the germline-specific Oct4-GFP transgene in normal and clone mouse embryos. 2004
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12: The fate of a genetically modified Pseudomonas strain and its transgene during the composting of poultry manure. 2004
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13: Expression of a transgene encoded on a non-viral episomal vector is not subject to epigenetic silencing by cytosine methylation. 2004
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14: Transgene expression of green fluorescent protein and germ line transmission in cloned calves derived from in vitro-transfected somatic cells. 2003
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15: [Whole amount in situ hybridization and transgene via microinjection in zebrafish] 2003
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16: [Transgenes and their medical applications] 2002
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17: HC-Pro suppression of transgene silencing eliminates the small RNAs but not transgene methylation or the mobile signal. 2001
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18: Transgene analysis proves mRNA trans-splicing at the complex mod(mdg4) locus in Drosophila. 2001
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19: [Impact of transgenes and cloning on xenografts] 2000
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20: Transgene vectors go retro. 1999
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21: Possible ecological risks of transgenic organism release when transgenes affect mating success: sexual selection and the Trojan gene hypothesis. 1999
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22: Timing is everything in life: conditional transgene expression in the cardiovascular system. 1998
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23: A bacteriophage T3 promoter can be linked to a lethal gene without detectable toxicity for eukaryotic cells. Interest for inducible transgenes. 1996
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24: Developmental expression of H-2K major histocompatibility complex class I transgenes requires the presence of proximal introns. 1995
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25: A new method for manipulating transgenes: engineering heat tolerance in a complex, multicellular organism. 1993
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26: Knock-in and knock-out. Transgenes, Development and Disease: A Keystone Symposium sponsored by Genentech and Immunex, Tamarron, CO, USA, January 12-18, 1991. 1991
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