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利用MySQL库分析关于水稻基因的研究(四)

已有 3416 次阅读 2014-10-4 20:49 |个人分类:linux|系统分类:科研笔记

     一篇文献里可能报道多个基因(或者准确的说会出现多个RAP_id),利用建立好的MySQL数据库可以产生一张新表,这张表可以给出每篇文章包含多少个RAP_id.这个表像下面这个样子:

journal_nameOryzaref_idyeartitle_namerap_id_number
Plant Physiol.311512006Whole-genome analysis of Oryza sativa reveals similar architecture of two-component signaling machinery with Arabidopsis.51
DNA Res.343212003Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana.52
Plant Mol. Biol.378572014Positive regulation of rice RING E3 ligase OsHIR1 in arsenic and cadmium uptakes.52
Genomics331722006Genome-wide analysis, evolutionary expansion, and expression of early auxin-responsive SAUR gene family in rice (Oryza sativa).54
BMC Plant Biol.336782010Classification of rice (Oryza sativa L. Japonica nipponbare) immunophilins (FKBPs, CYPs) and expression patterns under water stress.56
Gene375762013A collection of glycosyltransferases from rice (Oryza sativa) exposed to atrazine.59
Plant Physiol.357592012Posttranscriptional Control of Photosynthetic mRNA Decay under Stress Conditions Requires 3' and 5' Untranslated Regions and Correlates with Differential Polysome Association in Rice.59
Phytochemistry375722013Transcriptomic analysis of UV-treated rice leaves reveals UV-induced phytoalexin biosynthetic pathways and their regulatory networks in rice.60
PLoS ONE334642011The phytocyanin gene family in rice (Oryza sativa L.): genome-wide identification, classification and transcriptional analysis.62
BMC Genomics373012007MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress.64
BMC Genomics.318442008Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice.64
Molecular Genetics & Genomics (Molecular General Genetics up to 2001)218212004Organisation and structural evolution of the rice glutathione S-transferase gene family.64
Plant Physiol.335602012Characterization of genes involved in cytokinin signaling and metabolism from rice.67
Mol. Biol. Rep.343132012Genome-wide identification, classification and expression analysis of genes encoding putative fasciclin-like arabinogalactan proteins in Chinese cabbage (Brassica rapa L.).68
Mol Plant375122011Evolutionary history of the non-specific lipid transfer proteins.69
Plant Physiol.227412004A Rice WRKY Gene Encodes a Transcriptional Repressor of the Gibberellin Signaling Pathway in Aleurone Cells72
Mol Plant402262008Classification, expression pattern, and E3 ligase activity assay of rice U-box-containing proteins.74
Plant Physiol.329712009GRASSIUS: a platform for comparative regulatory genomics across the grasses74
Plant Physiol.227432005Annotations and Functional Analyses of the Rice WRKY Gene Superfamily Reveal Positive and Negative Regulators of Abscisic Acid Signaling in Aleurone Cells75
BMC Genomics402272008Genome-wide and expression analysis of protein phosphatase 2C in rice and Arabidopsis.77
Plant Mol. Biol.373062007Genome-wide identification and expression analysis of rice cell cycle genes.77
Plant Physiol.303482005Evolutionary expansion, gene structure, and expression of the rice wall-associated kinase gene family.77
Plant Cell Rep.305402006A comprehensive expression analysis of the WRKY gene superfamily in rice plants during defense response.78
BMC Genomics325142010Comprehensive expression analysis suggests overlapping and specific roles of rice glutathione S-transferase genes during development and stress responses79
FEBS J.376382013Genome-wide expressional and functional analysis of calcium transport elements during abiotic stress and development in rice.79
Biosci. Biotechnol. Biochem.219812004cDNA Microarray Analysis of Rice Anther Genes under Chilling Stress at the Microsporogenesis Stage Revealed Two Genes with DNA Transposon Castaway in the 5'-Flanking Region.82
Chin. Sci. Bull.217182004Cloning and analysis of expression profile of 13 WRKY genes in rice85
Plant Physiol.311242008Genomic survey and gene expression analysis of the basic leucine zipper transcription factor family in rice.88
DNA research : an international journal for rapid publication of reports on genes and genomes332532005The WRKY family of transcription factors in rice and Arabidopsis and their origins.94
BMC evolutionary biology332522005The WRKY transcription factor superfamily: its origin in eukaryotes and expansion in plants.95
Cell Stress Chaperones371092013Functional relevance of J-protein family of rice (Oryza sativa).95
Journal of integrative plant biology332542007The WRKY Gene Family in Rice (Oryza sativa)96
BMC Plant Biol321792009Characterization of WRKY co-regulatory networks in rice and Arabidopsis.100
Rice333952012Nomenclature report on rice WRKY's. -Conflict regarding gene names and its solution105
Plant OMICS373152012Analysis of GDSL lipase (GLIP) family genes in rice (Oryza sativa)108
BMC Genomics341642012Multifunctionality and diversity of GDSL esterase/lipase gene family in rice (Oryza sativa L. japonica) genome: new insights from bioinformatics analysis.110
Plant Physiol.311302006Genome-wide analysis of the ERF gene family in Arabidopsis and rice.123
Phytochemistry226572004The class III peroxidase multigenic family in rice and its evolution in land plants126
Trends Plant Sci.372862008Plant ABC proteins--a unified nomenclature and updated inventory.127
Mol. Genet. Genomics380152008Systematic sequence analysis and identification of tissue-specific or stress-responsive genes of NAC transcription factor family in rice.131
Bioenerg. Res.380162009A Bioinformatic Analysis of NAC Genes for Plant Cell Wall Development in Relation to Lignocellulosic Bioenergy Production138
Evol. Bioinform. Online340922012AP2/ERF Transcription Factor in Rice: Genome-Wide Canvas and Syntenic Relationships between Monocots and Eudicots.156
Plant Physiol.311482006Genome-wide analysis of basic/helix-loop-helix transcription factor family in rice and Arabidopsis.165
BMC Genomics335582012Genomic survey, expression profile and co-expression network analysis of OsWD40 family in rice.195
Plant J.217641994Toward cataloguing all rice genes: large-scale sequencing of randomly chosen rice cDNAs from a callus cDNA library.230
Plant Physiol.386532008The F-box gene family is expanded in herbaceous annual plants relative to woody perennial plants.613
Plant Physiol.311772007F-Box Proteins in Rice. Genome-Wide Analysis, Classification, Temporal and Spatial Gene Expression during Panicle and Seed Development, and Regulation by Light and Abiotic Stress.621
Proc. Natl. Acad. Sci. U.S.A.386552009Evolution of F-box genes in plants: different modes of sequence divergence and their relationships with functional diversification.683
PLoS ONE386542011Phylogenetic comparison of F-Box (FBX) gene superfamily within the plant kingdom reveals divergent evolutionary histories indicative of genomic drift.712

当然上面展示的表只是我生成的表的一部分。这个表给除了报道了50个以上的rap_id的文章。从文献的标题来看,一次报道这么多基因的文章,大多是基于基因家族的分析、生物信息学分析等。如果一个rap_id只在这样的文章中出现过,那么这个基因的功能仍然是未知的,或者具体到某个基因的功能,它的研究是不够的。换句话说,不能把它归到已经克隆基因里。通过数据库搜索可以发现这样的基因,共有1566个。

SQL查询语句如下:

SELECT * FROM  `rapid_numbers_title` , rap_id_refnumbers, genelist_14922, reflist_14922

WHERE rap_id_number >=50 AND ref_numbers =1 AND Oryzaref_id = Oryzabase_ref_id

AND Oryzabase_ID = genelist_14922.trait_gene_id AND rap_id_refnumbers.trait_gene_id = genelist_14922.trait_gene_id

用这个命令把结果搜出来,MySQL程序运行了好几个小时。







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