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EST Pipeline System: Detailed and Automated EST Data Processing and Mining

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genomics, Proteomics & bioinformatics 2003年第3期1卷 236-242页

作者： Hao Xu, Ling He, Yuanzhong Zhu, Wei Huang, Lijun Fang, Lin Tao, Yuedong Zhu, Lin Cai, Huayong Xu, Liang Zhang, Hong Yu, and Yan Zhouhangzhou genomics institute/James D. Watson institute of Genome Sciences, zhejiang university/key laboratory of bioinformatics of zhejiang province, hangzhou 310008, china. hangzhou genomics institute/James D. Watson institute of Genome Sciences Zhejiang University/Key Laboratory of Bioinformatics of Zhejiang Province Hangzhou 310008 China.

Expressed sequence tags (ESTs) are widely used in gene survey research these years. The EST Pipeline System, software developed by hangzhou genomics institute (HGI), can automatically analyze different scalar EST sequences by suitable methods. All the analysis reports, including those of vector masking, sequence assembly, gene annotation, Gene Ontology classification, and some other analyses, can be browsed and searched as well as downloaded in the Excel format from the web interface, saving research efforts from routine data processing for biological rules embedded in the data.

关键词： EST pipeline data mining relational database Java/J2EE

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A draft sequence of the rice (Oryza sativa ssp. indica) genome

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Chinese Science Bulletin 2001年第23期46卷 1937-1942页

作者： YU Jun, HU Songnian, WANG Jun,LI Songgang WONG Ka-Shu Gane, LIU Bin,DENG Yajun, DAI Li, ZHOU Yan,ZHANG Xiuqing, CAO Mengliang, LIU Jing,SUN Jiandong , TANG Jiabin, CHEN Yanjiong,HUANG Xiaobing, LIN Wei, YE Chen, TONG Wei,CONG Lijuan, GENG Jianing, HAN Yujun, LI Lin,LI Wei, HU Guangqiang, HUANG Xiangang,LI Wenjie, LI Jian, LIU Zhanwei, LI Long,LIU Jianping, Ql Qiuhui, LIU Jinsong, LI Li,WANG Xuegang, LU Hong, WU Tingling,ZHU Miao, Nl Peixiang, HAN Hua, DONG Wei,REN Xiaoyu, FENG Xiaoli, GUI Peng,LI Xianran, WANG Hao, XU Xin, ZHAI Wenxue,XU Zhao, ZHANG Jinsong, HE Sijie,ZHANG Jianguo, XU Jichen, ZHANG Kunlin,ZHENG Xianwu, DONG Jianhai, ZENG Wanyong,TAO Lin, CHEN Xuewei, HE Jun, LIU Daofeng,TIAN Wei, TIAN Chaoguang, XIA Hongai,LI Gang, GAO Hui, LI Ping, CHEN Wei ,WANG Xudong, ZHANG Yong, HU Jianfei,WANG Jing, LIU Song, YANG Jian,ZHANG Guangyu, XIONG Yuqing, LI Zhijie,MAO Long, ZHOU Chengshu, ZHU Zhen,CHEN Runsheng, HAO Bailin,ZHENG Weimou, CHEN Shouyi, QUO Wei,LI Guojie, LIU Siqi, HUANG Guyang,TAO Ming, WANG Jian, ZHU Lihuang,YUAN Longping& YANG HuanmingBeijing genomics institute/Center of genomics & bioinformatics, Chinese Academy of Sciences, Beijing 101300, china hangzhou genomics institute/institute of bioinformatics of zhejiang university/key laboratory of bioinformatics of zhejiang province, hangzhou 3.0007, china institute of Genetics, Chinese Academy of Sciences, Beijing 100101, china National Hybrid Rice R & D Center, Changsha 410125, china laboratory of bioinformatics, institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, china College of Life Sciences, Peking university, Beijing 100871, china institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 1Q0080, china Digital china Ltd., Beijing 100080, china institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, china Medical College, Xi’an Jiaotong university, Xi’an 710061, chinaThese authors contributed equally to this work.Corresponding author.Corresponden Beijing genomics institute/Center of genomics & bioinformatics Chinese Academy of Sciences Beijing China hangzhou genomics institute/institute of bioinformatics of zhejiang university/key laboratory of bioinformatics of zhejiang province Hangzhou China College of Life Sciences Peking University Beijing China Medical College Xi’an Jiaotong University Xi’an China institute of Genetics Chinese Academy of Sciences Beijing China laboratory of bioinformatics Institute of Biophysics Chinese Academy of Sciences Beijing China National Hybrid Rice R & D Center Changsha China institute of Theoretical Physics Chinese Academy of Sciences Beijing China Digital china Ltd. Beijing China institute of Computing Technology Chinese Academy of Sciences Beijing China

The sequence of the rice genome holds fundamental information for its biology, including physiology, genetics, development, and evolution, as well as information on many beneficial phenotypes of economic significance. Using a "whole genome shotgun" approach, we have pro-duced a draft rice genome sequence of Oryza sativa ssp. in-dica, the major crop rice subspecies in china and many other regions of Asia. The draft genome sequence is constructed from over 4.3 million successful sequencing traces with an accumulative total length of 2214.9 Mb. The initial assembly of the non-redundant sequences reached 409.76 Mb in length, based on 3.30 million successful sequencing traces with a total length of 1797.4 Mb from an indica variant cultivar 93-11, giving an estimated coverage of 95.29% of the rice genome with an average base accuracy of higher than 99%. The coverage of the draft sequence, the randomness of the sequence distribution, and the consistency of BIG-ASSEM-BLER, a custom-designed software package

关键词： rice genome draft sequences.

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Computational Identification of Protein-Protein Interactions in Rice Based on the Predicted Rice Interactome Network

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genomics,Proteomics & bioinformatics 2011年第Z2期 128-137页

作者： Pengcheng Zhu1, Haibin Gu1, Yinming Jiao1, Donglin Huang1,2, and Ming Chen1,2,3 1Department of bioinformatics, College of Life Sciences, zhejiang university, hangzhou 310058, china 2James D. Watson institute of Genome Sciences, zhejiang university, hangzhou 310058, china 3State key laboratory of Plant Physiology and Biochemistry, College of Life Sciences, zhejiang university, hangzhou 310058, china

Plant protein-protein interaction networks have not been identified by large-scale experiments. In order to better understand the protein interactions in rice, the Predicted Rice Interactome Network (PRIN; http://***/ prin/) presented 76,585 predicted interactions involving 5,049 rice proteins. After mapping genomic features of rice (GO annotation, subcellular localization prediction, and gene expression), we found that a well-annotated and biologically significant network is rich enough to capture many significant functional linkages within higher-order biological systems, such as pathways and biological processes. Furthermore, we took MADS-box do- main-containing proteins and circadian rhythm signaling pathways as examples to demonstrate that functional protein complexes and biological pathways could be effectively expanded in our predicted network. The expanded molecular network in PRIN has considerably improved the capability of these analyses to integrate existing knowledge and provide novel insights into the function and coordination of genes and gene networks.

关键词： protein-protein interactions rice interactome interolog sub-network expansion pathway clustering

The Rice Genome:Understanding the Progression From Sequence to Protein to Function

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The Rice Genome:Understanding the Progression From Sequence ...

中国蛋白质组学第二届学术大会

作者： Jun Wang, JianGuo Zhang, SiQi Liu, Jian Wang, HuanMing Yang, Jun Yu, Gane Ka-Shu Wong (Beijing institute of genomics, Chinese Academy of Sciences, Beijing 101300, china James D. Watson institute of zhejiang university, hangzhou genomics institute, key laboratory of bioinformatics of zhejiang province, hangzhou 3.0007, china)

We are releasing an integrated suite of genomic data for indica rice, including a sequence with essentially complete non-fragmented coverage of the genes, and confirmation for the genes through EST, SAGE, and proteomics. Comparisons with japonica rice indicate that differences in gene content between the subspecies are at most a few percent. In contrast, almost half the rice genes have no homolog (NH) in Arabidopsis, and these are confirmed even in proteomics. We argue that these so-called orphan genes are the by-products of an ongoing process of evolution by gene duplication. Although some orphan genes are likely to be dead, many others are evolving lineage-specific functions.

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Proteomic identification and function analysis of the silkworm,Bombyx mori

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Proteomic identification and function analysis of the silkwo...

中国生物化学与分子生物学会农业生物化学与分子生物学分会第八次学术研讨会

作者： Yaozhou Zhang~* Qingyou Xia~+ Jie Xu~* Lingying Kong~* Jian Chen~* Zuoming Nie~* Dan Wang~* Jianqing Chen~* Qingliang Zheng~* Qing Chen~* Xiaoyuan Ren~* Jiang Wang~* Zhengbing Lv~* Caiying Jiang~* Lili Liu~* Qing Sheng Yongfeng Jin~(**) Xiangfu Wu~* ~*The key laboratory of Bioreactor and Biopharmacy of zhejiang province institute of Biochemistry,zhejiang Sci-Tech university,hangzhou 310018,china ~+The key Sericultural laboratory of Agricultural Ministry The key laboratory for Sericultural Sciences and genomics of the Ministry of Education,College of Biotechnology,Southwest university,Beibei,Chongqing 400715,china ~(**)College of Life Sciences,zhejiang university,hangzhou 310029,china

Mass spectrometry (MS) is an effective method for large-scale proteomic identification and verification of protein-encoding genes present in a *** this study,peptide sequences identified by MS were matched with those from an ORF library of the silkworm (Bombyx mori) genome and a cDNA library to validate putative *** databases were *** first was based on a 6x draft sequence of the silkworm genome and contained 14,632 putative *** second was based on a *** pupal cDNA library that had 3,187 putative proteins,each composed of at least 30 amino acid *** this study,81,000 peptide sequences that had a threshold score of 60% were generated by MS/MS analysis,and 55,400 were chosen for sequence *** searching the two databases,6,649 and 250 protein were matches,and these accounted for approximately 45.4% and 7.8% *** analysis and cataloging of the identified proteins,which were carried out by using several bioinformatic tools,suggested that the matches included proteins with predicted transmembrane domains (TMDs;1,393) and preproteins with a signal peptide (SP,976).These results provide a fundamental understanding of gene expression and function analysis of silkworm proteins.

关键词： Bombyx mori pupae protein identification function analysis ORF genome proteomics

Effects of ELF magnetic fields on protein expression profile of human breast cancer cell MCF7

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Science china(Life Sciences) 2005年第5期48卷 506-514页

作者： LI Han1, ZENG Qunli1, 2, WENG Yu1, LU Deqiang1, JIANG Huai1 & XU Zhengping1, 2 1. Bioelectromagnetics laboratory, zhejiang university , hangzhou 310031, china 2. Research Center for Environmental genomics, zhejiang university School of Medicine, hangzhou 310031, china 1. Bioelectromagnetics laboratory Zhejiang University 310031 Hangzhou China 2. Research Center for Environmental genomics Zhejiang University School of Medicine 310031 Hangzhou China

Extremely Low Frequency Magnetic Fields (ELF MF) has been considered as a “possible human carcinogen” by International Agency for Research on Cancer (IARC) while credible mechanisms of its carcinogenicity remain unknown. In this study, a proteomics approach was employed to investigate the changes of protein expression profile induced by ELF MF in human breast cancer cell line MCF7, in order to determine ELF MF-responsive proteins. MCF7 cells were exposed to 50 Hz, 0.4 mT ELF MF for 24 h and the changes of protein profile were examined using two dimensional electrophoresis. Up to 6 spots have been statistically signifi-cantly altered (their expression levels were changed at least 5 fold up or down) compared with sham-exposed group. 19 ones were only detected in exposure group while 19 ones were missing. Three proteins were identified by LC-IT Tandem MS as RNA binding protein regulatory subunit、Proteasome subunit beta type 7 precursor and Translationally Controlled Tumor Protein. Our finding showed that 50 Hz, 0.4 mT ELF MF alternates the protein profile of MCF7 cell and may affect many physiological functions of normal cell and 2-DE coupled with MS is a promising ap-proach to elucidating cellular effects of electromagnetic fields.

关键词： ELF MF, MCF7, 2-DE, MS, protein expression profile.

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Proteomic Identification and Function Analysis of the Silkworm,Bombyx mori

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Proteomic Identification and Function Analysis of the Silkwo...

2008年全国生物化学与分子生物学学术大会

作者： Yao-zhou Zhang~1 Qing-you Xia~2 Jie Xu~1 Ling-ying Kong~1 Jian Chen~1 Zuo-ming Nie~1 Dan Wang~1 Jian-qing Chen~1 Qing-liang Zheng~1 Qing Chen~1 Xiao-yuan Ren~1 Jiang Wang~1 Zheng-bing Lü~1 Cai-ying Jiang~1 Li-li Liu~1 Qing Sheng Yong-feng Jin~3 Xiang-fu Wu~1 1 The key laboratory of Bioreactor and Biopharmacy of zhejiang province institute of Biochemistry,zhejiang Sci-Tech university,hangzhou 310018,china 2 The key Sericultural laboratory of Agricultural Ministry The key laboratory for Sericultural Sciences and genomics of the Ministry of Education,College of Biotechnology,Southwest university,Beibei,Chongqing 400715,china 3 College of Life Sciences,zhejiang university,hangzhou 310029,china

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Changes of genes activating cold exposure-induced thermogenesis in brown adipose tissue of mice by RNA-seq

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Changes of genes activating cold exposure-induced thermogene...

2011国际基因组学大会

作者： Xiaonuan Li~2 Yingfeng Luo~1 Linlin Pan~2 Tongwu Zhang~2 Songnian Hu~(1 2) and Jun Yu~(1 2) 1 CAS key laboratory of Genome Sciences and Information Beijing institute of genomics Chinese Academy of Sciences Beijing china 2 James D.Watson institute of Genome Sciences zhejiang university hangzhou china

＜正＞Brown adipose tissue（BAT） is a specialized tissue that can dissipate energy through the uncoupling effect of UCP1 and therefore is a therapeutic target to counteract obesity-associated *** identify genes activating the nonshivering thermogenesis of BAT,we performed RNA-Seq of mRNA samples collected from the BAT of cold-exposed mice（24h）（Bat-cold） and of mice kept at room temperature （Bat-normal） using next-generation sequencing technology（SOLID,Life Technologies）.We generated more than 2xl07 uniq-mapped tags for each sample;these tags were annotated to 15471 Bat-cold genes and 15202 Bat-normal genes based on mouse Ensembl *** identified 846 differentially expressed genes（q-value＜0.001,FC＞2,and absolute change＞50） by DEGseq program and found that 588 genes were down-regulated and 258 were up-regulated during cold *** up-regulated genes were over-represented in the Cholesterol Biosynthesis pathway and the Fatty Acid Biosynthesis pathway and the down-regulated genes were over-represented in the Apoptosis *** also considered genes expressed in intergenic regions of the mouse genome and identified about 5000 fragments in each *** results provide molecular evidence for the theory that during acute cold exposure the number of brown adipocytes increases through promoting proliferation and preventing apoptosis.

关键词： Brown adipose tissue(BAT) cold next-generation sequencing

Advance in genetical genomics

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Advance in genetical genomics

International Symposium on Green Technology and Ecosystem Health

作者： Xiuyan Liu 1,2,3,Zhenmiao Xie 1,Huizhe Chen 4,Shunpeng Li2 1School of Mechanical Engineering,hangzhou Dianzi university,hangzhou 310018,china 2 College of Life Science,Nanjing Agricultural university,Nanjing 210095 3 Ministry of Education key laboratory of Environmental Remediation and Ecological Health,College of Natural Resources and Environmental Science,zhejiang university,hangzhou 310029,china 4 china National Rice Research institute,hangzhou 310006,china

＜正＞Genetical genomics is combining of micriarray technology and quantitative trait loci （QTL） analysis, mapping expression QTL （eQTL） in global level. It provides a novel procedure for revealing the molecular m... 详细信息

关键词： microarray expression QTL (eQTL) regulatory network