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Biological networks to the analysis of microarray data

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Progress in Natural Science:Materials International 2006年第12期16卷 1242-1251页

作者： FANG Zhuo~1, LUO Qingming~1**, ZHANG Guoqing~1 and LI Yixue~2**(1. Hubei bioinformatics and Molecular Imaging Key Laboratory,Huazhong University of Science and technology, Wuhan 430074, china 2. shanghai center for Bioinformation and technology, shanghai 200235, china) [a]Hubei bioinformatics and Molecular Imaging Key Laboratory Huazhong University of Science and Technology Wuhan China [b]shanghai center for Bioinformation and technology Shanghai China

Microarray technology, which permits rapid and large-scale screening for patterns of gene expressions, usually generates a large amount of data. How to mine the biological meanings under these data is one of the main challenges in bioinformatics. Compared to the pure mathematical techniques, those methods incorporated with some prior biological knowledge generally bring better interpretations. Recently, a new analysis, in which the knowledge of biological networks such as metabolic network and protein interaction network is introduced, is widely applied to microarray data analysis. The microarray data analysis based on biological networks contains two main research aspects: identification of active components in biological networks and assessment of gene sets significance. In this paper, we briefly review the progress of these two categories of analyses, especially some representative methods.

关键词： biological networks microarray data analysis subnetwork gene set.

Semantic Search among Heterogeneous Biological Databases Based on Gene Ontology

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Acta Biochimica et Biophysica Sinica 2004年第5期36卷 365-370页

作者： Shun-Liang CAO, Lei QIN1, Wei-Zhong HE1, Yang ZHONG2, Yang-Yong ZHU, and Yi-Xue LI1,3* Department of Computing and Information technology, Fudan University, shanghai 200433, china shanghai center for Bioinformation 1 technology, shanghai 200235, china School of Life Sciences, Fudan University, shanghai 200433, china Bioinformation center of shanghai Institutes for Biological Sciences, the Chinese Academy of Sciences, shanghai 200031, china Department of Computing and Information technology Fudan University Shanghai China

Semantic search is a key issue in integration of heterogeneous biological databases. In this paper, we present a methodology for implementing semantic search in BioDW, an integrated biological data warehouse. Two tables are presented: the DB2GO table to correlate Gene Ontology (GO) annotated entries from BioDW data sources with GO, and the semantic similarity table to record similarity scores derived from any pair of GO terms. Based on the two tables, multifarious ways for semantic search are provided and the corresponding entries in heterogeneous biological databases in semantic terms can be expediently searched.

关键词： Gene Ontology semantic search BioDW

Functional analysis of schistosomes EF-hand domain-containing tegument proteins

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Chinese Science Bulletin 2007年第15期52卷 2100-2107页

作者： YU FuDong1,2,3,KANG Bin1,3,LI YuanYuan3,4 & LI YiXue1,3 1 bioinformatics center,Key Laboratory of Systems Biology,shanghai Institutes for Biological Sciences,Chinese Academy of Sci-ences,shanghai 200031,china 2 Graduate University of Chinese Academy of Sciences,shanghai 200031,china 3 shanghai center for Bioinformation technology,shanghai 200235,china 4 Key Laboratory of Systems Biology,shanghai Institutes for Biological Sciences,Chinese Academy of Sciences,shanghai 200031,china bioinformatics center Key Laboratory of Systems Biology Shanghai Institutesfor Biological Sciences Chinese Academy of Sciences Shanghai 200031 China

Schistosomes cause schistosomiasis disease which severely threatens human health. Little is known about the functions of EF-hand domain containing schistosomes tegument proteins other than as an-tigens. More possible functions of these tegument proteins were investigated with in silico analyses including protein-protein functional interaction,site-specific variation and glycosylation modification. The analysis results suggested that schistosomes could actively modulate host immune responses for its own favor through functional interactions with host proteins with immunomodulatory function,and passively regulate host immune responses through sequence variation under positive selection and glycosylating the recognition sites of host immune attack. In addition,the analysis of the C-terminal domain of these tegument proteins indicated that they could assist schistosomes in escaping host immune attacks through inhibiting chemotaxis and non-complement fixing antibody (IgG4) responses. In summary,our results suggested that these tegument antigen proteins could assist schistosomes in escaping and modulating host immune responses for self-protection during the process of host-para-site interaction.

关键词：寄生虫血吸虫皮蛋白质健康

Effect of heat-treatment on the surface properties of gallium phosphide nanosolids by Raman spectroscopy

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Rare Metals 2006年第3期25卷 253-259页

作者： ZHANG Zhaochun YUE Longyi GUO Jingkang School of Materials Science and technology Shanghai University Shanghai 200072 China bioinformatics Research center Shanghai University Shanghai 200072 China

Raman spectra of gallium phosphide （GAP） nanosolids （unheated and heat-treated at 598 and 723 K, respectively） were investigated. It was observed that both the longitudinal optical mode （LO） and the transverse optical mode （TO） displayed an asymmetry on the low-wavenumber side. The scattering bands were fitted to a sum of four Lorentzians which were assigned to the LO mode, surface phonon mode, TO mode, and a combination of Ga-O-P symmetric bending and sum band formed from the X-point TA ＋ LA phonons, respectively. Analysis of the characteristic of surface phonon mode revealed that the surface phonon peak of the GaP nanosolids could be confirmed. In the infrared spectrum of the GaP nanoparticles, we observed the bands on account of symmetric stretching and bending of PO2, as well as stretching of Ga-O The Raman scattering intensity arising from the Ga-O-P linkages increased as increasing the heat-treatment temperature.

关键词： semiconductor materials nanosolids Raman spectrum gallium phosphide

The contribution of cis-regulatory elements to head-to-head gene pairs' co-expression pattern

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Science china(Life Sciences) 2009年第1期52卷 74-79页

作者： HAO Pei1,2,YU Yao2,3,ZHANG XiaoYan4,TU Kang2,FAN HaiWei2 & ZHONG Yang1 1 School of Life Sciences,Fudan University,shanghai 200433,china 2 bioinformatics center,Key Lab of Systems Biology,shanghai Institutes for Biological Sciences,Chinese Academy of Sciences,shanghai 200031,china 3 shanghai center for Bioinformation technology,shanghai 200235,china 4 School of Life Sciences,Tongji University,shanghai 200092,china 1. School of Life Sciences Fudan University Shanghai 200433 China 2. bioinformatics center Key Lab of Systems Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200031 China 3. shanghai center for Bioinformation technology Shanghai 200235 China 4. School of Life Sciences Tongji University Shanghai 200092 China

Transcription regulation is one of the most critical pipelines in biological process,in which cis-elements play the role as gene expression *** attempt to deduce the principles underlying the co-expression of "head-to-head" gene pairs by analyzing activities or behaviors of the shared cis-elements.A network component analysis was performed to estimate the impact of cis-elements on gene promoters and their activities under different *** discoveries reveal how biological system uses those regulatory elements to control the expression pattern of "head-to-head" gene pairs and the whole transcription regulation system.

关键词： transcription regulation cis-elements "head-to-head" gene pairs

Preparation of PFSA/PSf hollow fiber composite membranes with recovered PFSA for the pervaporation separation of EtOH/H_2O

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Science china Chemistry 2010年第1期53卷 273-280页

作者： LANG WanZhong1,2,TONG Wei2,XU ZhenLiang2 & GUO YaJun1 1Department of Chemistry,shanghai Normal University,shanghai 200234,china 2Chemical Engineering Research center,East china University of Science and technology,shanghai 200237,china 1. Department of Chemistry Shanghai Normal University Shanghai 200234 China2. Chemical Engineering Research Center East China University of Science and Technology Shanghai 200237 China

Perfluorosulfonic acid/Polysulfone(PFSA/PSf) hollow fiber composite membranes have been prepared by dip-coating method using PSf ultrafiltration(UF) membrane as substrate with recovered *** composite membranes were applied to the pervaporation separation of 95% ethanol(EtOH)/H2O *** images show that the thickness of the PFSA skin layer of the composite membranes is about 2 μm,much thinner than those of other PFSA composite membranes revealed in the *** of annealing temperature,coating solution concentration and counter-ions of PFSA on the pervaporation performances of the composite membranes were *** total flux decreases and separation factor increases with the increase of annealing *** highest permeation flux of 3230 g m-2 h-1 and a separation factor of 5.4 is obtained for the composite membrane annealed at 80°*** lowest permeation flux of 396 g m-2 h-1 and a separation factor of 27.7 is obtained for the composite membrane annealed at 160°*** permeation performances of the PFSA/PSf composite membrane are evidently influenced by the counter-ions of *** flux sequence of the PFSA/PSf composite membranes with different counter-ions is H+>Li+>Ca2+>Mg2+>Na+>K+>Ba2+>Fe3+>Al3+,and the separation factor sequence is H+2+2+2+Na+>K+.There are very little variations of △Eapp values between the composite membranes with three divalent counterions(Mg2+,Ca2+ and Ba2+),and the △Eapp values of the composite membranes with two trivalent counterions(Fe3+ and Al3+) are relatively high.

关键词： pervaporation hollow fiber composite membrane perfluorslulfonic acid(PFSA) ethanol(EtOH)/H2O mixture

Phylogeographic analysis of human papillomavirus 58

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Science china(Life Sciences) 2009年第12期52卷 1164-1172页

作者： LI YanYun1, LI ZuoFeng2, HE YiFeng1, KANG Yu1, ZHANG XiaoYan1, CHENG MingJun1, ZHONG Yang2, 3· & XU CongJian1· 1 Obstetrics and Gynecology Hospital of Fudan University, shanghai 200011, china 2 shanghai Bioinformation Research center, shanghai 200235, china 3 School of Life Sciences, Fudan University, shanghai 200433, china Obstetrics and Gynecology Hospital of Fudan University Shanghai 200011 China shanghai Bio-information Research center Shanghai 200235 China School of Life Sciences Fudan University Shanghai 200433 China

Human papillomavirus 58 (HPV58) is one type of HPV with high risk of causing cervical cancer. Unusually high prevalence of HPV58 has been reported in Asia, Africa and some other areas. However, due to the scattered distribution of global data, in addition to the lack of data of some HPV58 high-incidence nations and regions, like china's Mainland, a comprehensive analysis of the global geographical distribution of HPV58 remains blank so far. In this study, HPV58 from the human cervical cancer tissue was detected in china's Mainland, and 14 new HPV58-E6/L1 gene sequences were obtained. Moreover, phylogeographic analysis has been conducted combining the HPV58 sequences that have been deposited in GenBank since 1985. The study result shows that the sequences detected from the shanghai, Jiangsu and Sichuan areas are homologous with those found in the past from Hong Kong and Xi'an, china, as well as Japan and other Southeast Asian areas. Furthermore, Western Africa is considered to be the "root" source of the HPV58 variant, while china's Mainland and Southeast Asia are "transit points" and the new sources of HPV58 after receiving the isolates from the "root" source; like HPV16 and HPV18, the HPV58 might also be one of the major HPV types associated with the development and spread of cervical cancer.

关键词： human papillomavirus 58 (HPV58) cervical cancer phylogeography molecular evolution

Performance and mechanism study for low-temperature SCR of NO with propylene in excess oxygen over Pt/TiO_2 catalyst

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Journal of Environmental Sciences 2010年第9期22卷 1441-1446页

作者： Zhixiang Zhang,Mingxia Chen,Zhi Jiang,Wenfeng Shangguan Research center for Combustion and Environmental technology,shanghai Jiao Tong University,shanghai 200240,china. [a] Research center for Combustion Environmental technology Shanghai Jiao Tong University Shanghai 200240 China

A 0.5 wt.% Pt/TiO2 catalyst was prepared and used for the low-temperature selective catalytic reduction （SCR） of NO with C3H6 in the presence of excess oxygen. The effects of Pt loading and 02 concentration on Pt/TiO2 catalytic performance for low-temperature SCR were investigated. It was found that optimal Pt loading was 0.5 wt.% and excess 02 favored low-temperature SCR of NOx. The mechanism of low-temperature SCR of NO with C3H6 was investigated with respect to the behavior of adsorbed species over Pt/TiO2 at 150~C using in situ DRIFTS. The results indicated that surface nitrosyl species （Pt~＋-NO and Ti3＋-NO） and pt2＋-CO are main reaction intermediates during the interactions of NO, C3H6 and 02. A simplified NO decomposition mechanism for the low-temperature SCR of NO with C3H6 was proposed.

关键词： NO low-temperature SCR Pt/TiO2 in situ DRIFTS

Photocatalytic energy storage ability of TiO_2-WO_3 composite prepared by wet-chemical technique

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Journal of Environmental Sciences 2010年第3期22卷 454-459页

作者： Linglin Cao, Jian Yuan, Mingxia Chen, Wenfeng Shangguan Research center for Combustion and Environment technology, shanghai Jiao Tong University, shanghai 200240, china. [a] Research center for Combustion Environment technology Shanghai Jiao Tong University Shanghai 200240 China

TiO2-WO3 hybrid photocatalysts were prepared using wet-chemical technique, and their energy storage performance was characterized by electrochemical galvanostatic method. TiO2 powder was coupled with WO3 powder, which was used as electron pool and the reductive energy could be stored in. As a result, the prepared TiO2-WO3 had good energy storage ability while pure TiO2 showed no capacity and pure WO3 showed quite low performance. The energy storage ability was affected by the crystal structure of WO3 and calcination temperature. The photocatalyst had better capacity when WO3 had low degree of crystallinity, since its loose structure made it easier for electrons and cations to pass through. The photocatalytic energy storage performance was also affected by the molar ratio of TiO2 to WO3. Energy storage capacity was significantly dependent on the composition, reaching the maximum value at TiO2/WO3 1：1 （mol/mol）.

关键词： photocatalyst TiO2-WO3 energy storage