VERMONT INBRE: BIOINFORMATICS CORE

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 佛蒙特州遗传学网络生物信息学核心（BC）亮点 2006年九  二○ ○七年四月十一日 对于三个BC目标中的每一个，我们重新打印目标，然后总结重点。 目标1提供生物信息学服务，使研究人员更有竞争力的研究资金。 服务包括实验设计以及数据管理和分析。 这些服务将包括对涉及寡核苷酸微阵列、LC-质谱和蛋白质结构/功能的实验项目的支持。 更一般地，BC支持定制数据库的开发。 由于VGN微阵列设施的巨大成功，生物信息学核心服务强调了微阵列数据分析。 VGN用INBRE基金支持了一个微阵列数据分析职位，这个职位现在已经基本上转移到了医学院支持和联邦研究赠款的结合。 因此，我们利用INBRE基金增加了一个微阵列数据分析职位，随后转向自我维持。 亮点： + 微阵列用户24 NIH资助的研究人员（FY 2006），17个部门的UVM，和初级研究人员的比例很高（表1）。 大约一半的服务支持人类表达或基因型分析（下表），但这些设施也支持特殊利益，如牛，变形链球菌和弓形虫研究。 + 支持美国国立卫生研究院R 01赠款的研究员（格雷斯Spatafora）在米德尔伯里学院。 除了表达统计的计算之外，服务还包括基于相关表达模式的共调节的鉴定，以及新开放阅读框架的鉴定。 五名米德尔伯里学院的本科生参加了这项研究。 + 一项新的BCRF资助海曼·穆斯博士对人类乳腺癌样本进行微阵列研究。 + 美国农业部资助托马斯·麦克法登博士进行牛微阵列研究。 + 一项NIH R 01基金授予马修兰德博士用于甲基汞毒性的基因芯片研究。 + 一个COBRE奖拉尔夫巴德博士的免疫生物学研究，包括基因芯片研究。 三名参与COBRE的研究人员在他们的研究中使用微阵列。 + 支持一名初级教员，吉赛尔·肖勒博士，参与临床研究，包括神经母细胞瘤治疗的I期临床试验。 目标2：向学士学位机构提供实验室/讲座单元。 生物信息学核心为VGN外展协调员Janet Murray博士提供了一些咨询服务，在她的生物信息学和微阵列模块的持续开发期间。 然而，Murray博士现在独立运作得非常好，因此外展核心应该为生物信息学和微阵列外展模块的成功而获得充分的信任。 目标3：支持发展电子网络的行政基础设施。 VGN发起了佛蒙特州科学和技术专家数据库的建设，该数据库的范围已经扩大到成为VGN ERIS项目。简要地说，ERIS的基本思想是利用公共人员目录，书目引用数据库，赠款奖励数据库和日历中的信息，提供有关人们的专业知识和兴趣，研究项目，出版物和事件的信息。 这些信息将通过全州范围内的电子邮件通知、网页和自动通知参与者新条目的机器人进行交换。在本报告所述期间，ERIS被用来发布13项全州范围的公告。 PI类别 # 教职员工 41 NIH资助，FY 06 24 初级教师 13 机构 3 UVM部门 17 表1. 主要研究者（PI）参与微阵列项目。 芯片 Number ATH1-121501 27 牛 52 DrosGenome1 8 果蝇_2 6 公司简介 123 HG-U133A_2 94 HG-U133_Plus_2 8 MG_U74Av2 34 MOE430A 34 Mapping250K_Nsp 34 Mapping250K_Sty 5 小鼠430A_2 38 老鼠430_2 6 Mu11KsubA 4 RAE230A 38 RG_U34A 19 S_mutans530155 17 Tgondia520372 9 总 556 表2. 由VGN微阵列设施或VGN生物信息学核心处理的芯片

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Vermont Genetics Network Bioinformatics Core (BC) Highlights September 2006  April 11, 2007 For each of the three BC Aims we reprint the aim and then summarize highlights. AIM 1 Provide bioinformatics services that make investigators more competitive for research funding. Services include experimental design as well as data management and analysis. These services will include support for experimental programs involving oligonucleotide microarrays, LC-Mass spectrometry, and protein structure/function. More generally, the BC supports development of custom databases. Bioinformatics Core services have emphasized microarray data analysis because of the overwhelming success of the VGN Microarray Facility. The VGN supported a microarray data analysis position with INBRE funds, a position that has now moved largely to a combination of College of Medicine support and federal research grants to individual investigators. Thus we used INBRE funds to add a microarray data analysis position that subsequently moved to self-sustainability. Highlights: + The microarray user 24 NIH-funded investigators (FY2006), 17 departments of UVM, and a high proportion of junior investigators (Table 1). About half of the services support human expression or genotype analysis (bottom table) but these facilities also support special interests such as Bos Taurus, Streptococcus mutans, and Toxoplasma gondii research. + Support for an NIH R01 grant to an investigator (Grace Spatafora) at Middlebury College. In addition to calculation of expression statistics, services included identification of co-regulation based on correlated expression patterns, and identification of novel open reading frames. Five Middlebury College undergraduates participated in this research. + A new BCRF grant to Dr. Hyman Muss for microarray studies on human breast cancer samples. + A USDA grant to Dr. Thomas McFadden for bovine microarray studies. + An NIH R01 grant to Dr. Matthew Rand for GeneChip studies of methyl mercury toxicity. + A COBRE award to Dr. Ralph Budd for immunobiology research that includes GeneChip studies. Three of the investigators participating in this COBRE use microarray in their research. + Support for a junior faculty member, Dr. Giselle Sholler, involved in clinical research that includes a Phase I clinical trial of a neuroblatoma therapy. AIM 2 Provide laboratory/lecture modules to Baccalaureate Institutions (BPI). The Bioinformatics Core provided some consulting services to Dr. Janet Murray, VGN Outreach coordinator, during ongoing development of her Bioinformatics and Microarray modules. However, that Dr. Murray is now functioning exceptionally well independently so the Outreach Core deserves full credit for the success of Bioinformatics and Microarray Outreach Modules. AIM 3 Support the development of administrative infrastructure for electronic networks. The VGN initiated construction of a database of Vermont Experts in Science and Technology, which has since grown in scope to become the VGN ERIS Project. Briefly, the idea underlying ERIS is to take advantage of information in public personnel directories, bibliographic citation databases, grant award databases, and calendars to provide information about people's expertise and interests, research projects, publications, and events. This information will be exchanged through statewide email announcements, a web page, and robots that automatically notify participants of new entries. ERIS was used to make 13 statewide announcements during the reporting period. PI Category # Faculty members 41 NIH-funded, FY06 24 Junior faculty 13 Institutions 3 UVM Departments 17 Table 1. Principal Investigators (PI) on projects that involve microarrays. Chip Number ATH1-121501 27 Bovine 52 DrosGenome1 8 Drosophila_2 6 HG-U133A 123 HG-U133A_2 94 HG-U133_Plus_2 8 MG_U74Av2 34 MOE430A 34 Mapping250K_Nsp 34 Mapping250K_Sty 5 Mouse430A_2 38 Mouse430_2 6 Mu11KsubA 4 RAE230A 38 RG_U34A 19 S_mutans530155 17 Tgondiia520372 9 TOTAL 556 Table 2. Chips processed by the VGN Microarray Facility or by the VGN Bioinformatics Core