{"id":42,"date":"2016-06-02T15:51:31","date_gmt":"2016-06-02T15:51:31","guid":{"rendered":"http:\/\/labs.icahn.mssm.edu\/zhang-lab\/?page_id=42"},"modified":"2016-06-02T17:18:12","modified_gmt":"2016-06-02T17:18:12","slug":"applications-2","status":"publish","type":"page","link":"https:\/\/labs.icahn.mssm.edu\/zhang-lab\/research\/applications-2\/","title":{"rendered":"Applications"},"content":{"rendered":"<p class=\"style12\"><strong>Next-Generation Sequencing (NGS) Data Analysis<\/strong><br \/>\nwe provide data analysis for whole genome\/exome sequencing, ChIP-seq, RNA-seq and miRNA-seq using state of art commerical tools ( eg SoftGenetics <a href=\"http:\/\/www.softgenetics.com\/NextGENe.php\">NextGeNe<\/a>) and customized tools\/pipelines developed by our group. The services include \u00a0SNP\/Indel\/structural variation detection, ChIP peak calling, RNA\/miRNA quantification\/discovery, \u00a0variation\/expression comparison across samples and visulaization.<\/p>\n<p class=\"style12\"><span class=\"style12\"> <strong>Microarray Gene\/MiRNA Expression Analysis<\/strong><br \/>\nDNA Microarray\/GenChip is a cutting-edge high throughput technology that can be used to simultaneously detect expression of tens of thousands of genes or non-coding RNAs. Due to a number of systematic and experimental variations, the analysis of millions of data points is very complicated. To help the biologist concentrate on the biological experiments, we offer a full bioinformatics support from consultation on experimental design, data analysis using a number of state-of-art bioinformatics\/statistics tools to data publishing\/submission to GEO.<\/span><\/p>\n<p><strong>Pathway\/Network Analysis<\/strong><br \/>\nDownstream microarray\/proteomics data analysis (such as pathway\/network analysis and integration with diverse types of biological data) is crucial for deeper understanding of gene expression regulation. To facilitate microarray data analysis, we have licensed <a href=\"http:\/\/www.ingenuity.com\/\">Ingenuity System <\/a>, a cutting-edge tool for pathway analysis and visualization. Please contact Weijia Zhang to schedule an appointment to use this tool.<\/p>\n<p><strong>Array CGH\/Copy Number Change<\/strong><br \/>\nArray based C omparative G enomic Hybridization (array CGH) is a novel high throughput cytogenetics approach to study the chromosomal abnormality that occurs in many type of tumors. Data analysis of array CGH is challenging due to the lack of a standard statistical algorithm for detection of chromosomal gain or loss. We have developed a novel statistical approach to identify chromosomal alterations, as well as various visualization tools. We provide support in experimental design, data analysis and visualization for array CGH by two-color arrays or Affymetrix 100K\/500K SNP gene chips.<\/p>\n<p><strong>SNP Chip Analysis <\/strong><br \/>\nWe provide data analysis of SNP Chips including Illumina and Affymetrix 100K\/500K SNP arrays. The data analysis we provide includes association study, Copy Number, LOH analysis and knowledge-based SNP analysis.<\/p>\n<p class=\"style12\"><strong>MS proteomics <\/strong><br \/>\nWe offer protein idenfication, quantitaive analysis and integration of protein expression into gene expression profiles.<\/p>\n<p><span class=\"style12\"><strong>Integrative Gene Annotation<\/strong><br \/>\nTo make biological sense out of Microarray expression data, we developed a useful tool, Gene Annotator for Microarray Analysis (GAMA). GAMA retrieves various types of biological information from a number of public databases and deposits it into a local database that can be queried via web-based annotation tools. GAMA allows researchers to obtain a detailed description of categorized biological information for a single gene or orthologous genes. A researcher can also upload a list of genes out of data analysis into GAMA to retrieve various types of biological information of his choice so that gene expression data can be correlated with biological characteristics.<br \/>\n<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Next-Generation Sequencing (NGS) Data Analysis we provide data analysis for whole genome\/exome sequencing, ChIP-seq, RNA-seq and miRNA-seq using state of art commerical tools ( eg SoftGenetics NextGeNe) and customized tools\/pipelines developed by our group. The services include \u00a0SNP\/Indel\/structural variation detection, ChIP peak calling, RNA\/miRNA quantification\/discovery, \u00a0variation\/expression comparison across samples and visulaization. Microarray Gene\/MiRNA Expression Analysis [&hellip;]<\/p>\n","protected":false},"author":143,"featured_media":0,"parent":30,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-42","page","type-page","status-publish","hentry"],"aioseo_notices":[],"_links":{"self":[{"href":"https:\/\/labs.icahn.mssm.edu\/zhang-lab\/wp-json\/wp\/v2\/pages\/42","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/labs.icahn.mssm.edu\/zhang-lab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/labs.icahn.mssm.edu\/zhang-lab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/zhang-lab\/wp-json\/wp\/v2\/users\/143"}],"replies":[{"embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/zhang-lab\/wp-json\/wp\/v2\/comments?post=42"}],"version-history":[{"count":4,"href":"https:\/\/labs.icahn.mssm.edu\/zhang-lab\/wp-json\/wp\/v2\/pages\/42\/revisions"}],"predecessor-version":[{"id":68,"href":"https:\/\/labs.icahn.mssm.edu\/zhang-lab\/wp-json\/wp\/v2\/pages\/42\/revisions\/68"}],"up":[{"embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/zhang-lab\/wp-json\/wp\/v2\/pages\/30"}],"wp:attachment":[{"href":"https:\/\/labs.icahn.mssm.edu\/zhang-lab\/wp-json\/wp\/v2\/media?parent=42"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}