This information is over 2 years old. Information was current at time of publication.{"id":11654,"date":"2019-02-25T14:48:18","date_gmt":"2019-02-25T18:48:18","guid":{"rendered":"http:\/\/info.hsls.pitt.edu\/updatereport\/?p=11654"},"modified":"2019-03-07T09:37:09","modified_gmt":"2019-03-07T13:37:09","slug":"using-partek-to-analyze-chip-seq-data","status":"publish","type":"post","link":"https:\/\/info.hsls.pitt.edu\/updatereport\/using-partek-to-analyze-chip-seq-data\/","title":{"rendered":"Using Partek to Analyze ChIP-Seq Data"},"content":{"rendered":"<p>The HSLS Molecular Biology Information Service (<a href=\"https:\/\/www.hsls.pitt.edu\/molbio\">HSLS-MBIS<\/a>) provides access to many <a href=\"http:\/\/hsls.libguides.com\/molbio\/licensedtools\/resources\">bioinformatics analysis tools<\/a>, including <a href=\"http:\/\/hsls.libguides.com\/molbio\/partekflow\">Partek Flow<\/a>. University of Pittsburgh researchers are now able to perform chromatin immunoprecipitation sequencing (ChIP-Seq) analysis using Partek software to determine how proteins interact with DNA and regulate gene expression.<\/p>\n<p>ChIP-Seq uses high-throughput DNA sequencing to map protein-DNA interactions across the entire genome. The point-and-click user interface in Partek software helps researchers to quickly build a start-to-finish ChIP-Seq pipeline and:<!--more--><\/p>\n<ul>\n<li>identify enriched genomic regions<\/li>\n<li>filter and annotate genomic regions<\/li>\n<li>detect known motifs<\/li>\n<li>discover novel motifs<\/li>\n<li>visualize enriched genomic regions and motifs<\/li>\n<li>find enriched gene sets<\/li>\n<li>integrate with gene expression data<\/li>\n<\/ul>\n<p>Partek software allows for the easy <a href=\"http:\/\/www.partek.com\/how-to-integrate-chip-seq-and-rna-seq-data\/\">integration of ChIP-Seq and RNA-Seq studies into a single study<\/a>. First, peaks and transcription factor binding sites are identified in the ChIP-Seq data, then the peaks are annotated to the genome to locate the nearest transcription start site. Next, a targeted gene list generated from the ChIP-Seq data is compared to a list of differentially expressed genes from RNA-Seq data, followed by visualization using a Venn diagram. The Partek chromosome view allows for the combined visualization of peaks and differentially expressed genes. A <a href=\"http:\/\/www.partek.com\/webinar\/chip-seq-and-atac-seq-analysis-and-integration-with-gene-expression-data\/\">webinar<\/a> describing this process is available.<\/p>\n<figure style=\"width: 503px\" class=\"wp-caption alignnone\"><a href=\"http:\/\/www.partek.com\/webinar\/chip-seq-and-atac-seq-analysis-and-integration-with-gene-expression-data\/\"><img loading=\"lazy\" decoding=\"async\" src=\"http:\/\/www.partek.com\/wp-content\/uploads\/2018\/09\/ChIP-SeqATAC-Seq.jpg\" alt=\"\" width=\"503\" height=\"254\" \/><\/a><figcaption class=\"wp-caption-text\">View full image: <a href=\"http:\/\/www.partek.com\/webinar\/chip-seq-and-atac-seq-analysis-and-integration-with-gene-expression-data\/\">http:\/\/www.partek.com\/webinar\/chip-seq-and-atac-seq-analysis-and-integration-with-gene-expression-data\/<\/a><\/figcaption><\/figure>\n<p>Anyone with a University of Pittsburgh e-mail address can <a href=\"https:\/\/www.hsls.pitt.edu\/molbio\/software_registration\">register for access to Partek software<\/a> via the HSLS license. For more information, <a href=\"https:\/\/www.hsls.pitt.edu\/ask-a-molbio-specialist\">contact<\/a> the HSLS <a href=\"https:\/\/www.hsls.pitt.edu\/molbio\">Molecular Biology Information Service<\/a>.<\/p>\n<p>*Parts of this article content were derived from the <a href=\"http:\/\/www.partek.com\/application-page\/chip-seq\/\">Partek ChIP-Seq website<\/a>.<\/p>\n<p>~Carrie Iwema<\/p>\n","protected":false},"excerpt":{"rendered":"<p>The HSLS Molecular Biology Information Service (HSLS-MBIS) provides access to many bioinformatics analysis tools, including Partek Flow. University of Pittsburgh researchers are now able to perform chromatin immunoprecipitation sequencing (ChIP-Seq) analysis using Partek software to determine how proteins interact with DNA and regulate gene expression. ChIP-Seq uses high-throughput DNA sequencing to map protein-DNA interactions across [&hellip;]<\/p>\n","protected":false},"author":4,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"issue-archives","meta":{"footnotes":"","_links_to":"","_links_to_target":""},"categories":[134],"tags":[-1],"class_list":["post-11654","post","type-post","status-publish","format-standard","hentry","category-march-2019","avhec_catgroup-issue-archives"],"_links":{"self":[{"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/posts\/11654","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/users\/4"}],"replies":[{"embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/comments?post=11654"}],"version-history":[{"count":3,"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/posts\/11654\/revisions"}],"predecessor-version":[{"id":11688,"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/posts\/11654\/revisions\/11688"}],"wp:attachment":[{"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/media?parent=11654"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/categories?post=11654"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/info.hsls.pitt.edu\/updatereport\/wp-json\/wp\/v2\/tags?post=11654"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}