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gene_networks_inference [2020/01/06 16:30] – [Software] 107.1.85.154gene_networks_inference [2020/05/27 03:00] (current) – [iNETgrate] admin
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 ====== Gene networks inference ====== ====== Gene networks inference ======
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 ===== Objectives ===== ===== Objectives =====
 Biological processes in a cell often require intricate coordination between //multiple// genes and proteins. The goal of this project is to infer useful biological and clinical information from large networks of thousands of genes. We develop an integrative approach to analyze co-expression and DNA methylation patterns in a single model. The results will be useful in pinpointing the cause and mechanism of complex diseases such as cancer. Our findings can potentially open doors to new targets for novel treatment plans. \\ Biological processes in a cell often require intricate coordination between //multiple// genes and proteins. The goal of this project is to infer useful biological and clinical information from large networks of thousands of genes. We develop an integrative approach to analyze co-expression and DNA methylation patterns in a single model. The results will be useful in pinpointing the cause and mechanism of complex diseases such as cancer. Our findings can potentially open doors to new targets for novel treatment plans. \\
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 ===== Software ===== ===== Software =====
  
-**Pigengene:** This R package provides an efficient way to perform network analysis and to infer biological signatures from gene expression profiles. The signatures are independent from the underlying platform, e.g., it can infer the signatures using data from microarray and evaluate them in an independent RNA Seq dataset. It is approved by, and publicly available from, [[https://bioconductor.org/packages/Pigengene|Bioconductor]].+==== Pigengene ==== 
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 +This R package provides an efficient way to perform network analysis and to infer biological signatures from gene expression profiles. The signatures are independent from the underlying platform, e.g., it can infer the signatures using data from microarray and evaluate them in an independent RNA Seq dataset. It is approved by, and publicly available from, [[https://bioconductor.org/packages/Pigengene|Bioconductor]]. 
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 +==== iNETgrate ====
  
-**iNETgrate:** This R package is useful to integrate DNA methylation and gene expression data into //a single //network [[[:https:bitbucket.org_habilzare_genetwork_src_master|code]]]. This approach leads to identification of more robust gene modules compared to conventional coexpression networks. The package will be publicly available after review and approval by Bioconductor.+This R package is useful to integrate DNA methylation and gene expression data into //a single //network ([[https://bitbucket.org/habilzare/genetwork/src/master/code/Ghazal/iNETgrate/|code]]). This approach leads to identification of more robust gene modules compared to conventional coexpression networks. The package will be publicly available after review and approval by Bioconductor. A [[https://docs.google.com/document/d/17ZlnpNFm2QD58j4AI-GbyW_9TPXT_e5dsGYm_DPV2Fs/edit|checklist]] for package completion tasks.