Gene list enrichment analysis for Cellular Component Ontology using ToppGene.

The list of 100% probable proteins from each sample’s proteome was derived and gene list enrichment analysis was carried out using ToppFun (https://toppgene.cchmc.org/) for Cellular Component ontology. ToppGene Suite is being developed at Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center (BMI CCHMC), Cincinnati, OH 45229. For comparison we also analysed results from two proteomic data-sets [Vesiclepedia ID_44 and Vesiclepedia ID_353] derived from exosomes purified from human plasma using Size exclusion filtration followed by Sucrose density gradient ultracentrifugation (UC), as posted on Vesiclepedia (http://microvesicles.org/index.html). Cellular component ontology analysis using ToppFun (GO:0070062: Extracellular vesicular Exosome) for Vesiclepedia ID_44 and Vesiclepedia ID_353 derived exosomal proteome revealed p-values of 1.15E-09 and 1.92E-11 respectively. Similar analysis for GO:0065010 (Extracellular membrane-bounded organelle) from Vesiclepedia ID_44 and Vesiclepedia ID_353 derived exosomal proteome revealed p-values of 1.54E-09 and 2.66E-11 respectively. The %GO term means the percentage ratio of ‘list of proteins as input’ over the assigned list of genes for a specific annotation.
Gene list enrichment analysis for Cellular Component Ontology using ToppGene.