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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link="#0563C1" vlink="#954F72"><div class=WordSection1><p class=MsoNormal>Hi, <o:p></o:p></p><p class=MsoNormal>I am working on creating a Protein Protein Interaction Network for my lab and I am attempting to convert from String ID to the gene name.<o:p></o:p></p><p class=MsoNormal>I found this as a possible answer for how to convert the two ID forms (<a href="https://www.biostars.org/p/342160/">https://www.biostars.org/p/342160/</a>), but since I am using Neurospora Crassa and not Human models, I had to modify it a bit. This is the code that I used:<o:p></o:p></p><p class=MsoNormal><span style='font-family:Courant'>library("biomaRt")<o:p></o:p></span></p><p class=MsoNormal><span style='font-family:Courant'>listMarts(host = "<a href="https://fungi.ensembl.org">https://fungi.ensembl.org</a>", port = 443)<o:p></o:p></span></p><p class=MsoNormal><span style='font-family:Courant'>test <- c("EFNCRP00000000466", "EFNCRP00000000314", "EFNCRP00000000407", "EFNCRP00000000083")<o:p></o:p></span></p><p class=MsoNormal><span style='font-family:Courant'>ensembl_fungi <- useMart(host="<a href="https://fungi.ensembl.org">https://fungi.ensembl.org</a>", <o:p></o:p></span></p><p class=MsoNormal><span style='font-family:Courant'> biomart="fungi_mart", <o:p></o:p></span></p><p class=MsoNormal><span style='font-family:Courant'> port = 443,<o:p></o:p></span></p><p class=MsoNormal><span style='font-family:Courant'> dataset = "ncrassa_eg_gene")<o:p></o:p></span></p><p class=MsoNormal><span style='font-family:Courant'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-family:Courant'>conversion.table <- data.frame(getBM(attributes = c("ensembl_gene_id","ensembl_peptide_id", "uniprotswissprot", "uniprotsptrembl"),<o:p></o:p></span></p><p class=MsoNormal><span style='font-family:Courant'> filters = "ensembl_peptide_id",<o:p></o:p></span></p><p class=MsoNormal><span style='font-family:Courant'> values = list(test),<o:p></o:p></span></p><p class=MsoNormal><span style='font-family:Courant'> mart = ensembl_fungi))<o:p></o:p></span></p><p class=MsoNormal><span style='font-family:Courant'>head(conversion.table)<o:p></o:p></span></p><p class=MsoNormal>This results in an empty data frame. When I put the gene ID’s for each of these (previously known) in as the test and filter by “ensembl_gene_id”, it says the peptide IDs are: <span style='font-size:8.0pt;font-family:"DejaVu Sans",sans-serif;color:black'>EAA26917, <span style='background:white'>EAA26918, </span>EAA28465, <span style='background:white'>EAA28503</span></span><span style='font-size:8.0pt;color:black;background:white'>, </span><span style='color:black;background:white'>which is very different than what String says the ensembl peptide IDs should be.</span><span style='color:black;background:white'><o:p></o:p></span></p><p class=MsoNormal><span style='color:black;background:white'>Does anyone know why this is happening or how to convert from StringID to a gene name directly?<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal style='vertical-align:baseline'><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>Sam Altshuler </span><span style='font-size:9.0pt;font-family:"Segoe UI",sans-serif'><o:p></o:p></span></p><p class=MsoNormal style='vertical-align:baseline'><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>RPI Class of 2021 </span><span style='font-size:9.0pt;font-family:"Segoe UI",sans-serif'><o:p></o:p></span></p><p class=MsoNormal style='vertical-align:baseline'><span style='font-size:12.0pt;font-family:"Times New Roman",serif'>Bioinformatics and Molecular Biology </span><span style='font-size:9.0pt;font-family:"Segoe UI",sans-serif'><o:p></o:p></span></p><p class=MsoNormal style='vertical-align:baseline'><span style='font-size:9.0pt;font-family:"Segoe UI",sans-serif'><a href="mailto:Altshs@rpi.edu" target="_blank"><span style='font-size:12.0pt;font-family:"Times New Roman",serif;color:#0563C1'>Altshs@rpi.edu</span></a></span><span style='font-size:12.0pt;font-family:"Times New Roman",serif'> | 651-558-6327</span><span style='font-size:9.0pt;font-family:"Segoe UI",sans-serif'><o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>