Corey Hudson edited Methods.md  over 10 years ago

Commit id: 9da18313d6f9b570fe0f0290baf4c4119dbd5a11

deletions | additions      

       

Only a few hundred measurements were found from multiple sources for Arabidopsis, which did not cover the organelles explicitly and less than 10% of the known leaf proteome. As the data proved to be inadequate for this study, the Arabidopsis survey had to be set aside for this reason.   Uniprot identifiers were mapped to rice probe set identifiers. Many of the Uniprot identifiers were directly mappable to probe set (236 out of 554 identifiers: split among 123 chloroplast, 235 mature leaf, and 196 seedling leaf probes), using the Rice Coexpression Database \cite{Sato_2013}. The remaining Uniprot identifiers were manually mapped, BLASTP searching Uniprot sequence against the {\it Oryza \textit{Oryza  sativa} Nipponbare reference genome \cite{Kawahara_2013}. ###Translation Initiation Estimation for motifs  The interrelationship between Rice Gene, Protein in the Proteome set, and the MicroArray Probe set required several data sources. The Probe Set Annotation data for the Rice IVT Expression Array was extracted from the Probe Set Annotation CSV file provided by Affymetrix \cite{Liu_2003}. Because UniProt accessions drift over time, the Rice Proteome, which was generated circa 2004, had no protein accessions which were currently in uniprot. Data relationships to gene names and probe sets were assembled through multiple processes. Reviewing archival Rice Genome projects