Definition of features


Feature Description Feature Description
Accession AGI accession number; gene name Master Protein AGI protein accession number. This protein is the representative of a protein group that share a same set or a subset of peptides.
Description (TAIR) Description (Standard Annotation) retrieved from TAIR Description (curated) Curated description
Length number of amino acids Localization (SC) Subplastidial localization based on % of spectral count in Envelope, Stroma or Thylakoid subfractions (Ferro et al., 2010).
Localization (curated) Subcellular or subplastidial localization compiled from Ferro et al., 2010, previous proteomic studies, targeting prediction and bibliography. Calculated PI (PPDB) Calculated isoelectric point. Information retrieved from PPDB.
Calculated MW (PPDB) Molecular mass of the protein in kiloDalton. Information retrieved from PPDB. ENV (SC) Envelope Spectral Count: % of spectra recovered in the purified envelope fraction (Ferro et al., 2010).
STR (SC) Stroma Spectral Count: % of spectra recovered in the purified stroma fraction (Ferro et al., 2010). THY (SC) Thylakoid Spectral Count: % of spectra recovered in the purified thylakoid fraction (Ferro et al., 2010).
Total (SC) Total spectral count retrieved from the chloroplast proteins in Ferro et al., 2010. Function (curated) Manual annotation of the functional classification
References Literature references, crude data extracted from various protein databases, % of similarity with orthologues or paralogues, domains etc. MapManBin (PPDB) MapManBin functional classification. Information retrieved from PPDB.
Localization (TAIR) Subcellular or subplastidial localization as described in TAIR. ChloroP Prediction of plastid localization using ChloroP (http://www.cbs.dtu.dk/services/ChloroP/)
TargetP Prediction of subcellular localization using TargetP (http://www.cbs.dtu.dk/services/TargetP/) Curated localization (PPDB) Curated subcellular or subplastidial localization as stated in PPDB.
Aramemnon Number of transmembrane helices as found in the Aramemnon database (http://aramemnon.botanik.uni-koeln.de/) Publications (PPDB) List of most subcellular targeted proteomics studies (MedLine numbers) in which the protein was identified. Information retrieved from PPDB.
Reference of the experiment The reference name of this experiment such as "at_chloro_v1" (Ferro et al. 2010), "thylakoïd_sub_compartments" (Tomizioli et al., 2014) and "cam_bp" (Dell'Aglio et al., 2013). Reference date Reference date for a given experiment (release of the data).
Log Fold Change As described in Tomizioli et al., 2014 to discriminate proteins that are diffenretially distributed between BBY/grana and stroma-lamellae fractions. pValue As described in Tomizioli et al., 2014, a p-value <0.05 indicates that the proteins is diffenrentially distributed in the BBY/grana or the stroma-lamellae fractions.
Differentially distributed proteins high or medium Subthylakoid location (BBY = BBY/Grana fraction; LAM = stroma-lamellae fraction; see Tomizioli et al., 2014).

Definition of search properties


Evidence Exp1: data from Ferro et al., 2010
Evidence Exp2: data from Tomizioli et al., 2014


Property Description Property Description
Expname The reference name of the experiment such as "at_chloro_v1" (Ferro et al. 2010), "thylakoïd_sub_compartments" (Tomizioli et al., 2014) and "cam_bp" (Dell'Aglio et al., 2013). Evidence Exp2's DEP highmedium Differentially distributed proteins between strom-lamellae or BBY/Grana fractions. the different values can be BBY_high; BBY_medium; LAM_High; LAM_medium.
Protein Group's Accession AGI protein accession number. Protein Group's Public Annotation's ChloroP Prediction of plastid localization using ChloroP
Protein Group's Public Annotation's Curated Localization Ppdb Curated subcellular or subplastidial localization as stated in PPDB. Protein Group's Description Description of this protein
Protein Group's Curated Annotation's Description Curated Description. Protein Group's Public Annotation's Description TAIR Description (Standard Annotation) retrieved from TAIR
Protein Group's Curated Annotation's Function Curated Function. Protein Group's Curated Annotation's Localization Curated Curated Localization
Protein Group's Public Annotation's Location TAIR Localization retrieved from TAIR Protein Group's Public Annotation's Mapmanbin PPDB MapManBin functional classification. Information retrieved from PPDB.
Evidence Exp1's Scenvpercent Envelope Spectral Count: % of spectra recovered in the purified envelope fraction. Evidence Exp1's Scstrpercent Stroma Spectral Count: % of spectra recovered in the purified stroma fraction.
Evidence Exp1's Scthypercent Thylakoid Spectral Count: % of spectra recovered in the purified thylakoid fraction. Evidence Exp1's Localizationsc Subplastidial localization based on % of spectral count in Envelope, Stroma or Thylakoid subfractions.
Evidence Exp1's Totalspectralcount Total spectral count retrieved from the AT_CHLORO database. Protein Group's Public Annotation's Targetp Ppdb Prediction of subcellular localization using TargetP.