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). |