ApoplastP

Data sets used for training and evaluation

The positive training set (apoplastic plant and effector proteins) that was used for training ApoplastP can be found here: FASTA file.
The negative training set (non-apoplastic plant proteins) that was used for training ApoplastP can be found here: FASTA file.
The positive training set (apoplastic plant proteins) before homology reduction: FASTA file.
The negative training set (non-apoplastic plant proteins) before homology reduction: FASTA file.

The set of 29 apoplastic fungal effectors used in the training and evaluation: FASTA file.
The set of 19 apoplastic oomycete effectors used in the training and evaluation: FASTA file.
The set of 8 apoplastic nematode effectors used in the training and evaluation: FASTA file.
The set of 29 cytoplasmic fungal effectors used in the evaluation: FASTA file.
The set of 38 cytoplasmic oomycete effectors used in the evaluation: FASTA file.
The set of 358 RxLR effectors from a HMM model used in the evaluation: RxLR effectors FASTA file.

UniProt sets presented in the ApoplastP paper

The set of plant proteins with Golgi localization and a predicted signal peptide: FASTA file.
The set of plant proteins with ER localization and a predicted signal peptide: FASTA file.
The set of plant proteins with Vacuole localization and a predicted signal peptide: FASTA file.
The set of plant proteins with transmembrane localization and a predicted signal peptide: FASTA file.
The set of plant proteins with GPI-anchors and a predicted signal peptide: FASTA file.
The set of fungal proteins with Golgi localization and a predicted signal peptide: FASTA file.
The set of fungal proteins with ER localization and a predicted signal peptide: FASTA file.
The set of fungal proteins with Vacuole localization and a predicted signal peptide: FASTA file.
The set of fungal proteins with transmembrane localization and a predicted signal peptide: FASTA file.
The set of fungal proteins with GPI-anchors and a predicted signal peptide: FASTA file.
The set of mammalian extracellular proteins with a predicted signal peptide: FASTA file.
The set of mammalian proteins with GPI-anchors and a predicted signal peptide: FASTA file.
The set of human proteins: FASTA file.
The set of human proteins with >= 3.1% cysteine: FASTA file.
The set of human proteins with <= 3.8% glutamic acid: FASTA file.

Rust expression data presented in the ApoplastP paper

The set of secreted Puccinia graminis f. sp. tritici proteins encoded by genes with logFC >= 10 (haustoria vs. spores): FASTA file.
The set of secreted Puccinia graminis f. sp. tritici proteins encoded by genes with logFC >= 1 (haustoria vs. spores): FASTA file.
The set of secreted Puccinia graminis f. sp. tritici proteins encoded by genes with logFC >= 10 (spores vs. haustoria): FASTA file.
The set of secreted Puccinia graminis f. sp. tritici proteins encoded by genes with logFC >= 1 (spores vs. haustoria): FASTA file.

Proteomics and effector candidates data presented in the ApoplastP paper

Extracellular proteome of P. infestans (Meijer et al. 2014): FASTA file.
Extracellular proteome of P. infestans with SignalP 4.1 (Meijer et al. 2014): FASTA file.
Apoplastic proteome of M. oryzae (Kim et al. 2013): FASTA file.
Apoplastic proteome of M. oryzae with SignalP 4.1 (Kim et al. 2013): FASTA file.
Apoplastic proteome of Oryza sativa (Kim et al. 2013): FASTA file.
Apoplastic proteome of Oryza sativa with SignalP 4.1 (Kim et al. 2013): FASTA file.
Apoplastic proteome of Brassica napus (Floerl et al. 2008): FASTA file.
Apoplastic proteome of Brassica napus with SignalP 4.1 (Floerl et al. 2008): FASTA file.
Apoplastic proteome of Arabidopsis thaliana (Floerl et al. 2012): FASTA file.
Apoplastic proteome of Arabidopsis thaliana with SignalP 4.1 (Floerl et al. 2012): FASTA file.
Apoplastic proteome of Nicotiana benthamiana (Goulet et al. 2010): FASTA file.
Apoplastic proteome of Nicotiana benthamiana with SignalP 4.1 (Goulet et al. 2010): FASTA file.
Extracellular fluid proteome of sunflower (Pinedo et al. 2012): FASTA file.

Detailed results from secretome predictions presented in the ApoplastP paper

The 99 predicted secretomes used in the evaluation: zip file
The predicted apoplastic proteins from the 99 secretomes: zip file
The predicted non-apoplastic proteins from the 99 secretomes: zip file

Contact

For comments and suggestions please contact jana.sperschneider@csiro.au