ai: Data set to predict autophagy induction in _Podospora...
In Path2PPI: Prediction of pathway-related protein-protein interaction networks

Description Usage Format Details Value References Examples

This data set consists of all data files necessary to predict the putative interactions of the induction step of autophagy in Podospora anserina by means of the corresponding PPIs in human and yeast.

1	data("ai")

human.ai.irefindex: Data frames with 1694 observations of 54 variables. yeast.ai.irefindex: Data frames with 3840 observations of 54 variables. pa2human.ai.homologs: Data frames with 261 observations of 12 variables. pa2yeast.ai.homologs: Data frames with 98 observations of 12 variables. human.ai.proteins: Named character vector with 5 elements. yeast.ai.proteins: Named character vector with 7 elements.

Data frames human.ai.irefindex and yeast.ai.irefindex consists of all relevant interactions of the corresponding iRefIndex files. The two data frames pa2human.ai.homologs and pa2yeast.ai.homologs are the necessary parts of the result files from the BLAST searches of the P. anserina proteom against the proteoms of human and yeast. The named character vectors human.ai.proteins and yeast.ai.proteins consists of the proteins involved in the induction process of autophagy in human and yeast.

Four data frames and two named character vectors (see above).

Camacho, C. et al. (2009). BLAST+: architecture and applications. BMC Bioinformatics, 10(1), 421.

Razick, S. et al. (2008). iRefIndex: a consolidated protein interaction database with provenance. BMC Bioinformatics, 9(1), 405.