Feature Set Downloading:

• Here I share the derived feature sets (the 162 detailed version) to save others’ time if also interested in this problem.

> Feature Details in the data set

• Details about each feature here are in this link.

Group Index	# of features	Dataset	Attribute Property	Data Position in the set
1	20	Gene Expression	Real value: [-1, 1]	1-20
2	21	GO Molecular Function	{1, 0}	21- 41
3	33	GO Biological Process	{1, 0}	42 - 74
4	23	GO Component	{1, 0}	75 - 97
5	1	Protein Expression	Real Value – Non Negative	98
6	1	Essentiality	{2 , 1, 0}	99
7	1	HMS_PCI Mass *	{ 1, 0}	100
8	1	TAP Mass *	{ 1, 0}	101
9	1	Y2H	{ 1, 0}	102
10	1	Synthetic Lethal	{ 1, 0}	103
11	1	Gene Neighborhood / Gene Fusion / Gene Co-occur	{ 1, 0}	104
12	1	Sequence Similarity	Real value - Non negative	105
13	4	Homology based PPI	Discrete: Non-negative (Most 0, 1)	106 – 109
14	1	Domain-Domain Interaction	Real value between [0, 1]	110
15	16	Protein-DNA TF group binding	Non-negative discrete, most 0	111 – 126
16	25	MIPS Protein Class	{ 1, 0}	127 – 151
17	11	MIPS Mutant Phenotype	{ 1, 0}	151 - 162

* Matrix model for co-complex and co-pathway prediction. Spoke model for direct PPI prediction.

> Shared data sets

• Yeast Protein ORF list
• File format read me

• For physical Interaction Task in Detailed feature type
• Positive Set PPI list ( from DIP database )
• Positive Set feature set
• Random Negative Set Protein Pairs list (subset size ~230,000)
• Random Negative Set Protein Pairs Feature
• File format read me

• For co-complex Task in Detailed feature type
• Positive Set PPI list ( from MIPS database Complex catalogue )
• Positive Set feature set
• Random Negative Set Protein Pairs list (subset size ~230,000)
• Random Negative Set Protein Pairs Feature
• File format read me

• For co-pathway Task in Detailed feature type
• Positive Set PPI list ( from KEGG database pathway )
• Positive Set feature set
• Random Negative Set Protein Pairs list (subset size ~230,000)
• Random Negative Set Protein Pairs Feature
• File format read me
• Note: The co-pathway relation is an extreme simplified version for the protein-protein pair-wise relationships within a pathway (see paper for the reference work of this task). The main purpose using this task here is to make a comparison to the co-complex and the physical interaction tasks. For the future research, it is quite necessary to investigate the proteins’ interactions within pathways in a more detailed fashion.

> Note

· “-100” in the feature sets means a missing value in that position!

· Details about the gold standard positive sets shared above, please check “Gold Standard datasets” section in the paper.

· The negative data sets I put here is just a random subset containing ~230,000 yeast protein-protein pairs that are not in the positive PPI set of each specific task.

· In the paper, we assume the size ratio between the positive examples and the negative examples is roughly 1:600 (estimated based on experimental data) in building the train-test sets.

· This ratio is still questionable and need further discussion.

· If you happen to know a better answer other than the above strategy I used, it would be greatly appreciated if you could contact me.

·

· If you notice any mistakes in the data, please contact me as soon as possible. Thanks ahead !

· FAQ page