Table 2.
Overview of the different node and edge attributes in the PML-NB interaction network. In the 'field' column we present the attribute as it is assigned in the network. In the 'description' column we provide a brief explanation of what is embodied by the attribute. Finally, in the 'criteria' column the different sources of information are mentioned.
| Field | Description | Criteria (in order) |
|---|---|---|
| Node Attributes | ||
| ID | UniProtID 87 | Retrieved from UniProt |
| Canonical Name | Common name | Most used in literature > First designation in UniProt |
| Cellular Localization | Subcellular localization differentiates amongst the several organelles in the nucleus and cytoplasm. | GO (cellular component ontology) > Locate 88 (marked with “*”) > Literature > predicted localization by Locate |
| Simplified Cellular Localization | Only differentiates between nucleus, cytoplasm and shuttles between these two compartiments. | 'nucleus' (all nuclear organelles); 'cytoplasm' (all cytoplasmatic organelles) and 'shuttle' between cytoplasm and nucleus. |
| Function | For this attribute we used the UniProt ontology as a simplified version of the GO terms to provide a comprehensible overview. To annotate the network with the complete GO annotations we refer to Cytoscape plugins such as BINGO89. | UniProt Ontologies > Panther database 90 |
| Connection with disease | This field is filled in when mutations, knockout or other modifications of the protein resulting in disease. If a MIM number was available it is mentioned, otherwise there is reference to specific publications. This attribute is additional information and does not mean that the PML-NBs are explicitly involved in the disease process. | UniProt (General Annotation) and literature |
| Induction | Information from UniProt and literature about regulation by several (bio)chemical stimuli. | UniProt (General Annotation) and literature |
| SUMO Consensus | We manually searched if any PML-NB components contained a predicted negatively charged amino acid-dependent sumoylation motif (NDSM)91 or phosphorylation-dependent sumoylation motif (PDSM)92 and present these in this attribute. Proteins predicted by us are labeled as 'IS Lab'. | Literature |
| SUMO Isoform | Here we provide an overview of the conjugated isoform described in literature. Proteins marked in this attribute with 'pathway' are enzymes or actors of the SUMO conjugation machinery. | Literature |
| Remarks | In the 'Remarks' attribute we provide potentially important details about the protein | Literature and/or UniProt |
| Edge Attributes | ||
| Author(s) | Reference to the first author, year of publication and PubMedID. | PubMed |
| Source | Indication of source where a certain interaction was found. | Literature and/or database (IntAct, HPRD, BIOGRID, MINT and NPD) search |
| Methods | Gives an overview of the methods used to detect the interaction. As a designation for these methods we used the same evidence code as used on BIOGRID. | Literature and/or database (IntAct, HPRD, BIOGRID, MINT and NPD) search |
| Fluorescence Microscopy | Gives details about the conditions for co-localization studies e.g. endogenous levels, overexpression data and or partial overlap (if mentioned in the publication) | Literature |
| Cell type | Cell type used for PML interaction studies. | Literature |
| PML isoform | For PML interactions it is important to make reference of the PML isoform used if this data is available. | Literature |
| Remarks | In the 'Remarks' attribute we provide potentially important details interaction | Literature |