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Supporting Table 1

Supporting Table 2

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for online supplement of Albert et al., Computer-assisted generation of a protein-interaction database for nuclear receptors

Two tables are provided as an online supplement:

All_interactions

NR-NR_interactions

Columns are as follows:

ENTITY 1	The first "protein" in the tri-occurrence. The precision of the denotation is as apparent in the abstract, and can be at the family level, the gene locus/ protein level, or the variant level. In some cases, the species is indicated.
Merging of variants and species	Merging of ENTITY1 terms to gene level In this list, variants (e.g. splice variants, mutants) and proteins of different species were merged to a single entity at the gene locus level. Where in the abstract it has not been specified which gene (e.g. ERalpha or ERbeta) was referred to, this list will only hold subfamily terms.
Subfamily	Classification of ENTITY1 into Subfamilies. For this classification, the following receptors were summarized as families: TR (TR alpha and beta), RAR (RAR alpha, beta and gamma), PPAR (PPAR alpha, beta and gamma), ROR (ROR alpha and beta), LXR (LXR alpha and beta), HNF4 (HNF4 alpha and gamma), RXR (RXR alpha, beta and gamma), COUPTF (COUP-TF1 and 2), ER (ER alpha and beta) and ERR (ERR alpha, beta and gamma). Note: if ENTITY1 is at the family level, the classification will obviously be the same in the two columns.
NR/NRBP/X	Classification of ENTITY1 of the tri-occurrence as NR, NRBP or X (X = protein complex or fusion protein). This column is absent in the NR-NR and NRBP-NRBP table, since all proteins have the same classification within these tables.
ENTITY 2	The 2nd protein in the tri-occurrence. The precision of the denotation is as apparent in the abstract, and can be at the family level, the gene locus/ protein level, or the variant level. In some cases, the species is indicated.
INTERACTION TERM	affinity, assemble, associate, attach, bind, complex, contact, couple, dimerize, dissociate, dock, FRET, implied interaction, interact, link, mammalian two-hybrid system, precipitate, yeast two-hybrid system
CURATION STATUS	"shows the relation" OR "denies the relation"
SENTENCE	Sentence which shows the interaction between the proteins of ENTITY1 and ENTITY2.
CREATED BY	automatic = extracted by software, curator = manually added by the curators
IDDOC	Identification number of PubMed abstracts (PMID) for the retrieval of respective abstracts at PubMed.

All_interactions

This file contains tri-occurrences which show or deny an interaction between two proteins. There are seven sheets:

All interactions: list of all interactions retrieved

Pivot NRBP-NR interactions: interactive pivot table showing all interactions between NRBPs and NRs (Conditional formatting: 1-10 yellow, 11-20 orange, >20 red)

Pivot Interactions of NRs: table showing all interactions between NRs and NRs, NRBPs or X (complexes and fusion proteins) (Conditional formatting: 1-10 yellow, 11-50 orange, >50 red)

NRBP-NRBP interactions: list of all interactions between NRBPs. This is a subset of the list "All interactions"

Pivot NRBP-NRBP: table showing all interactions between two NRBPs. This is a subset of the list "All interactions". (Conditional formatting: 1-10 yellow, 11-20 orange, >20 red)

denied interactions: interactions that were reported not to take place.

Y2H details: this table gives details as to which interacting protein was picked up in which cDNA library in our screens.

NR-NR_interactions

This file contains only tri-occurrences which show an interaction between NRs. There are two sheets:

NR-NR interaction: list of all interactions between NRs

Pivot: table showing all interactions between two NRs (Conditional formatting: 1-10 yellow, 11-50 orange, >50 red)

How to use the pivot tables:

Pivot tables are interactive in Excel, allowing access to the underlying data. The interactive Pivot tables comprise interactions between two proteins. To see the data which describe a special interaction, double click on a number in the Pivot table: a new excel sheet will open containing all tri-occurrences found to show this protein-protein interaction. It will look like the general lists with the same columns. By copy/paste of the PMID at PubMed you can access the corresponding abstract(s).

Hyperlinks

The tables "all interactions" and "denied interactions" have hyperlinks in their righmost columns. Clicking these should open your internet browser and connect with PubMed for display of the respective reference, for your convenient access to the the literature source.

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