DroID - The Drosophila Interactions Database

Table Definitions

DroID contains three types of tables, including interaction data tables, Drosophila gene attribute tables, and interaction attributes tables. Table column names (used in downloaded text files), their short descriptive names (used on DroID web pages and in IM Browser when right clicking an interaction and choosing 'Edge attributes'), and their explanations are provided below. For a general description of each table see the database description page.

All of the data fields (columns) listed below are available in the interaciton list on the DroID web site. All fields can be used to search for or filter interaction networks using IM Browser.

Finley Yeast Two Hybrid Data

• FBGN_GENE1_BD (FBgn BD) - GENE1 was fused to a DNA Binding Domain.
• FBGN_GENE2_AD (FBgn AD) - GENE2 was fused to an Activation Domain.
• GENE1_INTERACTIONS_AS_BD (Interactions as BD) - Number of interactions in which GENE1 was fused to a DNA Binding Domain.
• GENE1_INTERACTIONS_TOTAL (Total Interactions for BD) - Number of interactions involving GENE1.
• GENE2_INTERACTIONS_AS_AD (Interactions as AD) - Number of interactions in which GENE2 was fused to an Activation Domain.
• GENE2_INTERACITONS_TOTAL (Total Interactions for AD) - Number of interactions involving GENE2.
• SCREEN (Screen) - Original interaction screen. Note that interactions may have been detected in multiple screens, but only the original is listed. The number of total times the interaction was detected from all screens is given in "IST_RFCS" and "MATRIX_DETECTIONS".
• REFERENCE (Reference) - Literature reference (PubMed ID) for this data set.
• DATE1 (Date) - Date this data was first published.
• C_LEU (C_LEU) - Integer numbers representing leu2 reporter gene signal strength. The LEU2 reporter activity was scored by growth in the absence of leucine, on a 0-3 scale. The background activity due to the BD alone was subtracted.
• C_LACZ (C_LACZ) - Integer numbers representing lacZ reporter gene signal strength. LacZ reporter activity was scored as the level of blue colors on X-Gal plates on a scale of 0 (white) to 5 (dark blue). The background activity due to the BD alone was subtracted
• C_SUM (Strength) - C_SUM is a sum of the leu and lacZ scores after the background has been subtracted, which is taken as an indicator of overall two-hybrid reporter activity (range 0-8).
• MATRIX (Matrix) - Interaction screening method in which the final interaction is verified in a one-on-one mating. Indicates whether this interaction was detected in a matrix screen (Yes or No). A single detection is reproducible, and thus the number of times detected is not particularly relevant. Occasionally, the same interaction was detected in a different screen, in which case the number of Matrix_Detections is greater than 2.
• IST (IST) - Interaction Sequence Tag. Indicates whether this interaction was detected in a library screen (Yes or No). In such a screen, after mating a BD strain with the AD library, individual yeast clones are selected based on reporter expression and the interacting AD fusion is sequenced. The same AD fusion can be identified several times; multiple ISTs for a given interaction are less likely to represent a false positive than a single IST.
• MATRIX_DETECTIONS (Matrix Detections) - The number of times this interaction was detected in one-on-one "matrix" assays.
• ISTS_RFCS (ISTS_RFCS) - This is essentially the total number of AD clones that were identified for the particular interaction. It is the sum of the number of ISTs and clones in an identical restriction fragment class (RFC) as the IST clone.
• DATA_VERSION (Version) - Version of current data.
• DATE_LAST_UPDATED (Date last updated) - Date of most recent update.
• PubMedURL
• Interaction Detection Methods - includes HUPO Protein Standards Initiative - Molecular Interaction (PSI-MI) term and ID when available.
• Interaction Type - PP for protein-protein, PD for protein-DNA interactions (as in transcritpion factor-gene interactions), RG for RNA-gene (as in miRNA-gene interactions), GG for genetic interactions.

Curagen Yeast Two Hybrid Data

• FBGN_GENE1_BD (FBgn BD) - see definition for Finley Yeast Two Hybrid Data.
• FBGN_GENE2_AD (FBgn AD) - see definition for Finley Yeast Two Hybrid Data.
• GENE1_INTEARCTIONS_AS_BD (Interactions as BD) - see definition for Finley Yeast Two Hybrid Data.
• GENE1_INTERACTIONS_TOTAL (Total Interactions for BD) - see definition for Finley Yeast Two Hybrid Data.
• GENE2_INTERACTIONS_AS_AD (Interactions as AD) - see definition for Finley Yeast Two Hybrid Data.
• GENE2_INTERACTIONS_TOTAL (Total Interactions for AD) - see definition for Finley Yeast Two Hybrid Data.
• SCREEN (Screen) - see definition for Finley Yeast Two Hybrid Data.
• REFERENCE (Reference) - see definition for Finley Yeast Two Hybrid Data.
• DATE1 (Date) - see definition for Finley Yeast Two Hybrid Data.
• CDNA (CDNA) - Indicates whether the interaction was detected by screening a cDNA library. Curagen conducted library screens by mating bait strains either with a cDNA library or a pool of ~11,00 individually cloned full length ORFs referred to as the "collection".
• COLLECTION (Collection) - Indicates whether the interaction was detected by screening the cololection of full-length clones (see above).
• HEXPERT (HEXPERT) - Indicates whether the interaction was part of a training set generated by human experts. 1 or 0 indicates whether it was in the true positive or false positive training set, respectively.
• YEXPERT (YEXPERT) - Indicates whether the interaction was part of a training set generated by a bioinformatics approach. 1 or 0 indicates whether it was in the true positive or false positive training set, respectively.
• CEXPERT (CEXPERT) - Indicates whether the interaction was part a training set generated by combing the human and bioinformatics sets. 1 or 0 indicates whether it was in the true positive or false positive training set, respectively.
• CURAGEN_CONFIDENCE (Curagen Confidence) - Confidence score (0-1) generated using a statistical model that determined attributes that correlate with the likelihood of being in the true or false positive training set. The dividing line between high confidence and low confidence interactions was set to 0.5.
• ISTS_RFCS (ISTS_RFCS) - see definition for Finley Yeast Two Hybrid Data.
• DATA_VERSION (Version) - Version of curent data.
• DATE_LAST_UPDATED (Date last updated) - Date of most recent update.
• PubMedURL
• Interaction Detection Methods - includes HUPO Protein Standards Initiative - Molecular Interaction (PSI-MI) term and ID when available.
• Interaction Type - PP for protein-protein, PD for protein-DNA interactions (as in transcritpion factor-gene interactions), RG for RNA-gene (as in miRNA-gene interactions), GG for genetic interactions.

Hybrigenics Yeast Two Hybrid Data

• FBGN_GENE1_BD (FBgn BD) - see definition for Finley Yeast Two Hybrid Data.
• FBGN_GENE2_AD (FBgn AD) - see definition for Finley Yeast Two Hybrid Data.
• GENE1_INTEARCTIONS_AS_BD (Interactions as BD) - see definition for Finley Yeast Two Hybrid Data.
• GENE1_INTERACTIONS_TOTAL (Total Interactions for BD) - see definition for Finley Yeast Two Hybrid Data.
• GENE2_INTERACTIONS_AS_AD (Interactions as AD) - see definition for Finley Yeast Two Hybrid Data.
• GENE2_INTERACTIONS_TOTAL (Total Interactions for AD) - see definition for Finley Yeast Two Hybrid Data.
• SCREEN (Screen) - see definition for Finley Yeast Two Hybrid Data.
• REFERENCE (Reference) - see definition for Finley Yeast Two Hybrid Data.
• DATE1 (Date) - see definition for Finley Yeast Two Hybrid Data.
• IST (IST) - see definition for Finley Yeast Two Hybrid Data.
• ISTS_RFCS (ISTS_RFCS) - see definition for Finley Yeast Two Hybrid Data.
• DATA_VERSION (Version) - Version of current data.
• PMID (PM ID) - PubMed ID of the article describing this data.
• URL_PUBMED (URL PubMed) - Web link to the article.
• DATE_LAST_UPDATED (Date last updated) - Date of most recent update.
• PubMedURL
• Interaction Detection Methods - includes HUPO Protein Standards Initiative - Molecular Interaction (PSI-MI) term and ID when available.
• Interaction Type - PP for protein-protein, PD for protein-DNA interactions (as in transcritpion factor-gene interactions), RG for RNA-gene (as in miRNA-gene interactions), GG for genetic interactions.

  Perrimon coAP complex

• FBgn_Bait - Flybase gene ID for the gene encoding the bait (TAP-tagged) protein.
• FBgn_Interactor - Flybase gene ID for the gene encoding the interacting protein co-affinity purified with the bait.
• SAINT Score (OVERALL_SAINT_PROB) - Overall score using the Signficance Analysis of Interactome (SAINT) method to score the interaction.
• Total Baits/Interactor (BAITS_TOTAL) - Number of baits that this interactor interacted with in this dataset.
• Biological Replicates (SAMPLES) - total number of experimental samples in which this interaction was detected.
• Total Spectral Count: sum of MS spectral counts for all experimental conditions.
• Average Spectral Count (AVE_SPECTRALCOUNT_TOTNORM) - sample-averaged spectral count normalized by sample total spectra.
• Average Spectral Count Bait (AVE_SPECTRALCOUNT_BAITNORM) - sample-averaged spectral count normalized by bait spectra.
• Conditions Interaction Detected (CONDITIONS_ISOLATED ) - experimental conditions in which this interaction was detected (number of separate samples in which the interaction was detected). "BS" – baaseline, Drosophila S2R+ cells untreated. "Insulin" – Drosophila S2R+ cells after 10 minutes of insulin stimulation. "Spitz/EGF" – Drosophila S2R+ cells after 10 minutes of sSpitz/EGF stimulation.
• SAINT baseline (SAINT_TIME_0) - SAINT score at baseline conditions (cells not treated with EGF or insulin).
• SAINT 10 min insulin (SAINT_TIME_I10) - SAINT score after 10 minutes insulin stimulation.
• SAINT 10 min EGF (SAINT_TIME_S10) - SAINT score after 10 minutes EGF stimulation.
• Dynamic prob insulin vs. baseline (DYNAMICS_PROB_I10_OVER_0) - calculated probability that the interaction is induced by insulin.
• Dynamic prob EGF vs. baseline (DYNAMICS_PROB_S10) - calculated probability that the interaction is induced by EGF.
• Dynamic prob insulin vs. EGF (DYNAMICS_PROB_I10_OVER_S10) - calculated probability that the interaction is more by insulin relative to EGF.
• Control_Samples - number of control samples in which this interactor was detected. A control is a pull-down with the affinity tag only and no bait protein.
• Control Spectral Count - sum of spectral counts for this interactor in all control pull downs.
• Control Ave Spectral Count (AVE_SPECTRALCOUNT_TOTNORM_CONT) - sample-averaged spectral count normalized by sample total spectra for this interactor in control pull downs.
• DATA_VERSION (Version) - Version of current data.
• Reference (PM ID) - PubMed ID of the article describing this data.
• DATE_LAST_UPDATED (Date last updated) - Date of most recent update.
• PubMed URL (URL_PUBMED) - Web link to the article.
• Interaction Detection Methods - includes HUPO Protein Standards Initiative - Molecular Interaction (PSI-MI) term and ID when available.
• Interaction Type - PP for protein-protein, PD for protein-DNA interactions (as in transcritpion factor-gene interactions), RG for RNA-gene (as in miRNA-gene interactions), GG for genetic interactions.

DPIM coAP complex

• FBgn Bait - Flybase gene ID for the gene encoding the bait (HA-tagged) protein.
• FBgn Interactor - Flybase gene ID for the gene encoding the interacting protein co-affinity purified with the bait.
• Bait URL - DPIM bait page
• Sample IDs - DPIM sample IDs
• Bait Clone IDs - DPIM clone IDs
• Bait Unique Peptides - unique bait peptides detected by MS/MS
• Bait total peptides - total bait peptides detected by MS/MS
• Bait Ave XCORR - SEQUEST Xcorr peptide identification score
• Bait Gene Redundancy (BAIT_AVG_GENE_REDUNDANCY) -
• Bait Isoforms - protein isoforms.
• Total Baits/Interactor (BAITS_TOTAL) - Number of baits that this interactor interacted with in this dataset. (DroID calculated).
• HGSCore - Hypergeometric Spectral Count Score
• Interactor Unique Peptides- unique peptides detected by MS/MS
• Interactor Total Peptides- total peptides detected by MS/MS
• Interactor Ave XCORR - SEQUEST Xcorr peptide identification score
• Interactor Ave Gene Redundancy -
• Interactor Isoforms - protein isoforms
• Data Source URL - link
• Interaction Source - source and download date.
• DATA_VERSION (Version) - Version of current data.
• Reference (PM ID) - PubMed ID of the article describing this data.
• DATE_LAST_UPDATED (Date last updated) - Date of most recent update.
• PubMed URL (URL_PUBMED) - Web link to the article.
• Interaction Detection Methods - includes HUPO Protein Standards Initiative - Molecular Interaction (PSI-MI) term and ID when available.
• Interaction Type - PP for protein-protein, PD for protein-DNA interactions (as in transcritpion factor-gene interactions), RG for RNA-gene (as in miRNA-gene interactions), GG for genetic interactions.

Genetic Interactions - from Flybase

• FLY_GENE1 (FBgn Gene1) - Fly FBgn of the first gene .
• FLY_GENE2 (FBgn Gene2) - Fly FBgn of the second gene.
• REFERENCE (Reference) - Flybase reference ids associated with this interaction.
• Flybase URL - links to the references
• DATA_VERSION (Version) - Version of current data.
• Reference (PM ID) - PubMed ID of the article describing this data.
• DATE_LAST_UPDATED (Date last updated) - Date of most recent update.
• PubMed URL (URL_PUBMED) - Web link to the article.
• Interaction Detection Methods - includes HUPO Protein Standards Initiative - Molecular Interaction (PSI-MI) term and ID when available.
• Interaction Type - PP for protein-protein, PD for protein-DNA interactions (as in transcritpion factor-gene interactions), RG for RNA-gene (as in miRNA-gene interactions), GG for genetic interactions.

Yeast Interologs

• FLY_GENE1 (FBgn Gene1) - Fly FBgn of the first gene in the predicted interaction.
• FLY_GENE2 (FBgn Gene2) - Fly FBgn of the second gene in the predicted interaction.
• YEAST_ORF1 (Yeast ORF1) - Yeast ORF corresponding to the first fly gene.
• YEAST_ORF2 (Yeast ORF2) - Yeast ORF corresponding to the second fly gene.
• YEAST_UNIPROT1 (Yeast uniprot_1) - Yeast UniProtKB accession number corresponding to the first fly gene.
• YEAST_UNIPROT2 (Yeast uniprot_2) - Yeast UniProtKB accession number corresponding to the second fly gene.
• ORTHOLOG_METHOD (Ortholog Method) - Orthology mapping method. InParanoid version 5.1, January 2007 was used to build tables in the current database.
• INTERACTION_PUBMEDS (Interaction Pubmed IDs) - PubMed IDs of articles discussing this interaction.
• INTERACTION_DETECT_METHODS (Interaction Detection Methods) - Methods employed in detecing this interaction.
• DATE_LAST_UPDATED (Date last updated) - Date of most recent update.
• DATA_VERSION (Version) - Version of current data.
• ORIGINAL_INTERACTION_SOURCE (Original interaction source) - Names of source databases containing this interaction, including date data was downloaded from the source databases.
• ORTHOLOG_FLY_GENE1_SCORE (Ortholog Fly gene1 score) - Scores assigned by InParanoid to denote confidence of ortholgy mapping.
• ORTHOLOG_YEAST_ORF1_SCORE (Ortholog Yeast ORF_1 score) - Scores assigned by InParanoid to denote confidence of ortholgy mapping.
• ORTHOLOG_FLY_GENE2_SCORE (Ortholog Fly gene2 score) - Scores assigned by InParanoid to denote confidence of ortholgy mapping.
• ORTHOLOG_YEAST_ORF1_SCORE (Ortholog Yeast ORF_2 score) - Scores assigned by InParanoid to denote confidence of ortholgy mapping.

Worm Interologs

• FLY_GENE1 (FBgn Gene1) - Fly FBgn of the first gene in the predicted interaction.
• FLY_GENE2 (FBgn Gene2) - Fly FBgn of the second gene in the predicted interaction.
• WORM_GENE1 (Worm gene_1) - Worm gene id corresponding to the first fly gene.
• WORM_GENE2 (Worm gene_2) - Worm gene idcorresponding to the second fly gene.
• WORM_PROTEIN1_UNIPROT (Worm uniprot_1) - Worm UniProtKB accession number corresponding to the first fly gene.
• WORM_PROTEIN2_UNIPROT (Worm uniprot_2) - UniProtKB accession number corresponding to the second fly gene.
• ORTHOLOG_METHOD (Ortholog Method) - See definition for Yeast Interologs.
• INTERACTION_PUBMEDS (Interaction Pubmed IDs) - See definition for Yeast Interologs.
• INTERACTION_DETECT_METHODS (Interaction Detection Methods) - See definition for Yeast Interologs.
• DATE_LAST_UPDATED (Date last updated) - Date of most recent update.
• DATA_VERSION (Version) - Version of current data.
• ORIGINAL_INTERACTION_SOURCE (Original interaction source) - See definition for Yeast Interologs.
• ORTHOLOG_FLY_GENE1_SCORE (Ortholog Fly gene1 score) - See definition for Yeast Interologs.
• ORTHOLOG_WORM_GENE1_SCORE (Ortholog Worm gene1 score) - See definition for Yeast Interologs.
• ORTHOLOG_FLY_GENE2_SCORE (Ortholog Fly gene2 score) - See definition for Yeast Interologs.
• ORTHOLOG_WORM_GENE2_SCORE (Ortholog Worm gene2 score) - See definition for Yeast Interologs.

Human Interologs

• FLY_GENE1 (FBgn Gene1) - Fly FBgn of the first gene in the predicted interaction.
• FLY_GENE2 (FBgn Gene2) - Fly FBgn of the second gene in the predicted interaction.
• HUMAN_PROTEIN1_ENSEMBL (Human Ensembl ID_1) - Human protein Ensembl ID corresponding to the first fly gene.
• HUMAN_PROTEIN2_ENSEMBL (Human Ensembl ID_2) - Human protein Ensembl ID corresponding to the second fly gene.
• HUMAN_PROTEIN1_UNIPROT (Human Uniprot AC_1) - Human protein UniprotKB accession number corresponding to the first fly gene.
• HUMAN_PROTEIN2_UNIPROT (Human Uniprot AC_2) - Human protein UniprotKB accession number corresponding to the second fly gene.
• ORTHOLOG_METHOD (Ortholog Method) - See definition for Yeast Interologs.
• INTERACTION_PUBMEDS (Interaction Pubmed IDs) - See definition for Yeast Interologs.
• INTERACTION_DETECT_METHODS (Interaction Detection Methods) - See definition for Yeast Interologs.
• DATE_LAST_UPDATED (Date last updated) - Date of most recent update.
• DATA_VERSION (Version) - Version of current data.
• ORIGINAL_INTERACTION_SOURCE (Original interaction source) - See definition for Yeast Interologs.
• ORTHOLOG_FLY_GENE1_SCORE (Ortholog Fly gene1 score) - See definition for Yeast Interologs.
• ORTHOLOG_HUMAN_PROTEIN1_SCORE (Ortholog Human protein1 score) - See definition for Yeast Interologs.
• ORTHOLOG_FLY_GENE2_SCORE (Ortholog Fly gene2 score) - See definition for Yeast Interologs.
• ORTHOLOG_HUMAN_PROTEIN2_SCORE (Ortholog Human protein2 score) - See definition for Yeast Interologs.

Gene Attributes

This table includes gene data periodically downloaded from Flybase and orthologs information from DroID.

• FLY_GENE (Primary FlyBase ID) - Primary FlyBase FBgn.
• SYMBOL (Symbol) - Gene symbol.
• FULL_NAME (Full Name) - Full name of the gene.
• URL (URL) - Web link to FlyBase page describing this gene.
• SECONDARY_FBGNS (Secondary FlyBase ID) - Secondary FlyBase FBgns associated with the primary FlyBase FBgns.
• GENE_CLASS (Class of Gene) - Class of the gene.
• GO_MOLECULAR_FUNCTION (GO Molecular Function) - Gene Ontology (GO) Molecular Function annotations. It was formatted as GO_id(GO_evidence)===GO_term,GO_id(GO_evidence)===GO_term... .
• GO_BIOLOGICAL_PROCESS (GO Biological Process) - GO Biological Function annotations,same format as Molecular Functions.
• GO_CELLULAR_PROCESS (GO Cellular Component) - GO Cellular Component annotations, same format as Molecular Functions.
• SYNONYMS (Synonyms) - Synonyms of the gene.
• PROTEIN_DOMAINS (Protein Domains) - Protein domain annotations obtained from Interpro.
• CG_SYMBOLS (CG Symbol) - CG symbols associated with this gene.
• Zebrafish orthologs - Danio rerio orthologs
• Yeast orthologs - S. cerevisiae orthologs
• Worm orthologs - C. elegans orthologs
• Mouse orthologs - Mus musculus orthologs
• Human orthologs - H. sapiens orthologs
• Protein Expression Stage - From Flybase controlled vocabulary
• Protein Expression Tissue - From Flybase controlled vocabulary
• RNA Expresion Stage - From Flybase controlled vocabulary
• RNA Expression Tissue - From Flybase controlled vocabulary
• Expression Data Link - Expression data at Flybase
• Phenotype Class - e.g., lethal, amaternal effect, female sterile, etc. From Flybase.
• Phenotype Manifest - Tissue or stage affected in mutants. From Flybase.
• DATE_LAST_UPDATED (Date last updated) - Date of most recent update.
• DATA_VERSION (Version) - Version of current data.

Home | About Us | Contact Info | Copyright