GUILDify uses network-topology based prioritization algorithms in GUILD to score relevance of gene products with respect to given keywords. First, BIANA knowledge base containing data integrated from publicly available major data repositories is queried for gene products associated with the keywords. Next, these gene products are fed to a species-specific interaction network (created using BIANA) as seed proteins. Finally, a score of relevance for each gene product in the network is calculated by the prioritization algorithm. See documentation page for details.

- Grouping multiple keywords TOGETHER using quotations

When the keywords are quoted together, GUILDify will only match entries that contain the quoted keywords together in their description. For instance, "lung carcinoma" (with quotation) will retrieve entries containing "lung carcinoma" together.

- Searching for a keyword AND another keyword using '+'

If we want to search entries containing multiple keywords but not necessarily together, we have to add '+' in front of the word. For instance, "+alzheimer +diabetes" will retrieve entries containing "alzheimer" AND "diabetes".

- Searching for a keyword OR another keyword using whitespaces

If we want to search entries containing at least one of the keywords specified, we have to separate them using whitespaces. For instance, "alzheimer diabetes" will retrieve entries containing "alzheimer" OR "diabetes".

- User-specified gene symbols using semicolons (';')

If the query contains ';', it will be considered as a list of genes separated by semicolons (e.g., TP53; BRCA1; BRCA2).

- User-specified gene symbols in a file

The user can introduce gene symbols in a text file separated by new lines ("\n").

The following examples have been calculated using all the seeds and the prioritization algorithm NetScore:

• From tgz file:

  R CMD INSTALL guildifyR.tgz

• From GitHub repository using devtools (in R):

  library(devtools)

  install_github("emreg00/guildifyR")

• query
  • Description: Get protein/gene info associated with the query keywords.
  • Usage:

    query(keywords, species = "9606", tissue = "all", network.source = "BIANA")

  • Example:

    result.table = query("alzheimer", species="9606", tissue="all", network.source = "BIANA")

• submit.job
  • Description: Submit job using the guildifyR query result table.
  • Usage:

    submit.job(result.table, species, tissue, network.source, scoring.options = list(netcombo = T))

  • Example:

    species="9606"

    tissue="all"

    network.source="BIANA"

    scoring.options = list(netscore=T, repetitionSelector=3, iterationSelector=2) # NetScore

    scoring.options = list(netzcore=T, repetitionZelector=3) # NetZcore

    scoring.options = list(netshort=T) # NetShort

    scoring.options = list(netcombo=T) # NetCombo

    job.id = submit.job(result.table, species, tissue, network.source, scoring.options)

• retrieve.job
  • Description: Retrieve results using job id.
  • Usage:

    retrieve.job(job.id, n.top = NULL, fetch.files = F, output.dir = NULL)

  • Example:

    result = retrieve.job(job.id)

    getSlots(class(result))

    head(gScores(result)) # Scores

    head(gFunctions(result)) # Functions

    head(gDrugs(result)) # Drugs

• retrieve.overlap
  • Description: Retrieve overlap between two results using two job ids.
  • Usage:

    retrieve.overlap(job.id1, job.id2, top.validated = T, fetch.files = F, output.dir = NULL)

  • Example:

    result = retrieve.overlap(job.id1, job.id2)

    getSlots(class(result)) # Scores

    head(gFunctions(result)) # Functions

    head(gDrugs(result)) # Drugs

Current version of GUILDify (2.0) uses BIANA integrated database release from May 2018 (includes UniProt, GO, OMIM, DisGeNET, Drugbank, HPRD, IntAct, DIP, BioGrid and HIPPIE databases). Please contact us in case you need to access data from the previous release of BIANA (from March 2013 ). Click here if you want to access to the previous version of GUILDify.

• GUILDify v2.0: A tool to identify the molecular networks underlying human diseases, their comorbidities and their druggable targets. J Mol Biol. 2019 Jun 14;431(13):2477-2484. PMID: 30851278.

• GUILDify: a web server for phenotypic characterization of genes through biological data integration and network-based prioritization algorithms. Bioinformatics. 2014 Jun 15;30(12):1789-90
• Biana: a software framework for compiling biological interactions and analyzing networks. BMC Bioinformatics. 2010 Jan 27;11:56
• Exploiting protein-protein interaction networks for genome-wide disease-gene prioritization. PLoS One. 2012;7(9):e43557