vignettes/longevityDrugs.knit.md
In tgirke/longevityDrugs: Drug Candidates Relevant for Longevity Genomics Project
title: "longevityDrugs: Database of Longevity-Associated Drugs (LAD)"
author: "Authors: Thomas Girke, Tyler Backman, Dan Evans"
date: "Last update: 25 May, 2016"
package: "longevityDrugs 1.0.0"
output:
BiocStyle::html_document:
toc: true
toc_depth: 3
fig_caption: yes
fontsize: 14pt
bibliography: bibtex.bib
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Introduction
This vignette is part of the NIA funded Longevity Genomics project. For more information on this project please visit its
website here. The GitHub repository of the corresponding R package
is available here and the most recent version of this
vignette can be found here.
The data package longevityDrugs contains molecular structures and annotation information
of longevity-associated drugs (LADs). An iterative process will be used to assemble, update and
curate this data set long-term [@Backman2011-uw; @Cao2008-zo]. Most small molecules will be identified by integrating several
large-scale community data sources such as data from drug databases (e.g.
Drugbank), bioassay databases (e.g. PubChem Bioassay, ChEMBL), literature,
drug-related gene expression fingerprints (e.g. LINCS), genetic (e.g. GWAS) and
phenotype resources. This will also include nearest neighbors of LADs sharing
with them structural, physicochemical or biological properties.
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Getting Started
Installation
The R software for running longevityDrugs and longevityTools can be downloaded from CRAN. The longevityTools package can be installed from the R console using the following biocLite install command.
source("http://bioconductor.org/biocLite.R") # Sources the biocLite.R installation script
biocLite("tgirke/longevityTools", build_vignettes=FALSE, dependencies=FALSE) # Installs package from GitHub
biocLite("tgirke/longevityDrugs", build_vignettes=FALSE, dependencies=FALSE)
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Loading of required packages
library(RSQLite); library(ChemmineR); library(longevityDrugs)
## Loading required package: DBI
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Load database
mypath <- system.file("extdata", "cmap.db", package="longevityDrugs")
conn <- initDb(mypath)
Query database
Retrieve compound structures
results <- getAllCompoundIds(conn)
sdfset <- getCompounds(conn, results, keepOrder=TRUE)
sdfset
## An instance of "SDFset" with 1309 molecules
plot(sdfset[1:4], print=FALSE)
as.data.frame(datablock2ma(datablock(sdfset)))[1:4,]
## instance_id batch_id cmap_name INN1 concentration..M. duration..h. cell2 array3
## 201 1 1 metformin INN 1.00e-05 6 MCF7 HG-U133A
## 202 21 2 phenformin INN 1.00e-05 6 MCF7 HG-U133A
## 203 22 2 phenyl biguanide 1.00e-05 6 MCF7 HG-U133A
## 204 23 2 valproic acid INN 1.00e-03 6 MCF7 HG-U133A
## perturbation_scan_id vehicle_scan_id4 scanner vehicle vendor catalog_number
## 201 EC2003090503AA EC2003090502AA HP GeneArray Scanner medium Sigma-Aldrich D5035
## 202 EC2003091104AA EC2003091102AA HP GeneArray Scanner medium Sigma-Aldrich P7045
## 203 EC2003091105AA EC2003091102AA HP GeneArray Scanner medium Sigma-Aldrich P19906
## 204 EC2003091106AA EC2003091102AA HP GeneArray Scanner medium Sigma-Aldrich P4543
## catalog_name SOURCE_DRUG UNIPROT P_SCORE DIRECTIONALITY
## 201 1,1-dimethylbiguanide hydrochloride Metformin ZN396_HUMAN 1.53601286 Stimulatory
## 202 phenformin hydrochloride Phenformin KI2L3_HUMAN -6.33081681 Inhibitory
## 203 1-phenylbiguanide hydrochloride PHENYL BIGUANIDE RHOC_HUMAN -4.21084571 Inhibitory
## 204 2-propylpentanoic acid Valproic Acid GSK3B_HUMAN -58.47057966 Inhibitory
## PUBCHEM_ID DRUGBANK_ID DRUGBANK_GROUP ATCCODES chembank_id chembank_name
## 201 CID4091 DB00331 approved A10BD11|A10BA02 1714 metformin
## 202 CID8249 DB00914 approved|withdrawn A10BA01 1018627 phenformin
## 203 CID4780 32656 phenylbiguanide
## 204 CID3121 DB00313 approved|investigational N03AG01 471 valproic acid
## match_distance smiles
## 201 0 CN(C)C(=N)NC(=N)N
## 202 0 NC(=N)NC(=N)NCCc1ccccc1
## 203 0 NC(=N)NC(=N)Nc1ccccc1
## 204 0 CCCC(CCC)C(=O)O
Retrieve compound properties
myfeat <- listFeatures(conn)
feat <- getCompoundFeatures(conn, results, myfeat)
feat[1:4,]
## compound_id aromatic cansmi cansmins formula hba1 hba2 hbd
## 1 201 0 CN(C(=N)NC(=N)N)C CN(C(=N)NC(=N)N)C C4H11N5 5 5 4
## 2 202 1 N=C(NC(=N)N)NCCc1ccccc1 N=C(NC(=N)N)NCCc1ccccc1 C10H15N5 5 5 5
## 3 203 1 N=C(Nc1ccccc1)NC(=N)N N=C(Nc1ccccc1)NC(=N)N C8H11N5 5 5 5
## 4 204 0 CCCC(C(=O)O)CCC CCCC(C(=O)O)CCC C8H16O2 2 2 1
## inchi logp
## 1 InChI=1S/C4H11N5/c1-9(2)4(7)8-3(5)6/h1-2H3,(H5,5,6,7,8) 0.2565
## 2 InChI=1S/C10H15N5/c11-9(12)15-10(13)14-7-6-8-4-2-1-3-5-8/h1-5H,6-7H2,(H6,11,12,13,14,15) 1.9181
## 3 InChI=1S/C8H11N5/c9-7(10)13-8(11)12-6-4-2-1-3-5-6/h1-5H,(H6,9,10,11,12,13) 1.8800
## 4 InChI=1S/C8H16O2/c1-3-5-7(6-4-2)8(9)10/h7H,3-6H2,1-2H3,(H,9,10) 2.2874
## mr mw ncharges nf r2nh r3n rcch rcho rcn rcooh rcoor rcor rings rnh2 roh ropo3 ror
## 1 36.9285 129.1636 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0
## 2 61.3212 205.2596 0 0 2 0 0 0 0 0 0 0 1 0 0 0 0
## 3 53.2452 177.2064 0 0 2 0 0 0 0 0 0 0 1 0 0 0 0
## 4 42.3418 144.2114 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
## title tpsa
## 1 metformin 88.99
## 2 phenformin 97.78
## 3 phenyl biguanide 97.78
## 4 valproic acid 37.30
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Funding
This project is funded by NIH grant U24AG051129 awarded by the National Intitute on Aging (NIA).
[Back to Table of Contents]()
Version information
sessionInfo()
## R version 3.2.2 (2015-08-14)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: CentOS Linux 7 (Core)
##
## locale:
## [1] C
##
## attached base packages:
## [1] stats graphics utils datasets grDevices methods base
##
## other attached packages:
## [1] longevityDrugs_1.0.0 ChemmineR_2.22.3 RSQLite_1.0.0 DBI_0.3.1
## [5] ggplot2_2.0.0 longevityTools_1.0.6 BiocStyle_1.8.0
##
## loaded via a namespace (and not attached):
## [1] Rcpp_0.12.3 knitr_1.12.3 magrittr_1.5 munsell_0.4.3 colorspace_1.2-6
## [6] rjson_0.2.15 stringr_1.0.0 plyr_1.8.3 tools_3.2.2 grid_3.2.2
## [11] gtable_0.1.2 htmltools_0.3 yaml_2.1.13 digest_0.6.9 formatR_1.2.1
## [16] bitops_1.0-6 codetools_0.2-14 RCurl_1.95-4.7 evaluate_0.8 rmarkdown_0.9.2
## [21] stringi_1.0-1 scales_0.3.0
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References
tgirke/longevityDrugs documentation built on May 31, 2019, 9:07 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
title: "longevityDrugs: Database of Longevity-Associated Drugs (LAD)" author: "Authors: Thomas Girke, Tyler Backman, Dan Evans" date: "Last update: 25 May, 2016" package: "longevityDrugs 1.0.0" output: BiocStyle::html_document: toc: true toc_depth: 3 fig_caption: yes
fontsize: 14pt bibliography: bibtex.bib
document.addEventListener("DOMContentLoaded", function() { document.querySelector("h1").className = "title"; }); document.addEventListener("DOMContentLoaded", function() { var links = document.links; for (var i = 0, linksLength = links.length; i < linksLength; i++) if (links[i].hostname != window.location.hostname) links[i].target = '_blank'; });Introduction
This vignette is part of the NIA funded Longevity Genomics project. For more information on this project please visit its website here. The GitHub repository of the corresponding R package is available here and the most recent version of this vignette can be found here.
The data package longevityDrugs contains molecular structures and annotation information
of longevity-associated drugs (LADs). An iterative process will be used to assemble, update and
curate this data set long-term [@Backman2011-uw; @Cao2008-zo]. Most small molecules will be identified by integrating several
large-scale community data sources such as data from drug databases (e.g.
Drugbank), bioassay databases (e.g. PubChem Bioassay, ChEMBL), literature,
drug-related gene expression fingerprints (e.g. LINCS), genetic (e.g. GWAS) and
phenotype resources. This will also include nearest neighbors of LADs sharing
with them structural, physicochemical or biological properties.
[Back to Table of Contents]()
Getting Started
Installation
The R software for running longevityDrugs and longevityTools can be downloaded from CRAN. The longevityTools package can be installed from the R console using the following biocLite install command.
source("http://bioconductor.org/biocLite.R") # Sources the biocLite.R installation script
biocLite("tgirke/longevityTools", build_vignettes=FALSE, dependencies=FALSE) # Installs package from GitHub
biocLite("tgirke/longevityDrugs", build_vignettes=FALSE, dependencies=FALSE)
[Back to Table of Contents]()
Loading of required packages
library(RSQLite); library(ChemmineR); library(longevityDrugs)
## Loading required package: DBI
[Back to Table of Contents]()
Load database
mypath <- system.file("extdata", "cmap.db", package="longevityDrugs")
conn <- initDb(mypath)
Query database
Retrieve compound structures
results <- getAllCompoundIds(conn)
sdfset <- getCompounds(conn, results, keepOrder=TRUE)
sdfset
## An instance of "SDFset" with 1309 molecules
plot(sdfset[1:4], print=FALSE)
as.data.frame(datablock2ma(datablock(sdfset)))[1:4,]
## instance_id batch_id cmap_name INN1 concentration..M. duration..h. cell2 array3
## 201 1 1 metformin INN 1.00e-05 6 MCF7 HG-U133A
## 202 21 2 phenformin INN 1.00e-05 6 MCF7 HG-U133A
## 203 22 2 phenyl biguanide 1.00e-05 6 MCF7 HG-U133A
## 204 23 2 valproic acid INN 1.00e-03 6 MCF7 HG-U133A
## perturbation_scan_id vehicle_scan_id4 scanner vehicle vendor catalog_number
## 201 EC2003090503AA EC2003090502AA HP GeneArray Scanner medium Sigma-Aldrich D5035
## 202 EC2003091104AA EC2003091102AA HP GeneArray Scanner medium Sigma-Aldrich P7045
## 203 EC2003091105AA EC2003091102AA HP GeneArray Scanner medium Sigma-Aldrich P19906
## 204 EC2003091106AA EC2003091102AA HP GeneArray Scanner medium Sigma-Aldrich P4543
## catalog_name SOURCE_DRUG UNIPROT P_SCORE DIRECTIONALITY
## 201 1,1-dimethylbiguanide hydrochloride Metformin ZN396_HUMAN 1.53601286 Stimulatory
## 202 phenformin hydrochloride Phenformin KI2L3_HUMAN -6.33081681 Inhibitory
## 203 1-phenylbiguanide hydrochloride PHENYL BIGUANIDE RHOC_HUMAN -4.21084571 Inhibitory
## 204 2-propylpentanoic acid Valproic Acid GSK3B_HUMAN -58.47057966 Inhibitory
## PUBCHEM_ID DRUGBANK_ID DRUGBANK_GROUP ATCCODES chembank_id chembank_name
## 201 CID4091 DB00331 approved A10BD11|A10BA02 1714 metformin
## 202 CID8249 DB00914 approved|withdrawn A10BA01 1018627 phenformin
## 203 CID4780 32656 phenylbiguanide
## 204 CID3121 DB00313 approved|investigational N03AG01 471 valproic acid
## match_distance smiles
## 201 0 CN(C)C(=N)NC(=N)N
## 202 0 NC(=N)NC(=N)NCCc1ccccc1
## 203 0 NC(=N)NC(=N)Nc1ccccc1
## 204 0 CCCC(CCC)C(=O)O
Retrieve compound properties
myfeat <- listFeatures(conn)
feat <- getCompoundFeatures(conn, results, myfeat)
feat[1:4,]
## compound_id aromatic cansmi cansmins formula hba1 hba2 hbd
## 1 201 0 CN(C(=N)NC(=N)N)C CN(C(=N)NC(=N)N)C C4H11N5 5 5 4
## 2 202 1 N=C(NC(=N)N)NCCc1ccccc1 N=C(NC(=N)N)NCCc1ccccc1 C10H15N5 5 5 5
## 3 203 1 N=C(Nc1ccccc1)NC(=N)N N=C(Nc1ccccc1)NC(=N)N C8H11N5 5 5 5
## 4 204 0 CCCC(C(=O)O)CCC CCCC(C(=O)O)CCC C8H16O2 2 2 1
## inchi logp
## 1 InChI=1S/C4H11N5/c1-9(2)4(7)8-3(5)6/h1-2H3,(H5,5,6,7,8) 0.2565
## 2 InChI=1S/C10H15N5/c11-9(12)15-10(13)14-7-6-8-4-2-1-3-5-8/h1-5H,6-7H2,(H6,11,12,13,14,15) 1.9181
## 3 InChI=1S/C8H11N5/c9-7(10)13-8(11)12-6-4-2-1-3-5-6/h1-5H,(H6,9,10,11,12,13) 1.8800
## 4 InChI=1S/C8H16O2/c1-3-5-7(6-4-2)8(9)10/h7H,3-6H2,1-2H3,(H,9,10) 2.2874
## mr mw ncharges nf r2nh r3n rcch rcho rcn rcooh rcoor rcor rings rnh2 roh ropo3 ror
## 1 36.9285 129.1636 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0
## 2 61.3212 205.2596 0 0 2 0 0 0 0 0 0 0 1 0 0 0 0
## 3 53.2452 177.2064 0 0 2 0 0 0 0 0 0 0 1 0 0 0 0
## 4 42.3418 144.2114 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
## title tpsa
## 1 metformin 88.99
## 2 phenformin 97.78
## 3 phenyl biguanide 97.78
## 4 valproic acid 37.30
[Back to Table of Contents]()
Funding
This project is funded by NIH grant U24AG051129 awarded by the National Intitute on Aging (NIA).
[Back to Table of Contents]()
Version information
sessionInfo()
## R version 3.2.2 (2015-08-14)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: CentOS Linux 7 (Core)
##
## locale:
## [1] C
##
## attached base packages:
## [1] stats graphics utils datasets grDevices methods base
##
## other attached packages:
## [1] longevityDrugs_1.0.0 ChemmineR_2.22.3 RSQLite_1.0.0 DBI_0.3.1
## [5] ggplot2_2.0.0 longevityTools_1.0.6 BiocStyle_1.8.0
##
## loaded via a namespace (and not attached):
## [1] Rcpp_0.12.3 knitr_1.12.3 magrittr_1.5 munsell_0.4.3 colorspace_1.2-6
## [6] rjson_0.2.15 stringr_1.0.0 plyr_1.8.3 tools_3.2.2 grid_3.2.2
## [11] gtable_0.1.2 htmltools_0.3 yaml_2.1.13 digest_0.6.9 formatR_1.2.1
## [16] bitops_1.0-6 codetools_0.2-14 RCurl_1.95-4.7 evaluate_0.8 rmarkdown_0.9.2
## [21] stringi_1.0-1 scales_0.3.0
[Back to Table of Contents]()
References
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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