README.md

tcmR

tcmR是一个用于中药网络药理学数据挖掘和分析的R包。 其功能包括:解析天然药有效活性成分、天然药化合物作用靶点以及常见疾病靶点、天然药与疾病的共作用靶点。

tcmR is an R package for TCM network pharmacology data mining and analyzing. Its functions include: analyzing the effective active ingredients of natural medicines, the targets of natural medicine compounds, common disease targets, and the co-action targets of natural medicines and diseases.

Authors

[周晓北] (Zhou Xiaobei)

[彭文杰] (Peng Wenjie)

Installation

for Linux,Mac or Win user:

install.packages("devtools")
devtools::install_github("pwj6/tcmR")

Relational graph of all functions and data

1627034863

Usage

library(tcmR)
h2m(x='huangqin',type='pinyin')

"x" is the name of traditional Chinese medicine, which can be the Chinese name(type='chinese') or Chinese Pinyin of traditional Chinese medicine(type='pinyin'), or the Latin name of traditional Chinese medicine(type='latin').

The function of hd2t is to query the corresponding targets of diseases and traditional Chinese medicine, the compounds included in traditional Chinese medicine and the common targets of diseases and traditional Chinese medicine,including molecule,molecule_id,cid.The results are as follows:

$huangqin
                                      molecule molecule_id       cid
  1:                                  Cosmetin   MOL000007   5280704
  2:                                  apigenin   MOL000008   5280443
  3:                          (+/-)-Isoborneol   MOL000018   6321405
  4:                            alpha-humulene   MOL000024   5281520
  5:                             beta-Selinene   MOL000035    442393
 ---                                                                
139: 2,6,2',4'-tetrahydroxy-6'-methoxychaleone   MOL002911        NA
140:                          darendoside B_qt   MOL002924        NA
141:                              epiberberine   MOL002897        NA
142:                        3,7-dimethylnonane   MOL012564 124556645
143:                             darendoside B   MOL002923        NA

m2t(x=c('445858','31423'),type='cid',tSource="tcmsp")

"x" is the name of the compound, which can be the id(type='molecule_id'), English name (type='molecule')or cid of the compound(type='cid').

"tSource" is the source of compound targets,including tcmsp and pubchem.

The function of m2t is to transform compounds into their corresponding targets and related information.The results are as follows:

 $`445858`
    molecule molecule_id    cid
 1:      FER   MOL000360 445858
 2:      FER   MOL000360 445858
 3:      FER   MOL000360 445858
 4:      FER   MOL000360 445858
 5:      FER   MOL000360 445858
 6:      FER   MOL000360 445858
 7:      FER   MOL000360 445858
 8:      FER   MOL000360 445858
 9:      FER   MOL000360 445858
10:      FER   MOL000360 445858
11:      FER   MOL000360 445858
12:      FER   MOL000360 445858
13:      FER   MOL000360 445858
14:      FER   MOL000360 445858
15:      FER   MOL000360 445858
16:      FER   MOL000360 445858
                                                 fullname   symbol
 1:                          Alpha-2A adrenergic receptor   ADRA2A
 2:                                    Chymotrypsinogen B    CTRB1
 3:            Sodium-dependent noradrenaline transporter   SLC6A2
 4:                          Alpha-1A adrenergic receptor   ADRA1A
 5:                          Alpha-2B adrenergic receptor   ADRA2B
 6:                 Sodium-dependent dopamine transporter   SLC6A3
 7:                            Beta-2 adrenergic receptor    ADRB2
 8:                  Urokinase-type plasminogen activator     PLAU
 9:                       Heat shock protein HSP 90-alpha HSP90AA1
10:                             Leukotriene A-4 hydrolase    LTA4H
11:                   Amine oxidase [flavin-containing] B     MAOB
12:                   Amine oxidase [flavin-containing] A     MAOA
13:                          Prostaglandin G/H synthase 1    PTGS1
14: cAMP-dependent protein kinase catalytic subunit alpha   PRKACA
15:                          Prostaglandin G/H synthase 2    PTGS2
16:                    Nitric-oxide synthase, endothelial     NOS3

$`31423`
   molecule molecule_id   cid                        fullname symbol
1:   pyrene   MOL005805 31423                   Interleukin-8   <NA>
2:   pyrene   MOL005805 31423 UDP-glucuronosyltransferase 1-1   <NA>
3:   pyrene   MOL005805 31423 UDP-glucuronosyltransferase 1-6   <NA>
h2t(x=c('Ziziphi Spinosae Semen','Abri Herba'),type='latin',tSource="tcmsp",output='both')

"x" is exactly the same as x in h2m.

"tSource" is the source of traditional Chinese medicine targets,including tcmsp and pubchem.

"output" is how much information is output.output='symbol' includes molecule,molecule_id,cid,fullname and symbol;

output='both' includes herb,molecule,molecule_id,cid,fullname,symbol,ob and dl.

The function of h2t is to transform traditional Chinese medicine into its corresponding targets and related information.The results are as follows:

$`Ziziphi Spinosae Semen`
                       herb        molecule molecule_id    cid                                    fullname symbol       ob       dl
  1: Ziziphi Spinosae Semen          Mairin   MOL000211  64971                       Progesterone receptor    PGR 55.37707 0.776100
  2: Ziziphi Spinosae Semen             FER   MOL000360 445858                Alpha-2A adrenergic receptor ADRA2A 39.55852 0.058069
  3: Ziziphi Spinosae Semen             FER   MOL000360 445858                          Chymotrypsinogen B  CTRB1 39.55852 0.058069
  4: Ziziphi Spinosae Semen             FER   MOL000360 445858  Sodium-dependent noradrenaline transporter SLC6A2 39.55852 0.058069
  5: Ziziphi Spinosae Semen             FER   MOL000360 445858                Alpha-1A adrenergic receptor ADRA1A 39.55852 0.058069
 ---                                                                                                                               
144: Ziziphi Spinosae Semen     zizyphusine   MOL001546     NA                           Androgen receptor     AR 41.52695 0.547170
145: Ziziphi Spinosae Semen     zizyphusine   MOL001546     NA                Prostaglandin G/H synthase 1  PTGS1 41.52695 0.547170
146: Ziziphi Spinosae Semen     zizyphusine   MOL001546     NA Sodium channel protein type 5 subunit alpha  SCN5A 41.52695 0.547170
147: Ziziphi Spinosae Semen     zizyphusine   MOL001546     NA                Prostaglandin G/H synthase 2  PTGS2 41.52695 0.547170
148: Ziziphi Spinosae Semen alphitolic acid   MOL001549     NA                                        <NA>   <NA> 23.38245 0.765810

$`Abri Herba`
           herb            molecule molecule_id cid                                                               fullname symbol        ob       dl
  1: Abri Herba protocatechuic acid   MOL000105  72                                                                   <NA>   <NA> 25.366468 0.035092
  2: Abri Herba protocatechuic acid   MOL000105  72                                                               Lysozyme      E 25.366468 0.035092
  3: Abri Herba protocatechuic acid   MOL000105  72 Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase   cobT 25.366468 0.035092
  4: Abri Herba protocatechuic acid   MOL000105  72                                       Maltase-glucoamylase, intestinal   MGAM 25.366468 0.035092
  5: Abri Herba protocatechuic acid   MOL000105  72                                                              Trypsin-3  PRSS3 25.366468 0.035092
 ---                                                                                                                                                
365: Abri Herba    kudzusapogenol A   MOL003655  NA                                                                   <NA>   <NA> 16.848452 0.711260
366: Abri Herba     Abrisapogenol F   MOL013317  NA                                                                   <NA>   <NA> 16.366658 0.758840
367: Abri Herba     Abrisapogenol B   MOL013316  NA                                                                   <NA>   <NA> 14.743140 0.735340
368: Abri Herba     Abrisapogenol E   MOL003668  NA                                                                   <NA>   <NA> 17.578022 0.735780
369: Abri Herba       Soyasaponin V   MOL013328  NA                                                                   <NA>   <NA>  2.210538 0.048624
m2h(x=c('thalifendine','rosthorin A'),type='molecule',OB='10',DL='0.01')

"OB" and "DL" are the oral bioavailability and drug-like properties of compounds, respectively.Their default values are OB='30' and DL='0.18' respectively. You can also set thresholds according to your own needs.

The function of m2h is to query how many Chinese medicines a compound is contained in and the Latin names of these Chinese medicines.The results are as follows:

$thalifendine
                            herb molecule_id     molecule cid       ob      dl
1: Phellodendri Amurensis Cortex   MOL006422 thalifendine  NA 44.41094 0.72588
2: Phellodendri Chinrnsis Cortex   MOL006422 thalifendine  NA 44.41094 0.72588
3:  Thalictri Glandulosissimi Et   MOL006422 thalifendine  NA 44.41094 0.72588
4:          Semiaquilegiae Radix   MOL006422 thalifendine  NA 44.41094 0.72588

$`rosthorin A`
           herb molecule_id    molecule cid       ob      dl
1: Ricini Semen   MOL008144 rosthorin A  NA 28.65893 0.56412

```r
d2t(x=c('C0009375','C0271979'),type='diseaseID',score=0.4)

"x" is the name of the disease, and can be the English name(type='disease') or id(type='diseaseID') of the disease.

"score" is the score of disease targets, which can be used to screen targets. The default value is 0.3, and you can also set thresholds according to your actual needs.

The function of d2t is to query the targets corresponding to the disease and relevant information.The results are as follows:

$C0009375
    symbol score
 1:    APC  0.60
 2:   BCL2  0.56
 3: CDKN1A  0.40
 4: CTNNB1  0.40
 5:  DNMT1  0.52
 6:   EGFR  0.40
 7:   KRAS  0.40
 8:   MLH1  0.40
 9:   MMP9  0.54
10:    MYC  0.53
11:  PPARG  0.40
12:  PTGS2  0.60
13:   TP53  0.50
14:  VEGFA  0.40

$C0271979
   symbol score
1:   HBA2   0.4
2:    HBB   0.4
hd2t(hb=c('mahuang','huangqi'),Disease='C0019209',htype='pinyin',dtype='diseaseID',tSource='tcmsp')

"hb" is exactly the same as x in h2m;"Disease" is exactly the same as x in d2t;"htype" is exactly the same as type in h2m;"dtype" is exactly the same as type in d2t;"tSource" is exactly the same as tSource in h2t.

The function of hd2t is to query the corresponding targets of diseases and traditional Chinese medicine, the compounds included in traditional Chinese medicine and the common targets of diseases and traditional Chinese medicine.The results are as follows:

$mahuang
$mahuang$drug_target
               herb                                molecule molecule_id       cid                           fullname symbol       ob       dl
   1: Ephedra Herba                                luteolin   MOL000006   5280445                               <NA>   <NA> 36.16263 0.245520
   2: Ephedra Herba                                luteolin   MOL000006   5280445                   Insulin receptor   INSR 36.16263 0.245520
   3: Ephedra Herba                                luteolin   MOL000006   5280445                DNA topoisomerase 1   topA 36.16263 0.245520
   4: Ephedra Herba                                luteolin   MOL000006   5280445                   Heme oxygenase 1  pbsA1 36.16263 0.245520
   5: Ephedra Herba                                luteolin   MOL000006   5280445         72 kDa type IV collagenase   MMP2 36.16263 0.245520
  ---                                                                                                                                        
3816: Ephedra Herba 1,5,8-trimethyl-1,2-dihydro-naphthalene   MOL010789 137331948       Prostaglandin G/H synthase 1  PTGS1 53.22308 0.059796
3817: Ephedra Herba 1,5,8-trimethyl-1,2-dihydro-naphthalene   MOL010789 137331948            D(1A) dopamine receptor   DRD1 53.22308 0.059796
3818: Ephedra Herba 1,5,8-trimethyl-1,2-dihydro-naphthalene   MOL010789 137331948       Prostaglandin G/H synthase 2  PTGS2 53.22308 0.059796
3819: Ephedra Herba 1,5,8-trimethyl-1,2-dihydro-naphthalene   MOL010789 137331948 Nitric-oxide synthase, endothelial   NOS3 53.22308 0.059796
3820: Ephedra Herba                               cinerolon   MOL011873  92966642                               <NA>   <NA> 75.62580 0.036324

$mahuang$disease_target
      symbol diseaseID      disease score
 1:     A1BG  C0019209 Hepatomegaly   0.3
 2:      AHR  C0019209 Hepatomegaly   0.3
 3:      ALB  C0019209 Hepatomegaly   0.3
 4:  ALDH1B1  C0019209 Hepatomegaly   0.3
 5:   CAMK2A  C0019209 Hepatomegaly   0.3
 6:    CRYGD  C0019209 Hepatomegaly   0.3
 7:   MAPK14  C0019209 Hepatomegaly   0.3
 8:     CYBA  C0019209 Hepatomegaly   0.4
 9:   CYP1A1  C0019209 Hepatomegaly   0.3
10:   CYP1A2  C0019209 Hepatomegaly   0.3
11:   CYP1B1  C0019209 Hepatomegaly   0.3
12:   ADAM3A  C0019209 Hepatomegaly   0.3
13:    DSCAM  C0019209 Hepatomegaly   0.3
14:    FGF12  C0019209 Hepatomegaly   0.3
15:    NR5A2  C0019209 Hepatomegaly   0.3
16:      HDC  C0019209 Hepatomegaly   0.3
17:     IGKC  C0019209 Hepatomegaly   0.3
18:      LEP  C0019209 Hepatomegaly   0.3
19:     LEPR  C0019209 Hepatomegaly   0.3
20:    MYO1B  C0019209 Hepatomegaly   0.3
21:   TRIM37  C0019209 Hepatomegaly   0.4


pwj6/tcmR documentation built on Dec. 22, 2021, 10:53 a.m.