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Table 2 Significant associations of gene expression and logGI50 of Indian Natural Products in the NCI-60 cell line panel

From: Pharmacogenomics of in vitro response of the NCI-60 cancer cell line panel to Indian natural products

NSC

Gene

Spearman ρ

Original p value

FDR adjusted p value

Dendrogram subtree

Active molecule

328426

MYB

-0.66

1.7e-08

0.004

Subtree 1

Phyllanthoside

328426

BEND7

0.65

2.8e-08

0.005

Subtree 1

Phyllanthoside

308606

ZBTB33

-0.67

1.0e-07

0.012

Subtree 1

Cucurbitacin D

328426

NHS

0.62

2.0e-07

0.014

Subtree 1

Phyllanthoside

328426

WWC1

0.61

3.0e-07

0.019

Subtree 1

Phyllanthoside

94743

TRMT112

0.65

4.0e-07

0.022

Subtree 1

Cucurbitacin A

328426

RBMS2

0.60

5.0e-07

0.022

Subtree 1

Phyllanthoside

342443

EHD2

0.66

6.0e-07

0.025

Subtree 1

S3’-desacetyl-phyllanthoside

328426

PROSER2

0.60

8.0e-07

0.027

Subtree 1

Phyllanthoside

328426

SMAP2

-0.60

8.0e-07

0.027

Subtree 1

Phyllanthoside

328426

BAGE

-0.59

8.0e-07

0.027

Subtree 1

Phyllanthoside

328426

C6orf89

-0.59

9.0e-07

0.027

Subtree 1

Phyllanthoside

328426

EGFR

0.59

1.0e-06

0.027

Subtree 1

Phyllanthoside

328426

PDLIM1

0.59

1.0e-06

0.027

Subtree 1

Phyllanthoside

94743

ZNF48

0.63

1.0e-06

0.027

Subtree 1

Cucurbitacin A

328426

CNPPD1

-0.59

1.1e-06

0.029

Subtree 1

Phyllanthoside

342443

CLMP

0.65

1.1e-06

0.029

Subtree 1

S3’-desacetyl-phyllanthoside

143925

ATP1A1

0.59

1.2e-06

0.030

Subtree 1

Pekilocerin A

342443

ADAM9

0.64

1.4e-06

0.031

Subtree 1

S3’-desacetyl-phyllanthoside

328426

MON1A

-0.58

1.4e-06

0.031

Subtree 1

Phyllanthoside

328426

ZNF319

0.58

1.6e-06

0.033

Subtree 1

Phyllanthoside

328426

HKDC1

0.58

1.8e-06

0.036

Subtree 1

Phyllanthoside

342443

CD151

0.64

2.0e-06

0.037

Subtree 1

S3’-desacetyl-phyllanthoside

328426

AJUBA

0.58

2.1e-06

0.038

Subtree 1

Phyllanthoside

112167

TLN1

-0.62

2.3e-06

0.040

Subtree 1

Elatericin B

328426

HESX1

-0.57

2.4e-06

0.040

Subtree 1

Phyllanthoside

328426

MMP24

0.57

2.5e-06

0.042

Subtree 1

Phyllanthoside

328426

TJP1

0.57

2.7e-06

0.043

Subtree 1

Phyllanthoside

328426

TNFRSF12A

0.57

2.7e-06

0.043

Subtree 1

Phyllanthoside

342443

ZFP36L1

0.63

2.9e-06

0.043

Subtree 1

S3’-desacetyl-phyllanthoside

342443

NNMT

0.63

3.0e-06

0.043

Subtree 1

S3’-desacetyl-phyllanthoside

328426

BIN1

0.57

3.0e-06

0.043

Subtree 1

Phyllanthoside

342443

MTCL1

0.63

3.1e-06

0.043

Subtree 1

S3’-desacetyl-phyllanthoside

342443

TNFRSF1A

0.62

3.8e-06

0.046

Subtree 1

S3’-desacetyl-phyllanthoside

342443

LOC101241902

0.62

3.8e-06

0.046

Subtree 1

S3’-desacetyl-phyllanthoside

328426

GOLGA6L5P

0.56

3.9e-06

0.046

Subtree 1

Phyllanthoside

521777

SLAMF6

0.56

3.9e-06

0.046

Subtree 1

Elatericin B

342443

UCKL1

-0.62

3.9e-06

0.046

Subtree 1

S3’-desacetyl-phyllanthoside

143925

ILF2P1

-0.56

4.0e-06

0.046

Subtree 1

Pekilocerin A

328426

NUAK2

0.56

4.0e-06

0.046

Subtree 1

Phyllanthoside

328426

PUS3

-0.56

4.1e-06

0.046

Subtree 1

Phyllanthoside

328426

C2CD2L

-0.56

4.3e-06

0.046

Subtree 1

Phyllanthoside

342443

NRP1

0.62

4.3e-06

0.046

Subtree 1

S3’-desacetyl-phyllanthoside

328426

LRRN4

0.56

4.3e-06

0.046

Subtree 1

Phyllanthoside

328426

SLC35F3

0.56

4.4e-06

0.046

Subtree 1

Phyllanthoside

328426

ZNF639

-0.56

4.6e-06

0.046

Subtree 1

Phyllanthoside

143925

FNIP1

0.56

4.7e-06

0.046

Subtree 1

Pekilocerin A

94743

ZNF629

0.60

4.8e-06

0.046

Subtree 1

Cucurbitacin A

328426

FRAT2

-0.56

5.6e-06

0.048

Subtree 1

Phyllanthoside

342443

NR2F2

0.61

5.8e-06

0.049

Subtree 1

S3’-desacetyl-phyllanthoside

342443

ITGB1

0.61

5.9e-06

0.049

Subtree 1

S3’-desacetyl-phyllanthoside

328426

CLDN1

0.56

5.9e-06

0.049

Subtree 1

Phyllanthoside

844

ZNF823

0.65

5.0e-07

0.022

Subtree 2

Nesol

62794

FOXN4

-0.62

1.2e-06

0.030

Subtree 2

Beta carotene

327430

OGFOD2

-0.64

1.7e-06

0.035

Subtree 2

Resveratrol

90487

SDHC

0.57

3.6e-06

0.046

Subtree 2

Lupeol

643160

LCP1

-0.62

4.0e-06

0.046

Subtree 2

3-Bromo-4-dimethylamino-alpha-benzoyl cinnamonitrite

844

PBX4

0.60

4.2e-06

0.046

Subtree 2

Nesol

90487

PFKFB2

0.56

5.3e-06

0.048

Subtree 2

Lupeol

619043

KIR2DL2

-0.63

5.6e-06

0.049

Subtree 2

Phyllanthin

236613

SLC7A11

0.79

1.0e-13

0.000

Subtree 3

Plumbagin

32982

ATAD3B

-0.67

1.3e-08

0.003

Subtree 3

Curcumin

309909

PDCD11

-0.66

2.3e-08

0.005

Subtree 3

Nimbolide

32982

HNRNPR

-0.66

3.0e-08

0.005

Subtree 3

Curcumin

309909

RPL34P6

-0.64

1.0e-07

0.009

Subtree 3

Nimbolide

32982

RPL11

-0.64

1.0e-07

0.012

Subtree 3

Curcumin

32982

PNRC2

-0.64

1.0e-07

0.012

Subtree 3

Curcumin

236613

HDHD2

-0.63

1.0e-07

0.013

Subtree 3

Plumbagin

309909

RPL34

-0.63

1.0e-07

0.013

Subtree 3

Nimbolide

309909

HNRNPA1P55

-0.63

2.0e-07

0.014

Subtree 3

Nimbolide

87868

NOLC1

-0.68

2.0e-07

0.014

Subtree 3

Phenethyl mustard oil

87868

NPM3

-0.68

2.0e-07

0.014

Subtree 3

Phenethyl mustard oil

236613

NR2F1

0.62

2.0e-07

0.014

Subtree 3

Plumbagin

742021

ERICH1

-0.62

2.0e-07

0.017

Subtree 3

Curcumin tri adamantylaminoethylcarbonate

87868

SRPK1

-0.67

3.0e-07

0.018

Subtree 3

Phenethyl mustard oil

309909

RPS10P2

-0.62

3.0e-07

0.018

Subtree 3

Nimbolide

87868

RBMXP1

-0.67

3.0e-07

0.018

Subtree 3

Phenethyl mustard oil

742020

RPL21P134

-0.61

3.0e-07

0.018

Subtree 3

Ethoxycurcumin trithiadiazolaminomethylcarbonte

705537

C5orf15

-0.63

4.0e-07

0.022

Subtree 3

Daturaolone

742022

CCDC149

0.61

4.0e-07

0.022

Subtree 3

Curcumin tri trithiadiazolaminoethylcarbonate

742020

RPL13AP3

-0.61

5.0e-07

0.022

Subtree 3

Ethoxycurcumin trithiadiazolaminomethylcarbonte

87868

ADAT2

-0.66

5.0e-07

0.022

Subtree 3

Phenethyl mustard oil

87868

HIF1A

0.66

5.0e-07

0.022

Subtree 3

Phenethyl mustard oil

236613

SLC7A11-AS1

0.60

5.0e-07

0.022

Subtree 3

Plumbagin

32982

SPEN

-0.60

7.0e-07

0.027

Subtree 3

Curcumin

236613

ACTN4P1

0.60

7.0e-07

0.027

Subtree 3

Plumbagin

643769

SMARCC1

-0.65

7.0e-07

0.027

Subtree 3

O-Bromo-alpha-benzoyl cinnamonitrile

643769

RPSAP56

-0.65

7.0e-07

0.027

Subtree 3

O-Bromo-alpha-benzoyl cinnamonitrile

87868

RPL10AP2

-0.65

8.0e-07

0.027

Subtree 3

Phenethyl mustard oil

87868

HNRNPA1P64

-0.65

8.0e-07

0.027

Subtree 3

Phenethyl mustard oil

87868

RPL34P18

-0.65

8.0e-07

0.027

Subtree 3

Phenethyl mustard oil

32982

SRRM1

-0.60

8.0e-07

0.027

Subtree 3

Curcumin

643023

FBXL2

0.66

8.0e-07

0.027

Subtree 3

Alpha-Phenyl-2,5-dimethoxy-alpha-cinnamonitrile

742020

RSL24D1

-0.59

9.0e-07

0.027

Subtree 3

Ethoxycurcumin trithiadiazolaminomethylcarbonte

236613

G6PD

0.59

9.0e-07

0.027

Subtree 3

Plumbagin

87868

HNRNPA1P55

-0.65

1.0e-06

0.027

Subtree 3

Phenethyl mustard oil

309909

NPM3

-0.60

1.0e-06

0.027

Subtree 3

Nimbolide

742022

PFN4

0.59

1.0e-06

0.027

Subtree 3

Curcumin tri trithiadiazolaminoethylcarbonate

87868

RPS4XP8

-0.64

1.0e-06

0.027

Subtree 3

Phenethyl mustard oil

87868

RPS4XP1

-0.64

1.2e-06

0.030

Subtree 3

Phenethyl mustard oil

309909

RPS10P5

-0.59

1.2e-06

0.030

Subtree 3

Nimbolide

643023

ETNK2

0.65

1.4e-06

0.031

Subtree 3

Alpha-Phenyl-2,5-dimethoxy-alpha-cinnamonitrile

742020

HNRNPA1P4

-0.59

1.4e-06

0.031

Subtree 3

Ethoxycurcumin trithiadiazolaminomethylcarbonte

309909

HNRNPA1L2

-0.59

1.4e-06

0.031

Subtree 3

Nimbolide

742019

ITGAV

0.59

1.4e-06

0.031

Subtree 3

Ethoxycurcumin tribenzimidazolmethylcarbonte

742020

RPL27AP

-0.58

1.4e-06

0.031

Subtree 3

Ethoxycurcumin trithiadiazolaminomethylcarbonte

643769

RPSA

-0.64

1.5e-06

0.032

Subtree 3

O-Bromo-alpha-benzoyl cinnamonitrile

742019

RPL21P44

-0.58

1.5e-06

0.032

Subtree 3

Ethoxycurcumin tribenzimidazolmethylcarbonte

236613

SRXN1

0.58

1.7e-06

0.034

Subtree 3

Plumbagin

365798

TSKU

0.64

1.8e-06

0.036

Subtree 3

Piceatannol

705537

SGF29

0.60

1.8e-06

0.036

Subtree 3

Daturaolone

742022

PDCD11

-0.58

1.9e-06

0.036

Subtree 3

Curcumin tri trithiadiazolaminoethylcarbonate

87868

RPS4XP2

-0.63

1.9e-06

0.036

Subtree 3

Phenethyl mustard oil

32982

HDAC10

-0.58

1.9e-06

0.036

Subtree 3

Curcumin

742020

EEF1B2P1

-0.58

2.0e-06

0.037

Subtree 3

Ethoxycurcumin trithiadiazolaminomethylcarbonte

742019

LINC00472

0.58

2.0e-06

0.037

Subtree 3

Ethoxycurcumin tribenzimidazolmethylcarbonte

742021

HMBOX1

-0.58

2.2e-06

0.039

Subtree 3

Curcumin tri adamantylaminoethylcarbonate

309909

NOLC1

-0.58

2.2e-06

0.039

Subtree 3

Nimbolide

643023

REEP3

0.64

2.3e-06

0.040

Subtree 3

Alpha.-Phenyl-2,5-dimethoxy-alpha-cinnamonitrile

87868

RPS4XP19

-0.63

2.4e-06

0.040

Subtree 3

Phenethyl mustard oil

32982

NOC2L

-0.58

2.4e-06

0.041

Subtree 3

Curcumin

309909

RPL34P18

-0.58

2.4e-06

0.041

Subtree 3

Nimbolide

87868

MYC

-0.63

2.6e-06

0.043

Subtree 3

Phenethyl mustard oil

236613

ALDH3A2

0.57

2.7e-06

0.043

Subtree 3

Plumbagin

32982

RCC2P4

-0.58

2.7e-06

0.043

Subtree 3

Curcumin

32982

KHDRBS1

-0.58

2.8e-06

0.043

Subtree 3

Curcumin

32982

DFFB

-0.58

2.8e-06

0.043

Subtree 3

Curcumin

87868

HNRNPA1P35

-0.62

3.0e-06

0.043

Subtree 3

Phenethyl mustard oil

643023

CAPN2

0.63

3.0e-06

0.043

Subtree 3

Alpha.-Phenyl-2,5-dimethoxy-alpha-cinnamonitrile

309909

ANLN

0.57

3.0e-06

0.043

Subtree 3

Nimbolide

32982

AHNAK2

0.57

3.1e-06

0.043

Subtree 3

Curcumin

236613

LOC344887

0.57

3.1e-06

0.043

Subtree 3

Plumbagin

309909

HNRNPA1P64

-0.57

3.2e-06

0.043

Subtree 3

Nimbolide

309909

EIF4BP9

-0.57

3.2e-06

0.043

Subtree 3

Nimbolide

309909

RPL29P7

-0.57

3.2e-06

0.043

Subtree 3

Nimbolide

742022

LOC100128816

-0.57

3.2e-06

0.043

Subtree 3

Curcumin tri trithiadiazolaminoethylcarbonate

742022

CUEDC1

0.57

3.3e-06

0.044

Subtree 3

Curcumin tri trithiadiazolaminoethylcarbonate

32982

CLIP4

0.57

3.3e-06

0.045

Subtree 3

Curcumin

112166

CRKL

0.61

3.4e-06

0.045

Subtree 3

Cucurbitacin K

236613

PGRMC1

0.57

3.4e-06

0.045

Subtree 3

Plumbagin

742019

RPL21P12

-0.57

3.5e-06

0.046

Subtree 3

Ethoxycurcumin tribenzimidazolmethylcarbonte

32982

ATAD3A

-0.57

3.7e-06

0.046

Subtree 3

Curcumin

236613

LRRC8A

0.57

3.7e-06

0.046

Subtree 3

Plumbagin

236613

AFAP1

0.57

3.8e-06

0.046

Subtree 3

Plumbagin

742022

CAMSAP2

0.56

3.9e-06

0.046

Subtree 3

Curcumin tri trithiadiazolaminoethylcarbonate

236613

NEU3

-0.56

3.9e-06

0.046

Subtree 3

Plumbagin

742019

RPS11P1

-0.56

3.9e-06

0.046

Subtree 3

Ethoxycurcumin tribenzimidazolmethylcarbonte

643023

MT2P1

0.63

4.1e-06

0.046

Subtree 3

Alpha-Phenyl-2,5-dimethoxy-alpha-cinnamonitrile

309909

ACTN4P1

0.57

4.1e-06

0.046

Subtree 3

Nimbolide

309909

IKZF5

-0.57

4.2e-06

0.046

Subtree 3

Nimbolide

87868

RPL34P31

-0.61

4.2e-06

0.046

Subtree 3

Phenethyl mustard oil

742019

FIGN

0.56

4.3e-06

0.046

Subtree 3

Ethoxycurcumin tribenzimidazolmethylcarbonte

236613

ELP2

-0.56

4.4e-06

0.046

Subtree 3

Plumbagin

309909

HNRNPCP3

-0.57

4.4e-06

0.046

Subtree 3

Nimbolide

643769

RPSAP47

-0.61

4.4e-06

0.046

Subtree 3

O-Bromo-alpha-benzoyl cinnamonitrile

309909

MTPAP

-0.57

4.4e-06

0.046

Subtree 3

Nimbolide

742020

RPL21P120

-0.56

4.5e-06

0.046

Subtree 3

Ethoxycurcumin trithiadiazolaminomethylcarbonte

742022

CRACR2A

-0.56

4.5e-06

0.046

Subtree 3

Curcumin tri trithiadiazolaminoethylcarbonate

236613

NQO1

0.56

4.5e-06

0.046

Subtree 3

Plumbagin

643769

RPS10

-0.61

4.5e-06

0.046

Subtree 3

O-Bromo-alpha-benzoyl cinnamonitrile

705537

PDGFC

-0.58

4.6e-06

0.046

Subtree 3

Daturaolone

742022

DARS

-0.56

4.6e-06

0.046

Subtree 3

Curcumin tri trithiadiazolaminoethylcarbonate

236613

ANXA2P1

0.56

4.7e-06

0.046

Subtree 3

Plumbagin

309909

EIF4BP5

-0.57

4.7e-06

0.046

Subtree 3

Nimbolide

87868

PDSS1

-0.61

4.7e-06

0.046

Subtree 3

Phenethyl mustard oil

309909

RPL7AP12

-0.56

4.8e-06

0.046

Subtree 3

Nimbolide

383468

RCC2P4

-0.56

4.8e-06

0.046

Subtree 3

Andrographis Paniculata

32982

RASAL2

0.56

4.8e-06

0.046

Subtree 3

Curcumin

309909

RPL34P31

-0.56

5.0e-06

0.047

Subtree 3

Nimbolide

87868

COL4A1

0.61

5.0e-06

0.047

Subtree 3

Phenethyl mustard oil

309909

SFXN2

-0.56

5.0e-06

0.047

Subtree 3

Nimbolide

643769

HNRNPM

-0.61

5.2e-06

0.048

Subtree 3

O-Bromo-alpha-benzoyl cinnamonitrile

87868

PDGFD

0.61

5.2e-06

0.048

Subtree 3

Phenethyl mustard oil

87868

RPL36AP39

-0.61

5.2e-06

0.048

Subtree 3

Phenethyl mustard oil

87868

HNRNPA1P13

-0.61

5.3e-06

0.048

Subtree 3

Phenethyl mustard oil

309909

SNORA14B

-0.56

5.3e-06

0.048

Subtree 3

Nimbolide

87868

BICC1

0.61

5.4e-06

0.048

Subtree 3

Phenethyl mustard oil

87868

PRSS23

0.61

5.4e-06

0.048

Subtree 3

Phenethyl mustard oil

742022

RPL6

-0.56

5.5e-06

0.048

Subtree 3

curcumin tri trithiadiazolaminoethylcarbonate

87868

RPL34P6

-0.61

5.5e-06

0.048

Subtree 3

Phenethyl mustard oil

87868

HNRNPA1P8

-0.61

5.5e-06

0.048

Subtree 3

Phenethyl mustard oil

309909

TAF5

-0.56

5.6e-06

0.048

Subtree 3

Nimbolide

32982

PRTG

0.56

5.6e-06

0.048

Subtree 3

Curcumin

643023

ITGA3

0.62

5.7e-06

0.049

Subtree 3

Alpha.-Phenyl-2,5-dimethoxy-alpha-cinnamonitrile

643769

CTSD

0.61

5.7e-06

0.049

Subtree 3

O-Bromo-alpha-benzoyl cinnamonitrile

309909

GALNT10

0.56

5.8e-06

0.049

Subtree 3

Nimbolide

742020

TFAP4

-0.56

6.0e-06

0.050

Subtree 3

Ethoxycurcumin trithiadiazolaminomethylcarbonte

309909

RPL10AP2

-0.56

6.0e-06

0.050

Subtree 3

Nimbolide

  1. Listed are the genes whose expression was associated with logGI50 of INPs with FDR adjusted p < 0.05. For each product, the subtree from hierarchical clustering shown in Fig. 1 is provided. The product of Ricinus communis (NSC 15384) was not included in the hierarchical clustering as its screening concentration units differed from all other INPs. ρ, Spearman correlation coefficient