Name: Mohammad Turhan Pathan

Group:5
Gene of interest: BMP1 in STAD
 B
A

All cancer
All normal
Adipose-cancer
dipose-normal
drenal-gland cancer
drenal-gland normal
Bladder-cancer
Bladder-normal
Blood-cancer
Blood-Normal
Bone-cancer
Bone-normal
Brain-cancer
Brain-normal
Breast-cancer
Breast-normal
Cervix cancer
Cervix normal
Colon cancer
Colon normal
Endometrium cancer
Endometrium normal
Esophagus cancer
Esophagus normal
Eye cancer
Eye normal
Gall bladder cancer
Gall bladder cancer
Head&neck cancer
Head&neck normal
Kidney cancer
Kidney cancer
Liver cancer
Liver normal
Lung cancer
Lung normal
Lymphnode cancer
Lymph node normal
Muscle cancer
Muscle normal
Oral cancer
Oral normal
Ovary cancer
Ovary normal
Pancreas cancer
Pancreas normal
Pharynx cancer
Pharynx normal
Placenta normal
Prostate cancer
Prostate normal
Skin cancer
Skin normal
Small intestine cancer
Small intestine normal
Spleen cancer
Spleen normal
Stomach cancer
Stomach normal
Teeth cancer
Teeth normal
Testis cancer
Testis normal
Thyroid cancer
Thyroid normal
Tongue cancer
Tongue normal
Uterus cancer
Uterus normal
Vagina cancer
Vagina normal
A P-value=2.88E-7 Fold change= B P-value=5.85E-8 Fold change= 2.211 C P-value=8.19E-6 Fold change= 6.465
2.279

Gastric Gastric mucosa Gastric Gastric Cancer (12)

tissue(19)
Gastric tissue(19) Diffuse Gastric (12) tissue(3)
adenocarcinoma(3
D P-value=7.26E-5 Fold change= 3.743
1)
E P-value=3.29E-11 Fold change= 4.302 G

<1E-12

Gastric mucosa (31) Diffuse Gastric

Gastric mucosa
adenocarcinoma(6) Gastric intestinal
(31) Primary
type Normal
F adenocarcinoma(2 (N=34)
Tumor
(n=415)
6) B TCGA
Samples

STAD=408 Normal=36

Stomach 1
Stomach 1
HPA014572
HPA014572 Male, age 39 Stomach,
Male, age 72
upper (T-62350) Carcinoid,
Stomach, upper (T-62350)
malignant, NOS (M-82403)
Normal tissue, NOS (M-00100)
Normal tissue, NOS (M-00100)
Patient id: 2583
Patient id: 3368 Glandular cells
Glandular cells
Staining: Medium
Staining: Medium
Intensity:Moderate
Intensity: Moderate
Quantity: >75%
Quantity: >75%
Location: Cytoplasmic/
Location: Cytoplasmic/
membranous
membranous
 A
B C Individual Race
Sample Types Cancer
<1E-12 stages <1E-12
1.62E-12
Transcripts per million

Transcripts per million

1.62E-12 1.62E-12 9.48E-10

Transcripts per million

2.05E-7 1.53E-03

Normal Primary Normal Stage1 Stage2 Stage3 Stage4

Normal Caucasian African- Asian
(N=34) Tumor (N=34) (N=18) (N=123)(N=169) (N=41)
(N=34) (n=260) American N=87
(n=415) TCGA N=12
TCGA
Samples TCGA
Samples
Samples
Patient’s E E Tumor
D gender Patient’s grade
1.62E-12 age <1E-12 1.27E-02

Transcripts per million

<1E-12 <1E-12
Transcripts per million
1.62E-12 1.62E-12
2.67E-02
3.21E-09

Normal Male Female 21-40 41-60 61-80 81-100 Normal Grade 1 Grade 2 Grade 3
(N=34) N=268 N=147 N=4 N=128 N=253 N=25 (N=34) N=12 N=148 N=246
TCGA TCGA TCGA
Samples Samples Samples

G H
H.Pylori infection Histological
subtypes
Transcripts per million

<1E-12 2.88E-12
Transcripts per million

<1E-12 <1E-12
3.2E-05
1.11E-16 1.62E-12 7.15E-07
1.60E-02
1.01E-02

D i e n o
A d eno d e n o
e n o A d e n o
Int Ad
s Pa
o r m N O A t t Ad I nt i n o u d e n o
N e n o ffu s e i g n e In ul ar M u c nt A
Ad ) S S T u b ) I
l
a 34 = 6 9 g N O ) = 2 0 i ll ar y
= S ( n R i n 7 3 ) n = 7 6 (n p
(N 1 5 5 ) 1 2 ) (n = ( = 7 )
(n = ( n= (n
)
Normal With W/0 Unavailbl
(N=34) H.pylori H.pylori e
infection infection N=153
N=20 N=157
TCGA
Samples
 C Patient’s race
A B Individual cancer stages
5.7E-01 6.7E-01 6.7E-01 8.0E-01 5.7E-01
6.7E-01
6.3E-01
8.9E-01

Beta value
Beta value

Beta value
Primary Normal Stage1 Stage2 Stage3 Stage4
tumor Normal Caucasi African – Asian(n=
(n=2) (n=52) (n=125) (n=174)(n=33)
(n=395) (n=2) an America 89)
(n=253) n(n=13
E Patient’s age F
Patient’s gender Tumor Grade
D 2.7E-01 7.2E-01
6.3E-01 7.9E-01 5.9E-01
7.0E-01 6.4E-01
4.6E-01

Beta value
value
9.5E-01
Beta value

Betavalue
Beta

Normal Male Femal Normal 21-40 41-60 61-80 81-100 Normal Grade 1 Grade 2 Grade 3
(n=2) (n=259) (n=136) (n=2) N=4 N=127 N=237 N=22 (N=34) N=12 N=148 N=246
TCGA samples TCGA samples TCGA samples

G Nodal Metastasis status

6.3E-01
7.3E-01 7.2E-01 6.5E-01
value
Betavalue
Beta

Normal N0 N1 N2 N3
(n=2) (n=124) (n=101) (n=79) (n=28)
TCGA samples
A 202701_at B 202701_at C 202701_at

OS,
OS,
OS, ALL HER2 (-)
HER2 (+)

d 202701_at E 202701_at
F 202701_at

OS, Poorly OS, Moderately

OS, well
differentiated differentiated
differentiated

g 202701_at 202701_at
H

OS, Male OS, female

A B

Log2(LIF TPM)
Log2(bmp1 TPM)

C
D

LIF-BMP1
Pearsons’s rho
R=.4548(p=2.393e-24
Spearman’s rank rho
Rho=.4415(p=6.837e-23
A c

BMP1-EXPRESSION-RNA SEQ V2
C G A
ch T G A a ch
m a 18 (TC o m
Sto N 2 0 a ch St A)
NC A Sto m CG
OA ) (T
pu b

B
 PATHWAYS
A Reactome 2016 B KEGG 2019 HUMAN

C NCI-NATURE 2016 D Panther 2016

E ONTOLOGIES
GO Biological process 2018
GO Molecular function 2018
F

G
GO Cellular component 2018