Schematic overview of the cellular and molecular mechanisms involved in the cancer progression, including the proposed cellular and molecular mechanisms in cancer cells trajectory. AT1: alveolar type 1 cells; AT2: alveolar type 2 cells; AAH: atypical adenomatous hyperplasia; AIS: adenocarcinoma in situ; MIA: minimally invasive adenocarcinoma; IA: invasive adenocarcinoma; EMT: epithelial-mesenchymal transition

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	Gene summary
	Malignant transformation analysis
	Malignant transformation related pathway analysis
	Cell-cell communication analysis
	Single-cell gene regulatory network inference analysis
	Somatic mutation of malignant transformation related genes
	Related drugs of malignant transformation related genes

Gene: BST2

Gene summary for BST2

Gene summary.

Gene information	Species	Human
	Gene symbol	BST2
	Gene ID	684
	Gene name	bone marrow stromal cell antigen 2
	Gene Alias	CD317
	Cytomap	19p13.11
	Gene Type	protein-coding
	GO ID	GO:0001558
	UniProtAcc	A0A024R7H5

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Malignant transformation analysis

Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells

Malignant transformation involving gene list.

Entrez ID	Symbol	Replicates	Species	Organ	Tissue	Adj P-value	Log2FC	Malignancy
684	BST2	GSM4909281	Human	Breast	IDC	1.43e-66	1.11e+00	0.21
684	BST2	GSM4909285	Human	Breast	IDC	2.68e-03	3.19e-01	0.21
684	BST2	GSM4909286	Human	Breast	IDC	4.25e-04	-2.79e-01	0.1081
684	BST2	GSM4909287	Human	Breast	IDC	1.79e-42	1.08e+00	0.2057
684	BST2	GSM4909290	Human	Breast	IDC	8.98e-16	7.07e-01	0.2096
684	BST2	GSM4909291	Human	Breast	IDC	1.61e-09	6.49e-01	0.1753
684	BST2	GSM4909293	Human	Breast	IDC	3.77e-25	6.66e-01	0.1581
684	BST2	GSM4909295	Human	Breast	IDC	8.54e-03	-2.78e-01	0.0898
684	BST2	GSM4909296	Human	Breast	IDC	3.07e-37	9.50e-01	0.1524
684	BST2	GSM4909297	Human	Breast	IDC	1.25e-14	5.10e-01	0.1517
684	BST2	GSM4909298	Human	Breast	IDC	5.72e-17	3.60e-01	0.1551
684	BST2	GSM4909301	Human	Breast	IDC	1.35e-03	-2.62e-01	0.1577
684	BST2	GSM4909302	Human	Breast	IDC	4.82e-05	4.72e-01	0.1545
684	BST2	GSM4909304	Human	Breast	IDC	1.07e-80	1.21e+00	0.1636
684	BST2	GSM4909305	Human	Breast	IDC	3.71e-02	3.65e-01	0.0436
684	BST2	GSM4909306	Human	Breast	IDC	2.34e-47	8.93e-01	0.1564
684	BST2	GSM4909307	Human	Breast	IDC	7.03e-77	1.23e+00	0.1569
684	BST2	GSM4909308	Human	Breast	IDC	8.45e-102	1.42e+00	0.158
684	BST2	GSM4909309	Human	Breast	IDC	6.25e-34	9.86e-01	0.0483
684	BST2	GSM4909311	Human	Breast	IDC	3.60e-07	-8.83e-02	0.1534

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Breast		IDC: Invasive ductal carcinoma
		DCIS: Ductal carcinoma in situ
		Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers
Cervix		CC: Cervix cancer
		HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions
		N_HPV: HPV-infected normal cervix
Colorectum (GSE201348)		FAP: Familial adenomatous polyposis
		CRC: Colorectal cancer
Colorectum (HTA11)		AD: Adenomas
		SER: Sessile serrated lesions
		MSI-H: Microsatellite-high colorectal cancer
		MSS: Microsatellite stable colorectal cancer
Endometrium		AEH: Atypical endometrial hyperplasia
		EEC: Endometrioid Cancer
Esophagus		ESCC: Esophageal squamous cell carcinoma
		HGIN: High-grade intraepithelial neoplasias
		LGIN: Low-grade intraepithelial neoplasias
GC		CAG: Chronic atrophic gastritis
		CAG with IM: Chronic atrophic gastritis with intestinal metaplasia
		CSG: Chronic superficial gastritis
		GC: Gastric cancer
		SIM: Severe intestinal metaplasia
		WIM: Wild intestinal metaplasia
Liver		HCC: Hepatocellular carcinoma
		NAFLD: Non-alcoholic fatty liver disease
Lung		AAH: Atypical adenomatous hyperplasia
		AIS: Adenocarcinoma in situ
		IAC: Invasive lung adenocarcinoma
		MIA: Minimally invasive adenocarcinoma
Oral Cavity		EOLP: Erosive Oral lichen planus
		LP: leukoplakia
		NEOLP: Non-erosive oral lichen planus
		OSCC: Oral squamous cell carcinoma
Prostate		BPH: Benign Prostatic Hyperplasia
Skin		AK: Actinic keratosis
		cSCC: Cutaneous squamous cell carcinoma
		SCCIS:squamous cell carcinoma in situ
Thyroid		ATC: Anaplastic thyroid cancer
		HT: Hashimoto's thyroiditis
		PTC: Papillary thyroid cancer

∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage.

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Malignant transformation related pathway analysis

Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer

Figure of enriched GO biological processes.

Tissue	Disease Stage	Enriched GO biological Processes
Colorectum	AD
Colorectum	SER
Colorectum	MSS
Colorectum	MSI-H
Colorectum	FAP

∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust).

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Enriched GO biological processes.

GO ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	Count
GO:00525488	Lung	IAC	regulation of endopeptidase activity	75/2061	432/18723	4.18e-05	1.01e-03	75
GO:00190798	Lung	IAC	viral genome replication	30/2061	131/18723	7.15e-05	1.51e-03	30
GO:00431235	Lung	IAC	positive regulation of I-kappaB kinase/NF-kappaB signaling	38/2061	186/18723	1.19e-04	2.25e-03	38
GO:00015586	Lung	IAC	regulation of cell growth	70/2061	414/18723	1.69e-04	3.01e-03	70
GO:19039008	Lung	IAC	regulation of viral life cycle	31/2061	148/18723	3.07e-04	4.89e-03	31
GO:00096156	Lung	IAC	response to virus	61/2061	367/18723	6.75e-04	9.12e-03	61
GO:00458618	Lung	IAC	negative regulation of proteolysis	58/2061	351/18723	1.04e-03	1.24e-02	58
GO:2000146	Lung	IAC	negative regulation of cell motility	56/2061	359/18723	4.58e-03	3.62e-02	56
GO:0030336	Lung	IAC	negative regulation of cell migration	54/2061	344/18723	4.65e-03	3.66e-02	54
GO:0051271	Lung	IAC	negative regulation of cellular component movement	57/2061	367/18723	4.67e-03	3.67e-02	57
GO:0040013	Lung	IAC	negative regulation of locomotion	60/2061	391/18723	4.94e-03	3.78e-02	60
GO:00354551	Lung	IAC	response to interferon-alpha	7/2061	21/18723	5.59e-03	4.12e-02	7
GO:00447661	Lung	IAC	multi-organism transport	7/2061	21/18723	5.59e-03	4.12e-02	7
GO:19025791	Lung	IAC	multi-organism localization	7/2061	21/18723	5.59e-03	4.12e-02	7
GO:00109518	Lung	IAC	negative regulation of endopeptidase activity	41/2061	252/18723	6.84e-03	4.75e-02	41
GO:001603213	Lung	AIS	viral process	85/1849	415/18723	4.74e-11	1.95e-08	85
GO:001905813	Lung	AIS	viral life cycle	68/1849	317/18723	5.39e-10	1.16e-07	68
GO:001604912	Lung	AIS	cell growth	83/1849	482/18723	3.26e-07	2.79e-05	83
GO:003295613	Lung	AIS	regulation of actin cytoskeleton organization	63/1849	358/18723	4.06e-06	2.09e-04	63
GO:003297013	Lung	AIS	regulation of actin filament-based process	68/1849	397/18723	4.49e-06	2.27e-04	68

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0517024	Breast	DCIS	Human immunodeficiency virus 1 infection	33/846	212/8465	6.49e-03	3.22e-02	2.37e-02	33
hsa0517034	Breast	DCIS	Human immunodeficiency virus 1 infection	33/846	212/8465	6.49e-03	3.22e-02	2.37e-02	33
hsa0517016	Cervix	CC	Human immunodeficiency virus 1 infection	55/1267	212/8465	1.80e-05	1.42e-04	8.40e-05	55
hsa0517017	Cervix	CC	Human immunodeficiency virus 1 infection	55/1267	212/8465	1.80e-05	1.42e-04	8.40e-05	55
hsa051704	Colorectum	MSS	Human immunodeficiency virus 1 infection	69/1875	212/8465	2.66e-04	1.98e-03	1.21e-03	69
hsa03250	Colorectum	MSS	Viral life cycle - HIV-1	23/1875	63/8465	6.55e-03	2.64e-02	1.62e-02	23
hsa051705	Colorectum	MSS	Human immunodeficiency virus 1 infection	69/1875	212/8465	2.66e-04	1.98e-03	1.21e-03	69
hsa032501	Colorectum	MSS	Viral life cycle - HIV-1	23/1875	63/8465	6.55e-03	2.64e-02	1.62e-02	23
hsa0517018	Endometrium	AEH	Human immunodeficiency virus 1 infection	43/1197	212/8465	8.19e-03	4.22e-02	3.09e-02	43
hsa0517019	Endometrium	AEH	Human immunodeficiency virus 1 infection	43/1197	212/8465	8.19e-03	4.22e-02	3.09e-02	43
hsa0517025	Endometrium	EEC	Human immunodeficiency virus 1 infection	44/1237	212/8465	8.86e-03	4.05e-02	3.02e-02	44
hsa0517035	Endometrium	EEC	Human immunodeficiency virus 1 infection	44/1237	212/8465	8.86e-03	4.05e-02	3.02e-02	44
hsa0517029	Esophagus	HGIN	Human immunodeficiency virus 1 infection	51/1383	212/8465	2.16e-03	1.90e-02	1.51e-02	51
hsa05170112	Esophagus	HGIN	Human immunodeficiency virus 1 infection	51/1383	212/8465	2.16e-03	1.90e-02	1.51e-02	51
hsa032509	Esophagus	ESCC	Viral life cycle - HIV-1	54/4205	63/8465	2.01e-09	2.17e-08	1.11e-08	54
hsa05170210	Esophagus	ESCC	Human immunodeficiency virus 1 infection	147/4205	212/8465	3.37e-09	3.53e-08	1.81e-08	147
hsa0325014	Esophagus	ESCC	Viral life cycle - HIV-1	54/4205	63/8465	2.01e-09	2.17e-08	1.11e-08	54
hsa0517038	Esophagus	ESCC	Human immunodeficiency virus 1 infection	147/4205	212/8465	3.37e-09	3.53e-08	1.81e-08	147
hsa032502	Liver	HCC	Viral life cycle - HIV-1	46/4020	63/8465	3.25e-05	1.88e-04	1.04e-04	46
hsa051709	Liver	HCC	Human immunodeficiency virus 1 infection	125/4020	212/8465	4.51e-04	1.94e-03	1.08e-03	125

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Cell-cell communication analysis

Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states

Ligand

Receptor

LRpair

Pathway

Tissue

Disease Stage

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Single-cell gene regulatory network inference analysis

Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states

Cell Type

Tissue

Disease Stage

Target Gene

RSS

Regulon Activity

∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression.

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Somatic mutation of malignant transformation related genes

Annotation of somatic variants for genes involved in malignant transformation

Hugo Symbol

Variant Class

Variant Classification

dbSNP RS

HGVSc

HGVSp

HGVSp Short

SWISSPROT

BIOTYPE

SIFT

PolyPhen

Tumor Sample Barcode

Tissue

Histology

Sex

Age

Stage

Therapy Types

Drugs

Outcome

BST2

SNV

Missense_Mutation

c.112G>C

p.Gly38Arg

p.G38R

Q10589

protein_coding

tolerated(0.4)

probably_damaging(1)

TCGA-AN-A0FK-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Unknown

BST2

SNV

Missense_Mutation

c.440G>A

p.Arg147Lys

p.R147K

Q10589

protein_coding

tolerated_low_confidence(0.97)

benign(0.129)

TCGA-JW-A5VL-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

BST2

SNV

Missense_Mutation

rs753915464

c.29N>A

p.Arg10Lys

p.R10K

Q10589

protein_coding

tolerated(1)

benign(0.001)

TCGA-VS-A959-01

Cervix

cervical & endocervical cancer

Female

>=65

I/II

Unknown

BST2

SNV

Missense_Mutation

c.494C>T

p.Ala165Val

p.A165V

Q10589

protein_coding

tolerated_low_confidence(0.3)

benign(0.025)

TCGA-AA-3833-01

Colorectum

colon adenocarcinoma

Female

<65

I/II

Unknown

BST2

SNV

Missense_Mutation

rs376557702

c.56G>A

p.Arg19His

p.R19H

Q10589

protein_coding

tolerated(0.1)

benign(0.017)

TCGA-A5-A0G2-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Unknown

BST2

SNV

Missense_Mutation

novel

c.248N>T

p.Asp83Val

p.D83V

Q10589

protein_coding

tolerated(0.27)

possibly_damaging(0.68)

TCGA-A5-A1OF-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

BST2

SNV

Missense_Mutation

novel

c.190C>T

p.Arg64Cys

p.R64C

Q10589

protein_coding

deleterious(0)

possibly_damaging(0.85)

TCGA-AJ-A3BH-01

Endometrium

uterine corpus endometrioid carcinoma

Female

Unknown

I/II

Unknown

BST2

SNV

Missense_Mutation

novel

c.108N>G

p.Ile36Met

p.I36M

Q10589

protein_coding

tolerated(0.1)

benign(0.145)

TCGA-AP-A059-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

BST2

SNV

Missense_Mutation

novel

c.437T>C

p.Val146Ala

p.V146A

Q10589

protein_coding

tolerated_low_confidence(1)

benign(0.001)

TCGA-AP-A1DK-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

BST2

SNV

Missense_Mutation

novel

c.351G>T

p.Glu117Asp

p.E117D

Q10589

protein_coding

tolerated(0.05)

possibly_damaging(0.73)

TCGA-AX-A1CE-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unspecific

Paclitaxel

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Related drugs of malignant transformation related genes

Identification of chemicals and drugs interact with genes involved in malignant transfromation

(DGIdb 4.0)

Entrez ID

Symbol

Category

Interaction Types

Drug Claim Name

Drug Name

PMIDs

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