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: OAS2

Gene summary for OAS2

Gene summary.

Gene information	Species	Human
	Gene symbol	OAS2
	Gene ID	4939
	Gene name	2'-5'-oligoadenylate synthetase 2
	Gene Alias	OAS2
	Cytomap	12q24.13
	Gene Type	protein-coding
	GO ID	GO:0001816
	UniProtAcc	P29728

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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
4939	OAS2	LZE5T	Human	Esophagus	ESCC	2.11e-02	1.80e-01	0.0514
4939	OAS2	LZE8T	Human	Esophagus	ESCC	4.92e-05	2.54e-01	0.067
4939	OAS2	LZE20T	Human	Esophagus	ESCC	5.84e-07	3.19e-01	0.0662
4939	OAS2	LZE24T	Human	Esophagus	ESCC	4.11e-29	1.16e+00	0.0596
4939	OAS2	LZE6T	Human	Esophagus	ESCC	1.85e-07	2.54e-01	0.0845
4939	OAS2	P2T-E	Human	Esophagus	ESCC	1.34e-56	1.18e+00	0.1177
4939	OAS2	P4T-E	Human	Esophagus	ESCC	1.88e-09	1.86e-01	0.1323
4939	OAS2	P5T-E	Human	Esophagus	ESCC	1.67e-13	2.54e-01	0.1327
4939	OAS2	P8T-E	Human	Esophagus	ESCC	1.28e-15	3.38e-01	0.0889
4939	OAS2	P9T-E	Human	Esophagus	ESCC	1.82e-22	5.74e-01	0.1131
4939	OAS2	P11T-E	Human	Esophagus	ESCC	2.04e-20	1.04e+00	0.1426
4939	OAS2	P15T-E	Human	Esophagus	ESCC	2.64e-06	2.57e-01	0.1149
4939	OAS2	P17T-E	Human	Esophagus	ESCC	7.38e-10	5.55e-01	0.1278
4939	OAS2	P20T-E	Human	Esophagus	ESCC	1.24e-13	5.84e-01	0.1124
4939	OAS2	P21T-E	Human	Esophagus	ESCC	2.56e-29	7.38e-01	0.1617
4939	OAS2	P22T-E	Human	Esophagus	ESCC	8.71e-09	1.83e-01	0.1236
4939	OAS2	P23T-E	Human	Esophagus	ESCC	5.49e-21	6.66e-01	0.108
4939	OAS2	P24T-E	Human	Esophagus	ESCC	2.21e-23	5.86e-01	0.1287
4939	OAS2	P27T-E	Human	Esophagus	ESCC	4.68e-27	5.68e-01	0.1055
4939	OAS2	P28T-E	Human	Esophagus	ESCC	2.28e-26	4.87e-01	0.1149

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Esophagus		ESCC: Esophageal squamous cell carcinoma
		HGIN: High-grade intraepithelial neoplasias
		LGIN: Low-grade intraepithelial neoplasias
Liver		HCC: Hepatocellular carcinoma
		NAFLD: Non-alcoholic fatty liver disease
Oral Cavity		EOLP: Erosive Oral lichen planus
		LP: leukoplakia
		NEOLP: Non-erosive oral lichen planus
		OSCC: Oral squamous cell carcinoma
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:0016032111	Esophagus	ESCC	viral process	301/8552	415/18723	3.34e-29	1.32e-26	301
GO:0006401110	Esophagus	ESCC	RNA catabolic process	204/8552	278/18723	3.39e-21	5.66e-19	204
GO:0019058111	Esophagus	ESCC	viral life cycle	226/8552	317/18723	1.17e-20	1.76e-18	226
GO:0034655110	Esophagus	ESCC	nucleobase-containing compound catabolic process	272/8552	407/18723	2.92e-18	2.90e-16	272
GO:004670018	Esophagus	ESCC	heterocycle catabolic process	286/8552	445/18723	1.12e-15	7.47e-14	286
GO:004427019	Esophagus	ESCC	cellular nitrogen compound catabolic process	288/8552	451/18723	3.03e-15	1.79e-13	288
GO:001943918	Esophagus	ESCC	aromatic compound catabolic process	295/8552	467/18723	1.09e-14	5.98e-13	295
GO:0019079111	Esophagus	ESCC	viral genome replication	102/8552	131/18723	4.31e-14	2.19e-12	102
GO:000961518	Esophagus	ESCC	response to virus	238/8552	367/18723	6.65e-14	3.32e-12	238
GO:190136118	Esophagus	ESCC	organic cyclic compound catabolic process	307/8552	495/18723	9.99e-14	4.80e-12	307
GO:0050792111	Esophagus	ESCC	regulation of viral process	119/8552	164/18723	2.19e-12	9.03e-11	119
GO:0048732111	Esophagus	ESCC	gland development	269/8552	436/18723	7.81e-12	2.95e-10	269
GO:1903900111	Esophagus	ESCC	regulation of viral life cycle	106/8552	148/18723	1.26e-10	3.72e-09	106
GO:0045069110	Esophagus	ESCC	regulation of viral genome replication	67/8552	85/18723	3.81e-10	1.04e-08	67
GO:00516075	Esophagus	ESCC	defense response to virus	171/8552	265/18723	3.91e-10	1.05e-08	171
GO:01405465	Esophagus	ESCC	defense response to symbiont	171/8552	265/18723	3.91e-10	1.05e-08	171
GO:003434013	Esophagus	ESCC	response to type I interferon	48/8552	58/18723	6.18e-09	1.26e-07	48
GO:00603375	Esophagus	ESCC	type I interferon signaling pathway	41/8552	50/18723	1.35e-07	2.17e-06	41
GO:00713575	Esophagus	ESCC	cellular response to type I interferon	42/8552	52/18723	2.15e-07	3.30e-06	42
GO:004852516	Esophagus	ESCC	negative regulation of viral process	66/8552	92/18723	3.49e-07	4.88e-06	66

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa05169210	Esophagus	ESCC	Epstein-Barr virus infection	151/4205	202/8465	1.55e-13	3.45e-12	1.77e-12	151
hsa0516425	Esophagus	ESCC	Influenza A	122/4205	171/8465	5.01e-09	4.79e-08	2.45e-08	122
hsa05171211	Esophagus	ESCC	Coronavirus disease - COVID-19	156/4205	232/8465	3.18e-08	2.68e-07	1.37e-07	156
hsa051609	Esophagus	ESCC	Hepatitis C	107/4205	157/8465	1.75e-06	1.08e-05	5.55e-06	107
hsa051629	Esophagus	ESCC	Measles	90/4205	139/8465	2.16e-04	7.87e-04	4.03e-04	90
hsa0462122	Esophagus	ESCC	NOD-like receptor signaling pathway	116/4205	186/8465	2.90e-04	1.03e-03	5.30e-04	116
hsa0516937	Esophagus	ESCC	Epstein-Barr virus infection	151/4205	202/8465	1.55e-13	3.45e-12	1.77e-12	151
hsa0516435	Esophagus	ESCC	Influenza A	122/4205	171/8465	5.01e-09	4.79e-08	2.45e-08	122
hsa05171310	Esophagus	ESCC	Coronavirus disease - COVID-19	156/4205	232/8465	3.18e-08	2.68e-07	1.37e-07	156
hsa0516016	Esophagus	ESCC	Hepatitis C	107/4205	157/8465	1.75e-06	1.08e-05	5.55e-06	107
hsa0516213	Esophagus	ESCC	Measles	90/4205	139/8465	2.16e-04	7.87e-04	4.03e-04	90
hsa0462132	Esophagus	ESCC	NOD-like receptor signaling pathway	116/4205	186/8465	2.90e-04	1.03e-03	5.30e-04	116
hsa0517142	Liver	HCC	Coronavirus disease - COVID-19	167/4020	232/8465	1.50e-14	4.19e-13	2.33e-13	167
hsa0516921	Liver	HCC	Epstein-Barr virus infection	128/4020	202/8465	3.17e-06	2.79e-05	1.55e-05	128
hsa0516021	Liver	HCC	Hepatitis C	94/4020	157/8465	1.11e-03	4.10e-03	2.28e-03	94
hsa0516421	Liver	HCC	Influenza A	101/4020	171/8465	1.41e-03	5.07e-03	2.82e-03	101
hsa0517152	Liver	HCC	Coronavirus disease - COVID-19	167/4020	232/8465	1.50e-14	4.19e-13	2.33e-13	167
hsa0516931	Liver	HCC	Epstein-Barr virus infection	128/4020	202/8465	3.17e-06	2.79e-05	1.55e-05	128
hsa0516031	Liver	HCC	Hepatitis C	94/4020	157/8465	1.11e-03	4.10e-03	2.28e-03	94
hsa0516431	Liver	HCC	Influenza A	101/4020	171/8465	1.41e-03	5.07e-03	2.82e-03	101

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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

OAS2

SNV

Missense_Mutation

rs200589437

c.686N>T

p.Thr229Met

p.T229M

P29728

protein_coding

deleterious(0)

probably_damaging(0.991)

TCGA-A8-A082-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

5-fluorouracil

OAS2

SNV

Missense_Mutation

c.220G>A

p.Asp74Asn

p.D74N

P29728

protein_coding

deleterious(0.02)

probably_damaging(0.997)

TCGA-A8-A08J-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

OAS2

SNV

Missense_Mutation

c.59N>C

p.Ile20Thr

p.I20T

P29728

protein_coding

deleterious(0)

possibly_damaging(0.498)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

OAS2

SNV

Missense_Mutation

rs568482198

c.433G>A

p.Ala145Thr

p.A145T

P29728

protein_coding

tolerated(0.06)

benign(0.264)

TCGA-AC-A62X-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

OAS2

SNV

Missense_Mutation

rs753242512

c.1586N>A

p.Arg529Gln

p.R529Q

P29728

protein_coding

deleterious(0.03)

benign(0.044)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

OAS2

SNV

Missense_Mutation

c.373G>C

p.Asp125His

p.D125H

P29728

protein_coding

tolerated(0.15)

benign(0.001)

TCGA-D8-A1JA-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

adriamycin

OAS2

SNV

Missense_Mutation

c.706N>T

p.Gly236Trp

p.G236W

P29728

protein_coding

deleterious(0.01)

probably_damaging(1)

TCGA-E9-A1NA-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cyclophosphamide

OAS2

SNV

Missense_Mutation

rs775523501

c.688N>A

p.Val230Met

p.V230M

P29728

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-GM-A2DA-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

fluorouracil

OAS2

SNV

Missense_Mutation

c.641N>A

p.Ile214Asn

p.I214N

P29728

protein_coding

tolerated(0.37)

benign(0)

TCGA-GM-A2DK-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

arimidex

OAS2

SNV

Missense_Mutation

novel

c.1916N>T

p.Ala639Val

p.A639V

P29728

protein_coding

deleterious(0)

probably_damaging(0.969)

TCGA-LL-A5YM-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Unspecific

letrozole

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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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