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: OAS3

Gene summary for OAS3

Gene summary.

Gene information	Species	Human
	Gene symbol	OAS3
	Gene ID	4940
	Gene name	2'-5'-oligoadenylate synthetase 3
	Gene Alias	p100
	Cytomap	12q24.13
	Gene Type	protein-coding
	GO ID	GO:0001816
	UniProtAcc	Q9Y6K5

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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
4940	OAS3	LZE4T	Human	Esophagus	ESCC	2.57e-04	1.68e-01	0.0811
4940	OAS3	LZE7T	Human	Esophagus	ESCC	1.36e-05	1.78e-01	0.0667
4940	OAS3	LZE20T	Human	Esophagus	ESCC	3.83e-11	4.29e-01	0.0662
4940	OAS3	LZE24T	Human	Esophagus	ESCC	5.63e-25	9.33e-01	0.0596
4940	OAS3	LZE21T	Human	Esophagus	ESCC	5.69e-03	2.42e-01	0.0655
4940	OAS3	P1T-E	Human	Esophagus	ESCC	4.19e-13	1.01e+00	0.0875
4940	OAS3	P2T-E	Human	Esophagus	ESCC	1.13e-56	1.10e+00	0.1177
4940	OAS3	P4T-E	Human	Esophagus	ESCC	5.08e-25	5.65e-01	0.1323
4940	OAS3	P5T-E	Human	Esophagus	ESCC	6.01e-16	3.13e-01	0.1327
4940	OAS3	P8T-E	Human	Esophagus	ESCC	1.24e-22	5.35e-01	0.0889
4940	OAS3	P9T-E	Human	Esophagus	ESCC	1.90e-21	4.39e-01	0.1131
4940	OAS3	P11T-E	Human	Esophagus	ESCC	9.48e-22	1.01e+00	0.1426
4940	OAS3	P15T-E	Human	Esophagus	ESCC	3.06e-08	1.57e-01	0.1149
4940	OAS3	P17T-E	Human	Esophagus	ESCC	2.02e-16	7.02e-01	0.1278
4940	OAS3	P20T-E	Human	Esophagus	ESCC	3.53e-17	5.17e-01	0.1124
4940	OAS3	P21T-E	Human	Esophagus	ESCC	2.01e-45	9.77e-01	0.1617
4940	OAS3	P22T-E	Human	Esophagus	ESCC	5.30e-11	1.87e-01	0.1236
4940	OAS3	P23T-E	Human	Esophagus	ESCC	5.32e-16	5.69e-01	0.108
4940	OAS3	P24T-E	Human	Esophagus	ESCC	3.44e-25	5.35e-01	0.1287
4940	OAS3	P26T-E	Human	Esophagus	ESCC	1.45e-09	2.14e-01	0.1276

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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:003952815	Thyroid	ATC	cytoplasmic pattern recognition receptor signaling pathway in response to virus	23/6293	34/18723	5.15e-05	3.99e-04	23
GO:000275315	Thyroid	ATC	cytoplasmic pattern recognition receptor signaling pathway	35/6293	60/18723	7.31e-05	5.56e-04	35
GO:000222114	Thyroid	ATC	pattern recognition receptor signaling pathway	80/6293	172/18723	2.89e-04	1.84e-03	80
GO:006075912	Thyroid	ATC	regulation of response to cytokine stimulus	76/6293	162/18723	2.92e-04	1.85e-03	76
GO:009858615	Thyroid	ATC	cellular response to virus	44/6293	84/18723	2.94e-04	1.87e-03	44
GO:000195912	Thyroid	ATC	regulation of cytokine-mediated signaling pathway	71/6293	150/18723	3.28e-04	2.04e-03	71
GO:003952914	Thyroid	ATC	RIG-I signaling pathway	18/6293	27/18723	4.53e-04	2.68e-03	18
GO:005160712	Thyroid	ATC	defense response to virus	115/6293	265/18723	5.31e-04	3.09e-03	115
GO:014054612	Thyroid	ATC	defense response to symbiont	115/6293	265/18723	5.31e-04	3.09e-03	115
GO:006033811	Thyroid	ATC	regulation of type I interferon-mediated signaling pathway	22/6293	36/18723	6.58e-04	3.73e-03	22
GO:003247913	Thyroid	ATC	regulation of type I interferon production	47/6293	95/18723	9.81e-04	5.21e-03	47
GO:003260613	Thyroid	ATC	type I interferon production	47/6293	95/18723	9.81e-04	5.21e-03	47
GO:000181924	Thyroid	ATC	positive regulation of cytokine production	189/6293	467/18723	1.00e-03	5.31e-03	189
GO:004508813	Thyroid	ATC	regulation of innate immune response	94/6293	218/18723	2.05e-03	9.71e-03	94
GO:003272811	Thyroid	ATC	positive regulation of interferon-beta production	22/6293	39/18723	2.84e-03	1.29e-02	22
GO:004507110	Thyroid	ATC	negative regulation of viral genome replication	29/6293	56/18723	3.76e-03	1.64e-02	29
GO:00327608	Thyroid	ATC	positive regulation of tumor necrosis factor production	48/6293	103/18723	4.14e-03	1.76e-02	48
GO:19035576	Thyroid	ATC	positive regulation of tumor necrosis factor superfamily cytokine production	49/6293	107/18723	5.79e-03	2.34e-02	49
GO:004852518	Thyroid	ATC	negative regulation of viral process	43/6293	92/18723	6.02e-03	2.42e-02	43
GO:000283213	Thyroid	ATC	negative regulation of response to biotic stimulus	49/6293	108/18723	7.19e-03	2.84e-02	49

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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

OAS3

SNV

Missense_Mutation

c.1527N>T

p.Gln509His

p.Q509H

Q9Y6K5

protein_coding

deleterious(0.03)

benign(0.069)

TCGA-A8-A097-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

tamoxiphen

OAS3

SNV

Missense_Mutation

novel

c.2035N>A

p.Glu679Lys

p.E679K

Q9Y6K5

protein_coding

tolerated(0.08)

possibly_damaging(0.622)

TCGA-AR-A2LE-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

tamoxiphen

OAS3

SNV

Missense_Mutation

novel

c.473N>T

p.Ser158Phe

p.S158F

Q9Y6K5

protein_coding

tolerated(0.05)

benign(0.282)

TCGA-BH-A2L8-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

OAS3

SNV

Missense_Mutation

c.1760N>T

p.Arg587Leu

p.R587L

Q9Y6K5

protein_coding

deleterious(0)

possibly_damaging(0.758)

TCGA-EW-A6SD-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

tch

OAS3

insertion

Frame_Shift_Ins

novel

c.2563_2564insTCTCCAGTCACAAA

p.Gln855LeufsTer22

p.Q855Lfs*22

Q9Y6K5

protein_coding

TCGA-A8-A08H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

OAS3

insertion

In_Frame_Ins

novel

c.369_370insGCCCCC

p.Gln123_Ser124insAlaPro

p.Q123_S124insAP

Q9Y6K5

protein_coding

TCGA-AN-A03X-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

OAS3

insertion

Nonsense_Mutation

novel

c.371_372insATGGTGGGAGCTGGAAGTAAAAGGACTGGCATAAT

p.Ser124ArgfsTer12

p.S124Rfs*12

Q9Y6K5

protein_coding

TCGA-AN-A03X-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

OAS3

SNV

Missense_Mutation

rs540377614

c.356N>T

p.Thr119Met

p.T119M

Q9Y6K5

protein_coding

deleterious(0.04)

benign(0.026)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

OAS3

SNV

Missense_Mutation

rs769603563

c.2369N>A

p.Arg790Gln

p.R790Q

Q9Y6K5

protein_coding

tolerated(0.51)

benign(0.033)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

OAS3

SNV

Missense_Mutation

c.1382N>T

p.Ser461Leu

p.S461L

Q9Y6K5

protein_coding

deleterious(0)

probably_damaging(0.987)

TCGA-IR-A3LH-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

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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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