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: MAVS

Gene summary for MAVS

Gene summary.

Gene information	Species	Human
	Gene symbol	MAVS
	Gene ID	57506
	Gene name	mitochondrial antiviral signaling protein
	Gene Alias	CARDIF
	Cytomap	20p13
	Gene Type	protein-coding
	GO ID	GO:0001816
	UniProtAcc	Q7Z434

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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
57506	MAVS	HTA11_2487_2000001011	Human	Colorectum	SER	6.18e-07	6.14e-01	-0.1808
57506	MAVS	HTA11_1938_2000001011	Human	Colorectum	AD	3.49e-05	5.62e-01	-0.0811
57506	MAVS	HTA11_347_2000001011	Human	Colorectum	AD	9.59e-27	9.03e-01	-0.1954
57506	MAVS	HTA11_411_2000001011	Human	Colorectum	SER	1.32e-02	7.91e-01	-0.2602
57506	MAVS	HTA11_3361_2000001011	Human	Colorectum	AD	5.34e-07	6.83e-01	-0.1207
57506	MAVS	HTA11_83_2000001011	Human	Colorectum	SER	5.76e-12	9.28e-01	-0.1526
57506	MAVS	HTA11_696_2000001011	Human	Colorectum	AD	9.58e-22	9.12e-01	-0.1464
57506	MAVS	HTA11_866_2000001011	Human	Colorectum	AD	6.46e-10	5.31e-01	-0.1001
57506	MAVS	HTA11_1391_2000001011	Human	Colorectum	AD	1.81e-09	6.82e-01	-0.059
57506	MAVS	HTA11_2992_2000001011	Human	Colorectum	SER	5.22e-03	6.74e-01	-0.1706
57506	MAVS	HTA11_546_2000001011	Human	Colorectum	AD	8.52e-04	6.09e-01	-0.0842
57506	MAVS	HTA11_866_3004761011	Human	Colorectum	AD	9.37e-03	3.96e-01	0.096
57506	MAVS	HTA11_9408_2000001011	Human	Colorectum	AD	8.16e-03	2.17e-01	0.0451
57506	MAVS	HTA11_7663_2000001011	Human	Colorectum	SER	8.30e-04	6.18e-01	0.0131
57506	MAVS	HTA11_99999973899_84307	Human	Colorectum	MSS	4.42e-02	5.61e-01	0.2585
57506	MAVS	HTA11_99999974143_84620	Human	Colorectum	MSS	1.06e-08	4.61e-01	0.3005
57506	MAVS	A002-C-010	Human	Colorectum	FAP	7.67e-04	-3.06e-01	0.242
57506	MAVS	A015-C-203	Human	Colorectum	FAP	1.62e-14	-1.09e-01	-0.1294
57506	MAVS	A002-C-201	Human	Colorectum	FAP	6.04e-05	-1.91e-01	0.0324
57506	MAVS	A001-C-108	Human	Colorectum	FAP	9.92e-10	-2.04e-01	-0.0272

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
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
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
Prostate		BPH: Benign Prostatic Hyperplasia
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:001907920	Oral cavity	OSCC	viral genome replication	95/7305	131/18723	6.35e-15	4.02e-13	95
GO:000961515	Oral cavity	OSCC	response to virus	215/7305	367/18723	1.63e-14	9.41e-13	215
GO:009031610	Oral cavity	OSCC	positive regulation of intracellular protein transport	110/7305	160/18723	2.10e-14	1.19e-12	110
GO:004312218	Oral cavity	OSCC	regulation of I-kappaB kinase/NF-kappaB signaling	155/7305	249/18723	7.79e-14	4.14e-12	155
GO:004682217	Oral cavity	OSCC	regulation of nucleocytoplasmic transport	79/7305	106/18723	1.04e-13	5.37e-12	79
GO:004312310	Oral cavity	OSCC	positive regulation of I-kappaB kinase/NF-kappaB signaling	122/7305	186/18723	1.68e-13	8.52e-12	122
GO:000724910	Oral cavity	OSCC	I-kappaB kinase/NF-kappaB signaling	169/7305	281/18723	4.69e-13	2.25e-11	169
GO:005079220	Oral cavity	OSCC	regulation of viral process	109/7305	164/18723	8.95e-13	4.10e-11	109
GO:190018210	Oral cavity	OSCC	positive regulation of protein localization to nucleus	66/7305	87/18723	2.74e-12	1.10e-10	66
GO:190018015	Oral cavity	OSCC	regulation of protein localization to nucleus	93/7305	136/18723	3.46e-12	1.35e-10	93
GO:190390020	Oral cavity	OSCC	regulation of viral life cycle	97/7305	148/18723	5.34e-11	1.67e-09	97
GO:00516074	Oral cavity	OSCC	defense response to virus	154/7305	265/18723	1.96e-10	5.63e-09	154
GO:01405464	Oral cavity	OSCC	defense response to symbiont	154/7305	265/18723	1.96e-10	5.63e-09	154
GO:004506917	Oral cavity	OSCC	regulation of viral genome replication	62/7305	85/18723	2.14e-10	6.04e-09	62
GO:00343405	Oral cavity	OSCC	response to type I interferon	46/7305	58/18723	4.17e-10	1.11e-08	46
GO:00603374	Oral cavity	OSCC	type I interferon signaling pathway	41/7305	50/18723	5.59e-10	1.46e-08	41
GO:00713574	Oral cavity	OSCC	cellular response to type I interferon	42/7305	52/18723	8.50e-10	2.13e-08	42
GO:00511709	Oral cavity	OSCC	import into nucleus	100/7305	159/18723	8.67e-10	2.15e-08	100
GO:00066069	Oral cavity	OSCC	protein import into nucleus	97/7305	155/18723	2.27e-09	5.30e-08	97
GO:00028317	Oral cavity	OSCC	regulation of response to biotic stimulus	177/7305	327/18723	1.73e-08	3.43e-07	177

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa05171	Colorectum	AD	Coronavirus disease - COVID-19	113/2092	232/8465	9.90e-16	2.55e-14	1.63e-14	113
hsa05160	Colorectum	AD	Hepatitis C	54/2092	157/8465	3.87e-03	1.96e-02	1.25e-02	54
hsa051711	Colorectum	AD	Coronavirus disease - COVID-19	113/2092	232/8465	9.90e-16	2.55e-14	1.63e-14	113
hsa051601	Colorectum	AD	Hepatitis C	54/2092	157/8465	3.87e-03	1.96e-02	1.25e-02	54
hsa051712	Colorectum	SER	Coronavirus disease - COVID-19	98/1580	232/8465	3.33e-17	8.50e-16	6.17e-16	98
hsa051713	Colorectum	SER	Coronavirus disease - COVID-19	98/1580	232/8465	3.33e-17	8.50e-16	6.17e-16	98
hsa051714	Colorectum	MSS	Coronavirus disease - COVID-19	108/1875	232/8465	6.50e-17	1.67e-15	1.03e-15	108
hsa051602	Colorectum	MSS	Hepatitis C	52/1875	157/8465	9.29e-04	5.58e-03	3.42e-03	52
hsa05169	Colorectum	MSS	Epstein-Barr virus infection	63/1875	202/8465	1.63e-03	8.98e-03	5.50e-03	63
hsa05161	Colorectum	MSS	Hepatitis B	48/1875	162/8465	1.53e-02	4.93e-02	3.02e-02	48
hsa051715	Colorectum	MSS	Coronavirus disease - COVID-19	108/1875	232/8465	6.50e-17	1.67e-15	1.03e-15	108
hsa051603	Colorectum	MSS	Hepatitis C	52/1875	157/8465	9.29e-04	5.58e-03	3.42e-03	52
hsa051691	Colorectum	MSS	Epstein-Barr virus infection	63/1875	202/8465	1.63e-03	8.98e-03	5.50e-03	63
hsa051611	Colorectum	MSS	Hepatitis B	48/1875	162/8465	1.53e-02	4.93e-02	3.02e-02	48
hsa051718	Colorectum	FAP	Coronavirus disease - COVID-19	78/1404	232/8465	9.94e-11	1.11e-08	6.73e-09	78
hsa051719	Colorectum	FAP	Coronavirus disease - COVID-19	78/1404	232/8465	9.94e-11	1.11e-08	6.73e-09	78
hsa0517110	Colorectum	CRC	Coronavirus disease - COVID-19	74/1091	232/8465	1.66e-14	2.78e-12	1.88e-12	74
hsa0517111	Colorectum	CRC	Coronavirus disease - COVID-19	74/1091	232/8465	1.66e-14	2.78e-12	1.88e-12	74
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

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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

MAVS

SNV

Missense_Mutation

novel

c.967C>A

p.Pro323Thr

p.P323T

Q7Z434

protein_coding

deleterious(0.02)

benign(0.047)

TCGA-A2-A0CP-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

MAVS

SNV

Missense_Mutation

novel

c.841N>G

p.Ile281Val

p.I281V

Q7Z434

protein_coding

tolerated(0.1)

benign(0)

TCGA-A2-A0YM-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

MAVS

SNV

Missense_Mutation

rs762014329

c.1460N>T

p.Ala487Val

p.A487V

Q7Z434

protein_coding

tolerated(0.18)

benign(0.087)

TCGA-AC-A62X-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

MAVS

SNV

Missense_Mutation

novel

c.1249G>C

p.Glu417Gln

p.E417Q

Q7Z434

protein_coding

deleterious(0.02)

possibly_damaging(0.728)

TCGA-E9-A3QA-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

MAVS

SNV

Missense_Mutation

novel

c.1216N>C

p.Asp406His

p.D406H

Q7Z434

protein_coding

deleterious(0)

probably_damaging(0.958)

TCGA-LL-A5YO-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

taxotere

MAVS

insertion

Frame_Shift_Ins

novel

c.965_966insCCCTCAGAAATATATAGTTGTCCATCTG

p.Ser324GlnfsTer15

p.S324Qfs*15

Q7Z434

protein_coding

TCGA-A2-A0CP-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

MAVS

SNV

Missense_Mutation

c.545N>G

p.Ser182Cys

p.S182C

Q7Z434

protein_coding

deleterious(0.04)

possibly_damaging(0.826)

TCGA-Q1-A73O-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

MAVS

SNV

Missense_Mutation

c.1438N>C

p.Glu480Gln

p.E480Q

Q7Z434

protein_coding

tolerated(0.22)

possibly_damaging(0.605)

TCGA-Q1-A73O-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

MAVS

SNV

Missense_Mutation

novel

c.835N>A

p.Glu279Lys

p.E279K

Q7Z434

protein_coding

tolerated(0.33)

benign(0.02)

TCGA-AA-3994-01

Colorectum

colon adenocarcinoma

Male

>=65

III/IV

Chemotherapy

capecitabine

MAVS

SNV

Missense_Mutation

c.1459N>A

p.Ala487Thr

p.A487T

Q7Z434

protein_coding

tolerated(0.27)

benign(0.034)

TCGA-AZ-4615-01

Colorectum

colon adenocarcinoma

Male

>=65

III/IV

Chemotherapy

xeloda

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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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