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: NFATC3

Gene summary for NFATC3

Gene summary.

Gene information	Species	Human
	Gene symbol	NFATC3
	Gene ID	4775
	Gene name	nuclear factor of activated T cells 3
	Gene Alias	NF-AT4c
	Cytomap	16q22.1
	Gene Type	protein-coding
	GO ID	GO:0000122
	UniProtAcc	B5B2S0

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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
4775	NFATC3	HTA11_3410_2000001011	Human	Colorectum	AD	1.69e-09	-4.47e-01	0.0155
4775	NFATC3	HTA11_3361_2000001011	Human	Colorectum	AD	8.35e-04	-5.21e-01	-0.1207
4775	NFATC3	HTA11_696_2000001011	Human	Colorectum	AD	2.75e-03	-2.68e-01	-0.1464
4775	NFATC3	HTA11_866_2000001011	Human	Colorectum	AD	1.37e-02	-2.69e-01	-0.1001
4775	NFATC3	HTA11_866_3004761011	Human	Colorectum	AD	1.41e-08	-4.96e-01	0.096
4775	NFATC3	HTA11_7696_3000711011	Human	Colorectum	AD	8.85e-12	-4.09e-01	0.0674
4775	NFATC3	HTA11_6818_2000001021	Human	Colorectum	AD	4.37e-03	-4.46e-01	0.0588
4775	NFATC3	HTA11_99999970781_79442	Human	Colorectum	MSS	1.41e-11	-4.16e-01	0.294
4775	NFATC3	HTA11_99999965104_69814	Human	Colorectum	MSS	4.61e-02	-1.97e-01	0.281
4775	NFATC3	HTA11_99999974143_84620	Human	Colorectum	MSS	2.16e-11	-4.60e-01	0.3005
4775	NFATC3	F007	Human	Colorectum	FAP	6.53e-03	-3.31e-01	0.1176
4775	NFATC3	A001-C-207	Human	Colorectum	FAP	3.41e-05	-3.05e-01	0.1278
4775	NFATC3	A015-C-203	Human	Colorectum	FAP	5.09e-31	-5.14e-01	-0.1294
4775	NFATC3	A015-C-204	Human	Colorectum	FAP	6.59e-04	-2.87e-01	-0.0228
4775	NFATC3	A014-C-040	Human	Colorectum	FAP	5.45e-07	-6.31e-01	-0.1184
4775	NFATC3	A002-C-201	Human	Colorectum	FAP	9.20e-16	-4.68e-01	0.0324
4775	NFATC3	A002-C-203	Human	Colorectum	FAP	5.10e-04	-2.34e-01	0.2786
4775	NFATC3	A001-C-119	Human	Colorectum	FAP	5.82e-06	-2.81e-01	-0.1557
4775	NFATC3	A001-C-108	Human	Colorectum	FAP	2.03e-18	-3.85e-01	-0.0272
4775	NFATC3	A002-C-205	Human	Colorectum	FAP	1.18e-19	-4.53e-01	-0.1236

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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
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:0061614	Colorectum	AD	pri-miRNA transcription by RNA polymerase II	24/3918	55/18723	1.22e-04	1.78e-03	24
GO:1902893	Colorectum	AD	regulation of pri-miRNA transcription by RNA polymerase II	23/3918	54/18723	2.60e-04	3.25e-03	23
GO:00616142	Colorectum	MSS	pri-miRNA transcription by RNA polymerase II	19/3467	55/18723	3.47e-03	2.59e-02	19
GO:19028932	Colorectum	MSS	regulation of pri-miRNA transcription by RNA polymerase II	18/3467	54/18723	6.70e-03	4.38e-02	18
GO:00616143	Colorectum	FAP	pri-miRNA transcription by RNA polymerase II	21/2622	55/18723	7.50e-06	2.25e-04	21
GO:19028933	Colorectum	FAP	regulation of pri-miRNA transcription by RNA polymerase II	20/2622	54/18723	2.09e-05	5.05e-04	20
GO:0048016	Colorectum	FAP	inositol phosphate-mediated signaling	16/2622	55/18723	2.78e-03	2.15e-02	16
GO:1902894	Colorectum	FAP	negative regulation of pri-miRNA transcription by RNA polymerase II	7/2622	17/18723	5.62e-03	3.61e-02	7
GO:00616144	Colorectum	CRC	pri-miRNA transcription by RNA polymerase II	18/2078	55/18723	1.53e-05	4.70e-04	18
GO:19028934	Colorectum	CRC	regulation of pri-miRNA transcription by RNA polymerase II	17/2078	54/18723	4.62e-05	1.10e-03	17
GO:19028941	Colorectum	CRC	negative regulation of pri-miRNA transcription by RNA polymerase II	7/2078	17/18723	1.46e-03	1.57e-02	7
GO:0097720	Colorectum	CRC	calcineurin-mediated signaling	13/2078	48/18723	1.72e-03	1.77e-02	13
GO:0033173	Colorectum	CRC	calcineurin-NFAT signaling cascade	12/2078	43/18723	1.93e-03	1.96e-02	12
GO:00480161	Colorectum	CRC	inositol phosphate-mediated signaling	14/2078	55/18723	2.21e-03	2.15e-02	14
GO:00616146	Liver	NAFLD	pri-miRNA transcription by RNA polymerase II	13/1882	55/18723	2.64e-03	2.42e-02	13
GO:19028936	Liver	NAFLD	regulation of pri-miRNA transcription by RNA polymerase II	12/1882	54/18723	6.44e-03	4.69e-02	12
GO:006161412	Liver	Cirrhotic	pri-miRNA transcription by RNA polymerase II	22/4634	55/18723	8.94e-03	4.12e-02	22
GO:006161422	Liver	HCC	pri-miRNA transcription by RNA polymerase II	35/7958	55/18723	1.26e-03	6.92e-03	35
GO:190289312	Liver	HCC	regulation of pri-miRNA transcription by RNA polymerase II	34/7958	54/18723	1.92e-03	9.78e-03	34
GO:19028942	Liver	HCC	negative regulation of pri-miRNA transcription by RNA polymerase II	13/7958	17/18723	4.77e-03	2.02e-02	13

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0517010	Lung	IAC	Human immunodeficiency virus 1 infection	40/1053	212/8465	4.26e-03	2.00e-02	1.33e-02	40
hsa043608	Lung	IAC	Axon guidance	34/1053	182/8465	9.31e-03	3.62e-02	2.41e-02	34
hsa0421813	Lung	IAC	Cellular senescence	40/1053	156/8465	4.44e-06	1.44e-04	9.59e-05	40
hsa0516717	Lung	IAC	Kaposi sarcoma-associated herpesvirus infection	46/1053	194/8465	8.58e-06	2.14e-04	1.42e-04	46
hsa0541717	Lung	IAC	Lipid and atherosclerosis	48/1053	215/8465	3.02e-05	6.14e-04	4.08e-04	48
hsa0516617	Lung	IAC	Human T-cell leukemia virus 1 infection	49/1053	222/8465	3.44e-05	6.38e-04	4.24e-04	49
hsa0401011	Lung	IAC	MAPK signaling pathway	62/1053	302/8465	3.54e-05	6.38e-04	4.24e-04	62
hsa0431011	Lung	IAC	Wnt signaling pathway	40/1053	171/8465	4.56e-05	7.06e-04	4.69e-04	40
hsa0516315	Lung	IAC	Human cytomegalovirus infection	47/1053	225/8465	2.01e-04	2.42e-03	1.61e-03	47
hsa0513515	Lung	IAC	Yersinia infection	32/1053	137/8465	2.63e-04	2.76e-03	1.83e-03	32
hsa046251	Lung	IAC	C-type lectin receptor signaling pathway	26/1053	104/8465	3.15e-04	3.11e-03	2.06e-03	26
hsa046591	Lung	IAC	Th17 cell differentiation	26/1053	108/8465	5.91e-04	5.34e-03	3.54e-03	26
hsa049211	Lung	IAC	Oxytocin signaling pathway	33/1053	154/8465	1.09e-03	7.82e-03	5.19e-03	33
hsa046601	Lung	IAC	T cell receptor signaling pathway	23/1053	104/8465	3.88e-03	1.88e-02	1.25e-02	23
hsa0517013	Lung	IAC	Human immunodeficiency virus 1 infection	40/1053	212/8465	4.26e-03	2.00e-02	1.33e-02	40
hsa0436011	Lung	IAC	Axon guidance	34/1053	182/8465	9.31e-03	3.62e-02	2.41e-02	34
hsa0431021	Lung	AIS	Wnt signaling pathway	39/961	171/8465	1.29e-05	3.32e-04	2.12e-04	39
hsa0541723	Lung	AIS	Lipid and atherosclerosis	46/961	215/8465	1.33e-05	3.32e-04	2.12e-04	46
hsa0421823	Lung	AIS	Cellular senescence	35/961	156/8465	5.09e-05	7.85e-04	5.03e-04	35
hsa0401021	Lung	AIS	MAPK signaling pathway	57/961	302/8465	6.41e-05	9.43e-04	6.03e-04	57

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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

TF	Cell Type	Tissue	Disease Stage	Target Gene	RSS	Regulon Activity
NFATC3	MAST	Colorectum	AD	RPS6KA5,UBA6-AS1,PRELID2, etc.	2.43e-01
NFATC3	TH1	Endometrium	ADJ	SMAGP,AC006064.2,S1PR1, etc.	8.94e-03
NFATC3	CD8TEFF	Endometrium	Healthy	SMAGP,AC006064.2,S1PR1, etc.	2.68e-02
NFATC3	BMEM	Endometrium	Healthy	SMAGP,AC006064.2,S1PR1, etc.	1.43e-01
NFATC3	BMEM	Liver	NAFLD	ZSCAN5A,AC116366.3,BICRAL, etc.	9.23e-02
NFATC3	AT1	Lung	Healthy	HAX1,CLDN18,ADIRF, etc.	1.30e-01
NFATC3	NK	Lung	IAC	BRWD3,TMEM14A,SBNO1, etc.	4.77e-02
NFATC3	CD4TN	Lung	IAC	BRWD3,TMEM14A,SBNO1, etc.	2.11e-01
NFATC3	CD8TEFF	Lung	MIAC	PPM1D,SAMD3,CCND3, etc.	9.86e-02
NFATC3	CD8TCM	Lung	MIAC	PPM1D,SAMD3,CCND3, etc.	3.66e-02

∗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

NFATC3

SNV

Missense_Mutation

novel

c.208N>T

p.His70Tyr

p.H70Y

Q12968

protein_coding

deleterious(0.03)

benign(0.041)

TCGA-5L-AAT1-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Hormone Therapy

letrozol

NFATC3

SNV

Missense_Mutation

c.1440G>T

p.Met480Ile

p.M480I

Q12968

protein_coding

tolerated(0.35)

benign(0.101)

TCGA-A2-A25A-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unspecific

Cytoxan

NFATC3

SNV

Missense_Mutation

novel

c.605N>T

p.Arg202Leu

p.R202L

Q12968

protein_coding

deleterious(0)

probably_damaging(0.991)

TCGA-A7-A26F-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

taxotere

NFATC3

SNV

Missense_Mutation

rs772602157

c.1652G>A

p.Arg551Gln

p.R551Q

Q12968

protein_coding

deleterious(0.01)

probably_damaging(0.996)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

NFATC3

SNV

Missense_Mutation

c.301N>C

p.Gly101Arg

p.G101R

Q12968

protein_coding

deleterious(0)

benign(0.244)

TCGA-AN-A0XN-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Unknown

NFATC3

SNV

Missense_Mutation

c.2125G>C

p.Glu709Gln

p.E709Q

Q12968

protein_coding

deleterious(0.01)

benign(0.358)

TCGA-BH-A0DZ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

docetaxel

NFATC3

SNV

Missense_Mutation

c.2314G>A

p.Glu772Lys

p.E772K

Q12968

protein_coding

tolerated_low_confidence(0.98)

benign(0.098)

TCGA-BH-A0DZ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

docetaxel

NFATC3

SNV

Missense_Mutation

c.1970N>A

p.Gly657Glu

p.G657E

Q12968

protein_coding

tolerated(0.9)

benign(0.027)

TCGA-E2-A1IH-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

aromasin

NFATC3

SNV

Missense_Mutation

novel

c.3076A>T

p.Ile1026Phe

p.I1026F

Q12968

protein_coding

deleterious_low_confidence(0)

benign(0.386)

TCGA-E2-A574-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

NFATC3

insertion

Frame_Shift_Ins

novel

c.2625_2626insT

p.Leu876SerfsTer25

p.L876Sfs*25

Q12968

protein_coding

TCGA-A8-A08Z-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Unknown

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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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