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: NOS1

Gene summary for NOS1

Gene summary.

Gene information	Species	Human
	Gene symbol	NOS1
	Gene ID	4842
	Gene name	nitric oxide synthase 1
	Gene Alias	IHPS1
	Cytomap	12q24.22
	Gene Type	protein-coding
	GO ID	GO:0000768
	UniProtAcc	A0PJJ7

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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
4842	NOS1	P1T-E	Human	Esophagus	ESCC	2.30e-04	4.03e-01	0.0875
4842	NOS1	P2T-E	Human	Esophagus	ESCC	1.92e-10	1.38e-01	0.1177
4842	NOS1	P12T-E	Human	Esophagus	ESCC	6.56e-11	1.23e-01	0.1122
4842	NOS1	P20T-E	Human	Esophagus	ESCC	1.45e-06	2.15e-01	0.1124
4842	NOS1	P21T-E	Human	Esophagus	ESCC	6.27e-14	2.52e-01	0.1617
4842	NOS1	P23T-E	Human	Esophagus	ESCC	2.67e-03	1.71e-01	0.108
4842	NOS1	P27T-E	Human	Esophagus	ESCC	2.79e-05	3.74e-02	0.1055
4842	NOS1	P28T-E	Human	Esophagus	ESCC	4.14e-05	5.92e-02	0.1149
4842	NOS1	P31T-E	Human	Esophagus	ESCC	5.57e-18	1.34e-01	0.1251
4842	NOS1	P47T-E	Human	Esophagus	ESCC	8.95e-04	2.68e-02	0.1067
4842	NOS1	P54T-E	Human	Esophagus	ESCC	5.11e-16	4.16e-01	0.0975
4842	NOS1	P62T-E	Human	Esophagus	ESCC	2.15e-25	5.09e-01	0.1302
4842	NOS1	P75T-E	Human	Esophagus	ESCC	2.42e-26	7.44e-01	0.1125
4842	NOS1	P76T-E	Human	Esophagus	ESCC	1.92e-03	9.37e-03	0.1207
4842	NOS1	P79T-E	Human	Esophagus	ESCC	5.13e-04	2.69e-02	0.1154
4842	NOS1	P80T-E	Human	Esophagus	ESCC	1.91e-21	8.61e-01	0.155
4842	NOS1	P82T-E	Human	Esophagus	ESCC	8.20e-09	4.57e-01	0.1072
4842	NOS1	P84T-E	Human	Esophagus	ESCC	1.34e-05	3.04e-01	0.0933
4842	NOS1	P107T-E	Human	Esophagus	ESCC	1.10e-10	2.16e-01	0.171
4842	NOS1	P127T-E	Human	Esophagus	ESCC	1.86e-18	3.18e-01	0.0826

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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

∗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:0098901	Colorectum	AD	regulation of cardiac muscle cell action potential	15/3918	27/18723	8.20e-05	1.29e-03	15
GO:0006809	Colorectum	AD	nitric oxide biosynthetic process	30/3918	76/18723	1.72e-04	2.33e-03	30
GO:0030048	Colorectum	AD	actin filament-based movement	44/3918	127/18723	2.31e-04	2.99e-03	44
GO:0046209	Colorectum	AD	nitric oxide metabolic process	31/3918	81/18723	2.61e-04	3.25e-03	31
GO:2001057	Colorectum	AD	reactive nitrogen species metabolic process	31/3918	82/18723	3.37e-04	3.94e-03	31
GO:0045429	Colorectum	AD	positive regulation of nitric oxide biosynthetic process	17/3918	40/18723	1.66e-03	1.38e-02	17
GO:1904407	Colorectum	AD	positive regulation of nitric oxide metabolic process	17/3918	41/18723	2.29e-03	1.79e-02	17
GO:0099173	Colorectum	AD	postsynapse organization	51/3918	168/18723	2.47e-03	1.90e-02	51
GO:0080164	Colorectum	AD	regulation of nitric oxide metabolic process	23/3918	64/18723	3.99e-03	2.80e-02	23
GO:0050808	Colorectum	AD	synapse organization	112/3918	426/18723	4.25e-03	2.92e-02	112
GO:0098974	Colorectum	AD	postsynaptic actin cytoskeleton organization	7/3918	12/18723	5.09e-03	3.38e-02	7
GO:0045428	Colorectum	AD	regulation of nitric oxide biosynthetic process	22/3918	62/18723	5.72e-03	3.64e-02	22
GO:0051353	Colorectum	AD	positive regulation of oxidoreductase activity	21/3918	59/18723	6.58e-03	4.08e-02	21
GO:0032411	Colorectum	AD	positive regulation of transporter activity	37/3918	120/18723	6.82e-03	4.22e-02	37
GO:00068091	Colorectum	SER	nitric oxide biosynthetic process	27/2897	76/18723	1.38e-05	4.28e-04	27
GO:00462091	Colorectum	SER	nitric oxide metabolic process	28/2897	81/18723	1.73e-05	5.15e-04	28
GO:20010571	Colorectum	SER	reactive nitrogen species metabolic process	28/2897	82/18723	2.24e-05	6.43e-04	28
GO:00300481	Colorectum	SER	actin filament-based movement	38/2897	127/18723	2.80e-05	7.56e-04	38
GO:00991731	Colorectum	SER	postsynapse organization	46/2897	168/18723	5.20e-05	1.25e-03	46
GO:00989011	Colorectum	SER	regulation of cardiac muscle cell action potential	12/2897	27/18723	3.27e-04	5.22e-03	12

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa05014210	Esophagus	ESCC	Amyotrophic lateral sclerosis	266/4205	364/8465	1.31e-20	2.20e-18	1.13e-18	266
hsa05022210	Esophagus	ESCC	Pathways of neurodegeneration - multiple diseases	318/4205	476/8465	6.10e-15	2.04e-13	1.05e-13	318
hsa05010210	Esophagus	ESCC	Alzheimer disease	263/4205	384/8465	1.80e-14	5.47e-13	2.80e-13	263
hsa0414530	Esophagus	ESCC	Phagosome	100/4205	152/8465	3.81e-05	1.72e-04	8.82e-05	100
hsa049268	Esophagus	ESCC	Relaxin signaling pathway	81/4205	129/8465	1.72e-03	5.09e-03	2.61e-03	81
hsa0501438	Esophagus	ESCC	Amyotrophic lateral sclerosis	266/4205	364/8465	1.31e-20	2.20e-18	1.13e-18	266
hsa0502238	Esophagus	ESCC	Pathways of neurodegeneration - multiple diseases	318/4205	476/8465	6.10e-15	2.04e-13	1.05e-13	318
hsa0501038	Esophagus	ESCC	Alzheimer disease	263/4205	384/8465	1.80e-14	5.47e-13	2.80e-13	263
hsa04145114	Esophagus	ESCC	Phagosome	100/4205	152/8465	3.81e-05	1.72e-04	8.82e-05	100
hsa0492616	Esophagus	ESCC	Relaxin signaling pathway	81/4205	129/8465	1.72e-03	5.09e-03	2.61e-03	81
hsa0501422	Liver	HCC	Amyotrophic lateral sclerosis	252/4020	364/8465	8.85e-18	7.41e-16	4.12e-16	252
hsa0501022	Liver	HCC	Alzheimer disease	254/4020	384/8465	3.75e-14	8.97e-13	4.99e-13	254
hsa0502222	Liver	HCC	Pathways of neurodegeneration - multiple diseases	298/4020	476/8465	6.59e-12	1.30e-10	7.22e-11	298
hsa0414521	Liver	HCC	Phagosome	93/4020	152/8465	4.27e-04	1.88e-03	1.05e-03	93
hsa0033021	Liver	HCC	Arginine and proline metabolism	33/4020	50/8465	6.28e-03	1.77e-02	9.83e-03	33
hsa049262	Liver	HCC	Relaxin signaling pathway	75/4020	129/8465	9.33e-03	2.46e-02	1.37e-02	75
hsa0501432	Liver	HCC	Amyotrophic lateral sclerosis	252/4020	364/8465	8.85e-18	7.41e-16	4.12e-16	252
hsa0501032	Liver	HCC	Alzheimer disease	254/4020	384/8465	3.75e-14	8.97e-13	4.99e-13	254
hsa0502232	Liver	HCC	Pathways of neurodegeneration - multiple diseases	298/4020	476/8465	6.59e-12	1.30e-10	7.22e-11	298
hsa0414531	Liver	HCC	Phagosome	93/4020	152/8465	4.27e-04	1.88e-03	1.05e-03	93

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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

NOS1

SNV

Missense_Mutation

c.3037N>C

p.Val1013Leu

p.V1013L

P29475

protein_coding

tolerated(0.32)

benign(0)

TCGA-A8-A07R-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Ancillary

zoledronic

NOS1

SNV

Missense_Mutation

c.752N>A

p.Pro251His

p.P251H

P29475

protein_coding

tolerated_low_confidence(0.26)

benign(0.176)

TCGA-A8-A09Z-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

NOS1

SNV

Missense_Mutation

novel

c.703N>T

p.Asp235Tyr

p.D235Y

P29475

protein_coding

deleterious_low_confidence(0)

possibly_damaging(0.855)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

NOS1

SNV

Missense_Mutation

c.3001N>T

p.Arg1001Cys

p.R1001C

P29475

protein_coding

tolerated(0.19)

benign(0.018)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

NOS1

SNV

Missense_Mutation

rs150227193

c.2312N>T

p.Ser771Leu

p.S771L

P29475

protein_coding

deleterious(0)

probably_damaging(0.993)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

NOS1

SNV

Missense_Mutation

c.1244N>A

p.Arg415Gln

p.R415Q

P29475

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-AN-A0FY-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

NOS1

SNV

Missense_Mutation

c.228N>A

p.Ser76Arg

p.S76R

P29475

protein_coding

deleterious_low_confidence(0)

possibly_damaging(0.724)

TCGA-B6-A0I6-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

NOS1

SNV

Missense_Mutation

c.1243N>T

p.Arg415Trp

p.R415W

P29475

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-BH-A0B3-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cyclophosphamide

NOS1

SNV

Missense_Mutation

novel

c.1474N>A

p.Gln492Lys

p.Q492K

P29475

protein_coding

tolerated(0.1)

benign(0.432)

TCGA-BH-A0B6-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

NOS1

SNV

Missense_Mutation

rs200664091

c.2695N>A

p.Asp899Asn

p.D899N

P29475

protein_coding

tolerated(0.72)

benign(0.003)

TCGA-E2-A14S-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

cytoxan

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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
4842	NOS1	DRUGGABLE GENOME, ENZYME		ibuprofen	IBUPROFEN	25502615
4842	NOS1	DRUGGABLE GENOME, ENZYME		BENZODIAZEPINE	BENZODIAZEPINE	15136793
4842	NOS1	DRUGGABLE GENOME, ENZYME		SOY PROTEIN		15328066
4842	NOS1	DRUGGABLE GENOME, ENZYME		PRAZOSIN	PRAZOSIN	9322222
4842	NOS1	DRUGGABLE GENOME, ENZYME		DHT	ANDROSTANOLONE	10725371
4842	NOS1	DRUGGABLE GENOME, ENZYME		DHEA	PRASTERONE	16836960
4842	NOS1	DRUGGABLE GENOME, ENZYME		RETINOIC ACID		9635256
4842	NOS1	DRUGGABLE GENOME, ENZYME		DEXTRAN SULFATE SODIUM		15613746,17160477
4842	NOS1	DRUGGABLE GENOME, ENZYME		SALT	VOLANESORSEN SODIUM	11243307
4842	NOS1	DRUGGABLE GENOME, ENZYME		ANTI-INFLAMMATORY DRUGS		7827327

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