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: SMARCA5

Gene summary for SMARCA5

Gene summary.

Gene information	Species	Human
	Gene symbol	SMARCA5
	Gene ID	8467
	Gene name	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5
	Gene Alias	ISWI
	Cytomap	4q31.21
	Gene Type	protein-coding
	GO ID	GO:0000183
	UniProtAcc	O60264

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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
8467	SMARCA5	LZE4T	Human	Esophagus	ESCC	1.11e-15	6.04e-01	0.0811
8467	SMARCA5	LZE5T	Human	Esophagus	ESCC	2.00e-05	4.84e-01	0.0514
8467	SMARCA5	LZE7T	Human	Esophagus	ESCC	1.05e-06	4.66e-01	0.0667
8467	SMARCA5	LZE8T	Human	Esophagus	ESCC	2.74e-10	1.63e-01	0.067
8467	SMARCA5	LZE20T	Human	Esophagus	ESCC	4.08e-03	1.38e-01	0.0662
8467	SMARCA5	LZE22D1	Human	Esophagus	HGIN	1.72e-02	-6.99e-02	0.0595
8467	SMARCA5	LZE22T	Human	Esophagus	ESCC	3.39e-05	2.82e-01	0.068
8467	SMARCA5	LZE24T	Human	Esophagus	ESCC	2.66e-14	3.91e-01	0.0596
8467	SMARCA5	LZE21T	Human	Esophagus	ESCC	7.14e-10	2.76e-01	0.0655
8467	SMARCA5	LZE6T	Human	Esophagus	ESCC	4.32e-04	1.64e-01	0.0845
8467	SMARCA5	P1T-E	Human	Esophagus	ESCC	4.06e-13	4.37e-01	0.0875
8467	SMARCA5	P2T-E	Human	Esophagus	ESCC	7.10e-63	1.24e+00	0.1177
8467	SMARCA5	P4T-E	Human	Esophagus	ESCC	2.45e-33	8.01e-01	0.1323
8467	SMARCA5	P5T-E	Human	Esophagus	ESCC	3.06e-23	3.37e-01	0.1327
8467	SMARCA5	P8T-E	Human	Esophagus	ESCC	2.84e-25	5.80e-01	0.0889
8467	SMARCA5	P9T-E	Human	Esophagus	ESCC	7.93e-16	3.45e-01	0.1131
8467	SMARCA5	P10T-E	Human	Esophagus	ESCC	4.38e-27	6.61e-01	0.116
8467	SMARCA5	P11T-E	Human	Esophagus	ESCC	1.27e-24	9.45e-01	0.1426
8467	SMARCA5	P12T-E	Human	Esophagus	ESCC	3.65e-50	1.14e+00	0.1122
8467	SMARCA5	P15T-E	Human	Esophagus	ESCC	2.56e-33	8.48e-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
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:000632516	Esophagus	HGIN	chromatin organization	92/2587	409/18723	1.05e-06	4.16e-05	92
GO:00069975	Esophagus	HGIN	nucleus organization	34/2587	133/18723	2.20e-04	4.00e-03	34
GO:00063523	Esophagus	HGIN	DNA-templated transcription, initiation	30/2587	130/18723	2.86e-03	2.79e-02	30
GO:19908308	Esophagus	HGIN	cellular response to leukemia inhibitory factor	23/2587	94/18723	3.92e-03	3.54e-02	23
GO:19908238	Esophagus	HGIN	response to leukemia inhibitory factor	23/2587	95/18723	4.51e-03	3.93e-02	23
GO:000699713	Esophagus	ESCC	nucleus organization	96/8552	133/18723	4.66e-10	1.21e-08	96
GO:000632517	Esophagus	ESCC	chromatin organization	240/8552	409/18723	6.52e-08	1.14e-06	240
GO:00400295	Esophagus	ESCC	regulation of gene expression, epigenetic	74/8552	105/18723	2.24e-07	3.42e-06	74
GO:000635211	Esophagus	ESCC	DNA-templated transcription, initiation	86/8552	130/18723	1.88e-06	2.19e-05	86
GO:199082316	Esophagus	ESCC	response to leukemia inhibitory factor	60/8552	95/18723	4.41e-04	2.48e-03	60
GO:199083015	Esophagus	ESCC	cellular response to leukemia inhibitory factor	59/8552	94/18723	6.19e-04	3.32e-03	59
GO:00708281	Esophagus	ESCC	heterochromatin organization	31/8552	46/18723	2.42e-03	1.06e-02	31
GO:0045814	Esophagus	ESCC	negative regulation of gene expression, epigenetic	32/8552	50/18723	6.90e-03	2.52e-02	32
GO:0006997	Liver	Cirrhotic	nucleus organization	48/4634	133/18723	2.27e-03	1.38e-02	48
GO:00069971	Liver	HCC	nucleus organization	82/7958	133/18723	6.32e-06	7.72e-05	82
GO:0006352	Liver	HCC	DNA-templated transcription, initiation	78/7958	130/18723	4.19e-05	4.11e-04	78
GO:000632511	Liver	HCC	chromatin organization	206/7958	409/18723	7.23e-04	4.41e-03	206
GO:0040029	Liver	HCC	regulation of gene expression, epigenetic	61/7958	105/18723	9.02e-04	5.31e-03	61
GO:00069974	Oral cavity	OSCC	nucleus organization	85/7305	133/18723	5.12e-09	1.12e-07	85
GO:19908237	Oral cavity	OSCC	response to leukemia inhibitory factor	58/7305	95/18723	1.10e-05	1.14e-04	58

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Enriched KEGG pathways.

Pathway ID

Tissue

Disease Stage

Description

Gene Ratio

Bg Ratio

pvalue

p.adjust

qvalue

Count

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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
SMARCA5	CD4TN	Colorectum	Healthy	TRIM73,POLR3B,SF3B1, etc.	2.31e-02
SMARCA5	CD4TN	Colorectum	MSI-H	TRIM73,POLR3B,SF3B1, etc.	3.63e-02
SMARCA5	PERI	Colorectum	FAP	NUP50,MRNIP,FAM149A, etc.	4.93e-02
SMARCA5	ICAF	Colorectum	MSI-H	NUP50,MRNIP,FAM149A, etc.	2.63e-01
SMARCA5	iATC	Thyroid	Healthy	USP9X,MYOF,ISG20L2, etc.	7.48e-02
SMARCA5	TH1	Thyroid	ADJ	ITGA4,GOLGB1,SMC5, etc.	2.43e-02
SMARCA5	GC	Thyroid	ADJ	ITGA4,GOLGB1,SMC5, etc.	2.52e-03
SMARCA5	TH1	Thyroid	ATC	ITGA4,GOLGB1,SMC5, etc.	8.90e-02
SMARCA5	INMON	Thyroid	HT	ITGA4,GOLGB1,SMC5, etc.	3.61e-02
SMARCA5	M2MAC	Thyroid	HT	ITGA4,GOLGB1,SMC5, etc.	2.09e-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

SMARCA5

SNV

Missense_Mutation

c.2629N>G

p.Pro877Ala

p.P877A

O60264

protein_coding

tolerated(0.36)

benign(0)

TCGA-5L-AAT1-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Hormone Therapy

letrozol

SMARCA5

SNV

Missense_Mutation

c.1759N>A

p.Leu587Ile

p.L587I

O60264

protein_coding

deleterious(0)

possibly_damaging(0.812)

TCGA-A8-A07W-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Hormone Therapy

exemestane

SMARCA5

SNV

Missense_Mutation

novel

c.2105A>C

p.Asn702Thr

p.N702T

O60264

protein_coding

tolerated(0.07)

benign(0.022)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SMARCA5

SNV

Missense_Mutation

c.1034A>G

p.His345Arg

p.H345R

O60264

protein_coding

deleterious(0.04)

benign(0.444)

TCGA-AN-A0XU-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

SMARCA5

SNV

Missense_Mutation

c.2401N>T

p.Pro801Ser

p.P801S

O60264

protein_coding

tolerated(0.07)

benign(0.219)

TCGA-AR-A24S-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

anastrozole

SMARCA5

SNV

Missense_Mutation

novel

c.2562N>G

p.Ile854Met

p.I854M

O60264

protein_coding

deleterious(0.02)

possibly_damaging(0.868)

TCGA-XX-A89A-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SMARCA5

deletion

Frame_Shift_Del

novel

c.957delN

p.Lys319AsnfsTer5

p.K319Nfs*5

O60264

protein_coding

TCGA-D8-A27V-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

tamoxiphen

SMARCA5

SNV

Missense_Mutation

rs764115299

c.371G>A

p.Arg124His

p.R124H

O60264

protein_coding

tolerated(0.07)

benign(0.022)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

SMARCA5

SNV

Missense_Mutation

rs868118261

c.1817G>A

p.Arg606His

p.R606H

O60264

protein_coding

deleterious(0)

probably_damaging(0.987)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

SMARCA5

SNV

Missense_Mutation

rs749535799

c.2405G>A

p.Arg802Gln

p.R802Q

O60264

protein_coding

tolerated(0.37)

benign(0.011)

TCGA-2W-A8YY-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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