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: SWAP70

Gene summary for SWAP70

Gene summary.

Gene information	Species	Human
	Gene symbol	SWAP70
	Gene ID	23075
	Gene name	switching B cell complex subunit SWAP70
	Gene Alias	HSPC321
	Cytomap	11p15.4
	Gene Type	protein-coding
	GO ID	GO:0001775
	UniProtAcc	B3KUB9

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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
23075	SWAP70	LZE4T	Human	Esophagus	ESCC	1.30e-08	2.96e-01	0.0811
23075	SWAP70	LZE5T	Human	Esophagus	ESCC	4.41e-02	2.54e-01	0.0514
23075	SWAP70	LZE8T	Human	Esophagus	ESCC	2.85e-05	2.63e-01	0.067
23075	SWAP70	LZE20T	Human	Esophagus	ESCC	2.57e-04	1.41e-01	0.0662
23075	SWAP70	LZE22T	Human	Esophagus	ESCC	6.46e-04	3.29e-01	0.068
23075	SWAP70	LZE24T	Human	Esophagus	ESCC	6.62e-20	4.52e-01	0.0596
23075	SWAP70	P1T-E	Human	Esophagus	ESCC	9.01e-07	4.38e-01	0.0875
23075	SWAP70	P2T-E	Human	Esophagus	ESCC	5.64e-26	5.06e-01	0.1177
23075	SWAP70	P4T-E	Human	Esophagus	ESCC	8.86e-14	2.20e-01	0.1323
23075	SWAP70	P5T-E	Human	Esophagus	ESCC	4.16e-13	1.76e-01	0.1327
23075	SWAP70	P8T-E	Human	Esophagus	ESCC	3.91e-10	1.79e-01	0.0889
23075	SWAP70	P9T-E	Human	Esophagus	ESCC	4.11e-08	3.60e-01	0.1131
23075	SWAP70	P10T-E	Human	Esophagus	ESCC	3.68e-29	6.87e-01	0.116
23075	SWAP70	P11T-E	Human	Esophagus	ESCC	5.42e-07	6.26e-01	0.1426
23075	SWAP70	P12T-E	Human	Esophagus	ESCC	4.56e-04	1.89e-01	0.1122
23075	SWAP70	P15T-E	Human	Esophagus	ESCC	2.27e-24	5.72e-01	0.1149
23075	SWAP70	P16T-E	Human	Esophagus	ESCC	3.42e-14	2.94e-01	0.1153
23075	SWAP70	P17T-E	Human	Esophagus	ESCC	4.79e-08	4.60e-01	0.1278
23075	SWAP70	P20T-E	Human	Esophagus	ESCC	1.75e-18	4.47e-01	0.1124
23075	SWAP70	P21T-E	Human	Esophagus	ESCC	1.49e-12	3.99e-01	0.1617

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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
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
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:0022411111	Esophagus	ESCC	cellular component disassembly	305/8552	443/18723	1.94e-23	4.57e-21	305
GO:0010563111	Esophagus	ESCC	negative regulation of phosphorus metabolic process	274/8552	442/18723	2.32e-12	9.41e-11	274
GO:0045936111	Esophagus	ESCC	negative regulation of phosphate metabolic process	273/8552	441/18723	3.18e-12	1.25e-10	273
GO:003298416	Esophagus	ESCC	protein-containing complex disassembly	151/8552	224/18723	3.45e-11	1.15e-09	151
GO:1902905111	Esophagus	ESCC	positive regulation of supramolecular fiber organization	142/8552	209/18723	5.51e-11	1.76e-09	142
GO:1902903111	Esophagus	ESCC	regulation of supramolecular fiber organization	237/8552	383/18723	9.06e-11	2.75e-09	237
GO:0010639110	Esophagus	ESCC	negative regulation of organelle organization	215/8552	348/18723	8.20e-10	2.01e-08	215
GO:001631110	Esophagus	ESCC	dephosphorylation	251/8552	417/18723	1.26e-09	2.99e-08	251
GO:005149520	Esophagus	ESCC	positive regulation of cytoskeleton organization	147/8552	226/18723	2.93e-09	6.38e-08	147
GO:000647018	Esophagus	ESCC	protein dephosphorylation	177/8552	281/18723	3.13e-09	6.72e-08	177
GO:000701527	Esophagus	ESCC	actin filament organization	259/8552	442/18723	2.37e-08	4.50e-07	259
GO:003253520	Esophagus	ESCC	regulation of cellular component size	227/8552	383/18723	4.77e-08	8.60e-07	227
GO:0035304111	Esophagus	ESCC	regulation of protein dephosphorylation	66/8552	90/18723	8.82e-08	1.48e-06	66
GO:0035303111	Esophagus	ESCC	regulation of dephosphorylation	88/8552	128/18723	1.04e-07	1.71e-06	88
GO:0032970111	Esophagus	ESCC	regulation of actin filament-based process	231/8552	397/18723	2.91e-07	4.20e-06	231
GO:0032956111	Esophagus	ESCC	regulation of actin cytoskeleton organization	210/8552	358/18723	4.40e-07	6.00e-06	210
GO:011005327	Esophagus	ESCC	regulation of actin filament organization	166/8552	278/18723	1.54e-06	1.85e-05	166
GO:005101727	Esophagus	ESCC	actin filament bundle assembly	100/8552	157/18723	3.87e-06	4.17e-05	100
GO:006157227	Esophagus	ESCC	actin filament bundle organization	101/8552	161/18723	9.22e-06	8.82e-05	101
GO:000815420	Esophagus	ESCC	actin polymerization or depolymerization	130/8552	218/18723	2.19e-05	1.88e-04	130

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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

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

SWAP70

SNV

Missense_Mutation

c.1300N>C

p.Glu434Gln

p.E434Q

Q9UH65

protein_coding

tolerated(0.68)

benign(0.079)

TCGA-A2-A0EQ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

SWAP70

SNV

Missense_Mutation

c.1174G>A

p.Glu392Lys

p.E392K

Q9UH65

protein_coding

tolerated(0.32)

probably_damaging(0.994)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SWAP70

SNV

Missense_Mutation

c.407N>T

p.Ser136Leu

p.S136L

Q9UH65

protein_coding

tolerated(0.11)

benign(0.001)

TCGA-B6-A0RV-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

SWAP70

insertion

In_Frame_Ins

novel

c.670_671insCCTTACTTCTTT

p.Arg224delinsProLeuLeuLeuTrp

p.R224delinsPLLLW

Q9UH65

protein_coding

TCGA-S3-AA17-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

anastrozole

SWAP70

insertion

In_Frame_Ins

novel

c.671_672insCATGATTACCCCGTGCTGCCCCCTGATGCT

p.Arg224_Lys225insMetIleThrProCysCysProLeuMetLeu

p.R224_K225insMITPCCPLML

Q9UH65

protein_coding

TCGA-S3-AA17-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

anastrozole

SWAP70

SNV

Missense_Mutation

c.763N>T

p.Leu255Phe

p.L255F

Q9UH65

protein_coding

tolerated(0.71)

benign(0)

TCGA-EK-A3GM-01

Cervix

cervical & endocervical cancer

Female

>=65

I/II

Unknown

SWAP70

SNV

Missense_Mutation

rs756309764

c.670N>T

p.Arg224Trp

p.R224W

Q9UH65

protein_coding

deleterious(0)

probably_damaging(0.995)

TCGA-A6-6653-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

SWAP70

SNV

Missense_Mutation

novel

c.879G>T

p.Lys293Asn

p.K293N

Q9UH65

protein_coding

deleterious(0.01)

probably_damaging(0.971)

TCGA-AA-A00N-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

SWAP70

SNV

Missense_Mutation

c.1310G>A

p.Arg437Lys

p.R437K

Q9UH65

protein_coding

tolerated(0.64)

benign(0)

TCGA-G4-6628-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

SWAP70

SNV

Missense_Mutation

novel

c.715A>C

p.Ile239Leu

p.I239L

Q9UH65

protein_coding

tolerated(1)

benign(0.007)

TCGA-A5-A0G1-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

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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