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: SFSWAP

Gene summary for SFSWAP

Gene summary.

Gene information	Species	Human
	Gene symbol	SFSWAP
	Gene ID	6433
	Gene name	splicing factor SWAP
	Gene Alias	SFRS8
	Cytomap	12q24.33
	Gene Type	protein-coding
	GO ID	GO:0000245
	UniProtAcc	Q12872

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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
6433	SFSWAP	C57	Human	Oral cavity	OSCC	1.08e-03	2.19e-01	0.1679
6433	SFSWAP	C06	Human	Oral cavity	OSCC	6.95e-03	6.38e-01	0.2699
6433	SFSWAP	C08	Human	Oral cavity	OSCC	8.32e-10	3.06e-01	0.1919
6433	SFSWAP	LN22	Human	Oral cavity	OSCC	2.26e-04	9.09e-01	0.1733
6433	SFSWAP	LN46	Human	Oral cavity	OSCC	3.24e-03	2.81e-01	0.1666
6433	SFSWAP	EOLP-1	Human	Oral cavity	EOLP	1.20e-09	2.02e-01	-0.0202
6433	SFSWAP	NEOLP-3	Human	Oral cavity	NEOLP	5.46e-03	1.32e-01	-0.0191
6433	SFSWAP	SYSMH1	Human	Oral cavity	OSCC	1.86e-17	3.45e-01	0.1127
6433	SFSWAP	SYSMH2	Human	Oral cavity	OSCC	3.39e-22	6.61e-01	0.2326
6433	SFSWAP	SYSMH3	Human	Oral cavity	OSCC	7.72e-27	6.22e-01	0.2442
6433	SFSWAP	SYSMH4	Human	Oral cavity	OSCC	2.00e-04	5.96e-02	0.1226
6433	SFSWAP	SYSMH5	Human	Oral cavity	OSCC	2.63e-07	2.31e-01	0.0647
6433	SFSWAP	SYSMH6	Human	Oral cavity	OSCC	4.51e-05	1.96e-01	0.1275
6433	SFSWAP	P1_S1_AK	Human	Skin	AK	1.66e-06	2.62e-01	-0.3399
6433	SFSWAP	P2_S3_AK	Human	Skin	AK	6.90e-05	2.20e-01	-0.3287
6433	SFSWAP	P4_S8_cSCC	Human	Skin	cSCC	5.53e-15	3.20e-01	-0.3095
6433	SFSWAP	P5_S10_cSCC	Human	Skin	cSCC	2.43e-11	2.28e-01	-0.299
6433	SFSWAP	P1_cSCC	Human	Skin	cSCC	2.69e-20	6.61e-01	0.0292
6433	SFSWAP	P2_cSCC	Human	Skin	cSCC	3.72e-12	3.70e-01	-0.024
6433	SFSWAP	P4_cSCC	Human	Skin	cSCC	7.14e-18	4.76e-01	-0.00290000000000005

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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
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:0022613111	Esophagus	ESCC	ribonucleoprotein complex biogenesis	365/8552	463/18723	1.74e-49	1.11e-45	365
GO:0008380111	Esophagus	ESCC	RNA splicing	336/8552	434/18723	1.74e-42	3.67e-39	336
GO:0000375111	Esophagus	ESCC	RNA splicing, via transesterification reactions	248/8552	324/18723	3.05e-30	1.49e-27	248
GO:0000377111	Esophagus	ESCC	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	244/8552	320/18723	2.52e-29	1.07e-26	244
GO:0000398111	Esophagus	ESCC	mRNA splicing, via spliceosome	244/8552	320/18723	2.52e-29	1.07e-26	244
GO:1903311110	Esophagus	ESCC	regulation of mRNA metabolic process	210/8552	288/18723	3.25e-21	5.56e-19	210
GO:0071826111	Esophagus	ESCC	ribonucleoprotein complex subunit organization	166/8552	227/18723	2.94e-17	2.42e-15	166
GO:0043484111	Esophagus	ESCC	regulation of RNA splicing	116/8552	148/18723	3.18e-16	2.38e-14	116
GO:0050684110	Esophagus	ESCC	regulation of mRNA processing	109/8552	137/18723	3.51e-16	2.59e-14	109
GO:0022618111	Esophagus	ESCC	ribonucleoprotein complex assembly	159/8552	220/18723	8.19e-16	5.71e-14	159
GO:0048024111	Esophagus	ESCC	regulation of mRNA splicing, via spliceosome	78/8552	101/18723	8.72e-11	2.66e-09	78
GO:005068615	Esophagus	ESCC	negative regulation of mRNA processing	26/8552	29/18723	8.98e-07	1.15e-05	26
GO:000038019	Esophagus	ESCC	alternative mRNA splicing, via spliceosome	55/8552	77/18723	4.07e-06	4.38e-05	55
GO:0033119111	Esophagus	ESCC	negative regulation of RNA splicing	22/8552	25/18723	1.33e-05	1.21e-04	22
GO:1903312111	Esophagus	ESCC	negative regulation of mRNA metabolic process	62/8552	92/18723	2.08e-05	1.80e-04	62
GO:004802517	Esophagus	ESCC	negative regulation of mRNA splicing, via spliceosome	17/8552	20/18723	3.43e-04	2.01e-03	17
GO:000024514	Esophagus	ESCC	spliceosomal complex assembly	48/8552	79/18723	4.93e-03	1.89e-02	48
GO:002261322	Liver	HCC	ribonucleoprotein complex biogenesis	355/7958	463/18723	7.76e-52	4.92e-48	355
GO:000838022	Liver	HCC	RNA splicing	313/7958	434/18723	1.36e-36	1.73e-33	313
GO:000037522	Liver	HCC	RNA splicing, via transesterification reactions	228/7958	324/18723	1.47e-24	4.06e-22	228

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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

SFSWAP

SNV

Missense_Mutation

novel

c.1058C>G

p.Ser353Cys

p.S353C

Q12872

protein_coding

deleterious(0.01)

possibly_damaging(0.741)

TCGA-A8-A07U-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Chemotherapy

5-fluorouracil

SFSWAP

SNV

Missense_Mutation

c.1903G>C

p.Glu635Gln

p.E635Q

Q12872

protein_coding

deleterious(0.01)

probably_damaging(0.996)

TCGA-AN-A0XW-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

SFSWAP

SNV

Missense_Mutation

novel

c.1015A>T

p.Thr339Ser

p.T339S

Q12872

protein_coding

tolerated(0.48)

benign(0.007)

TCGA-AR-A256-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

SFSWAP

SNV

Missense_Mutation

novel

c.1136G>T

p.Cys379Phe

p.C379F

Q12872

protein_coding

deleterious(0.01)

probably_damaging(0.997)

TCGA-B6-A2IU-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

SFSWAP

SNV

Missense_Mutation

novel

c.865N>A

p.Asp289Asn

p.D289N

Q12872

protein_coding

deleterious(0.03)

probably_damaging(0.962)

TCGA-D8-A1J8-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

nolvadex

SFSWAP

SNV

Missense_Mutation

c.1903N>A

p.Glu635Lys

p.E635K

Q12872

protein_coding

deleterious(0.04)

probably_damaging(0.99)

TCGA-D8-A1J8-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

nolvadex

SFSWAP

SNV

Missense_Mutation

novel

c.204N>T

p.Lys68Asn

p.K68N

Q12872

protein_coding

tolerated(0.33)

benign(0.054)

TCGA-E2-A1IK-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

SFSWAP

SNV

Missense_Mutation

c.1157N>A

p.Gly386Glu

p.G386E

Q12872

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-EW-A1J5-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

SFSWAP

insertion

Frame_Shift_Ins

novel

c.1704_1705insATATTTTTGCCATCTCCTAATAAAGA

p.Gly569IlefsTer13

p.G569Ifs*13

Q12872

protein_coding

TCGA-AN-A049-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

SFSWAP

insertion

Nonsense_Mutation

novel

c.2939_2940insAGTATAA

p.Thr981ValfsTer2

p.T981Vfs*2

Q12872

protein_coding

TCGA-AN-A0FX-01

Breast

breast invasive 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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