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: SART3

Gene summary for SART3

Gene summary.

Gene information	Species	Human
	Gene symbol	SART3
	Gene ID	9733
	Gene name	spliceosome associated factor 3, U4/U6 recycling protein
	Gene Alias	DSAP1
	Cytomap	12q23.3
	Gene Type	protein-coding
	GO ID	GO:0000244
	UniProtAcc	Q15020

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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
9733	SART3	LZE2T	Human	Esophagus	ESCC	6.99e-04	3.54e-01	0.082
9733	SART3	LZE4T	Human	Esophagus	ESCC	1.19e-12	2.84e-01	0.0811
9733	SART3	LZE7T	Human	Esophagus	ESCC	1.05e-06	3.70e-01	0.0667
9733	SART3	LZE24T	Human	Esophagus	ESCC	3.94e-11	2.81e-01	0.0596
9733	SART3	LZE21T	Human	Esophagus	ESCC	5.66e-03	2.39e-01	0.0655
9733	SART3	LZE6T	Human	Esophagus	ESCC	3.85e-04	2.20e-01	0.0845
9733	SART3	P1T-E	Human	Esophagus	ESCC	6.63e-03	2.34e-01	0.0875
9733	SART3	P2T-E	Human	Esophagus	ESCC	2.01e-41	7.64e-01	0.1177
9733	SART3	P4T-E	Human	Esophagus	ESCC	8.28e-15	3.82e-01	0.1323
9733	SART3	P5T-E	Human	Esophagus	ESCC	8.25e-09	1.82e-01	0.1327
9733	SART3	P8T-E	Human	Esophagus	ESCC	1.99e-12	2.75e-01	0.0889
9733	SART3	P9T-E	Human	Esophagus	ESCC	4.03e-08	1.08e-01	0.1131
9733	SART3	P10T-E	Human	Esophagus	ESCC	4.86e-14	2.79e-01	0.116
9733	SART3	P11T-E	Human	Esophagus	ESCC	1.52e-15	4.89e-01	0.1426
9733	SART3	P12T-E	Human	Esophagus	ESCC	1.94e-20	3.02e-01	0.1122
9733	SART3	P15T-E	Human	Esophagus	ESCC	1.25e-14	4.24e-01	0.1149
9733	SART3	P16T-E	Human	Esophagus	ESCC	3.32e-25	4.68e-01	0.1153
9733	SART3	P17T-E	Human	Esophagus	ESCC	6.69e-04	2.39e-01	0.1278
9733	SART3	P20T-E	Human	Esophagus	ESCC	8.28e-22	4.02e-01	0.1124
9733	SART3	P21T-E	Human	Esophagus	ESCC	3.48e-21	4.54e-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
Liver		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

∗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:001657015	Esophagus	ESCC	histone modification	323/8552	463/18723	2.61e-26	7.88e-24	323
GO:1903320111	Esophagus	ESCC	regulation of protein modification by small protein conjugation or removal	181/8552	242/18723	1.80e-20	2.60e-18	181
GO:0045862111	Esophagus	ESCC	positive regulation of proteolysis	256/8552	372/18723	7.88e-20	9.43e-18	256
GO:0071826111	Esophagus	ESCC	ribonucleoprotein complex subunit organization	166/8552	227/18723	2.94e-17	2.42e-15	166
GO:0022618111	Esophagus	ESCC	ribonucleoprotein complex assembly	159/8552	220/18723	8.19e-16	5.71e-14	159
GO:190332216	Esophagus	ESCC	positive regulation of protein modification by small protein conjugation or removal	99/8552	138/18723	4.39e-10	1.16e-08	99
GO:003105614	Esophagus	ESCC	regulation of histone modification	106/8552	152/18723	1.52e-09	3.55e-08	106
GO:000632517	Esophagus	ESCC	chromatin organization	240/8552	409/18723	6.52e-08	1.14e-06	240
GO:00310583	Esophagus	ESCC	positive regulation of histone modification	65/8552	92/18723	1.04e-06	1.31e-05	65
GO:0048872111	Esophagus	ESCC	homeostasis of number of cells	163/8552	272/18723	1.40e-06	1.69e-05	163
GO:007064612	Esophagus	ESCC	protein modification by small protein removal	95/8552	157/18723	1.25e-04	8.56e-04	95
GO:009008515	Esophagus	ESCC	regulation of protein deubiquitination	11/8552	12/18723	1.26e-03	6.06e-03	11
GO:00165783	Esophagus	ESCC	histone deubiquitination	18/8552	23/18723	1.50e-03	7.06e-03	18
GO:00165793	Esophagus	ESCC	protein deubiquitination	79/8552	139/18723	5.23e-03	1.97e-02	79
GO:00003875	Esophagus	ESCC	spliceosomal snRNP assembly	32/8552	50/18723	6.90e-03	2.52e-02	32

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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

SART3

SNV

Missense_Mutation

c.2214N>G

p.Ile738Met

p.I738M

Q15020

protein_coding

deleterious(0)

possibly_damaging(0.839)

TCGA-A2-A0CX-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

SART3

SNV

Missense_Mutation

c.2114N>T

p.Thr705Ile

p.T705I

Q15020

protein_coding

deleterious(0)

possibly_damaging(0.701)

TCGA-A2-A25E-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

cytoxan

SART3

SNV

Missense_Mutation

c.1739N>T

p.Arg580Ile

p.R580I

Q15020

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SART3

SNV

Missense_Mutation

novel

c.1396N>A

p.Glu466Lys

p.E466K

Q15020

protein_coding

tolerated(0.44)

probably_damaging(0.997)

TCGA-B6-A0I1-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SART3

SNV

Missense_Mutation

rs771158811

c.236C>T

p.Ser79Phe

p.S79F

Q15020

protein_coding

deleterious_low_confidence(0.01)

possibly_damaging(0.564)

TCGA-BH-A0BR-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

SART3

SNV

Missense_Mutation

rs765674787

c.2630A>G

p.Asn877Ser

p.N877S

Q15020

protein_coding

deleterious(0.01)

probably_damaging(0.995)

TCGA-D8-A1XQ-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SART3

insertion

In_Frame_Ins

novel

c.37_38insTTTCCTGTCAAGGATTGAGGTGGGGGAAGA

p.Glu13delinsValSerCysGlnGlyLeuArgTrpGlyLysLys

p.E13delinsVSCQGLRWGKK

Q15020

protein_coding

TCGA-A2-A0CQ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

SART3

insertion

In_Frame_Ins

novel

c.2150_2151insAACACAAGCTGTTCATCTCAG

p.Glu717_Pro718insThrGlnAlaValHisLeuArg

p.E717_P718insTQAVHLR

Q15020

protein_coding

TCGA-A8-A07Z-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unspecific

Exemestane

SART3

insertion

In_Frame_Ins

novel

c.2788_2789insTTTTCTATATTTTTTTAA

p.Ala930delinsValPheTyrIlePheLeuThr

p.A930delinsVFYIFLT

Q15020

protein_coding

TCGA-A8-A08H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SART3

insertion

Nonsense_Mutation

novel

c.2534_2535insACGAGAACACACTGTTTTTGAGACACAGTTGTCCAAATGTTTCTG

p.Tyr845delinsTer

p.Y845delins*

Q15020

protein_coding

TCGA-AR-A0TY-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unspecific

Paclitaxel

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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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