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: SRC

Gene summary for SRC

Gene summary.

Gene information	Species	Human
	Gene symbol	SRC
	Gene ID	6714
	Gene name	SRC proto-oncogene, non-receptor tyrosine kinase
	Gene Alias	ASV
	Cytomap	20q11.23
	Gene Type	protein-coding
	GO ID	GO:0000003
	UniProtAcc	P12931

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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
6714	SRC	LZE4T	Human	Esophagus	ESCC	4.17e-04	8.87e-02	0.0811
6714	SRC	LZE8T	Human	Esophagus	ESCC	6.35e-03	5.66e-02	0.067
6714	SRC	LZE20T	Human	Esophagus	ESCC	3.88e-06	1.87e-01	0.0662
6714	SRC	LZE22T	Human	Esophagus	ESCC	2.39e-03	1.69e-01	0.068
6714	SRC	LZE24T	Human	Esophagus	ESCC	4.07e-12	3.74e-01	0.0596
6714	SRC	P1T-E	Human	Esophagus	ESCC	1.99e-04	2.78e-01	0.0875
6714	SRC	P2T-E	Human	Esophagus	ESCC	3.86e-10	1.07e-01	0.1177
6714	SRC	P4T-E	Human	Esophagus	ESCC	2.75e-19	1.82e-01	0.1323
6714	SRC	P8T-E	Human	Esophagus	ESCC	3.27e-12	2.30e-01	0.0889
6714	SRC	P9T-E	Human	Esophagus	ESCC	1.69e-09	7.57e-02	0.1131
6714	SRC	P10T-E	Human	Esophagus	ESCC	4.36e-10	1.94e-01	0.116
6714	SRC	P11T-E	Human	Esophagus	ESCC	4.18e-12	3.10e-01	0.1426
6714	SRC	P12T-E	Human	Esophagus	ESCC	2.98e-17	3.51e-01	0.1122
6714	SRC	P15T-E	Human	Esophagus	ESCC	6.55e-13	2.98e-01	0.1149
6714	SRC	P16T-E	Human	Esophagus	ESCC	8.91e-15	2.73e-01	0.1153
6714	SRC	P17T-E	Human	Esophagus	ESCC	6.33e-06	2.31e-01	0.1278
6714	SRC	P20T-E	Human	Esophagus	ESCC	5.91e-17	3.27e-01	0.1124
6714	SRC	P21T-E	Human	Esophagus	ESCC	3.51e-20	4.69e-01	0.1617
6714	SRC	P22T-E	Human	Esophagus	ESCC	6.37e-11	2.23e-01	0.1236
6714	SRC	P23T-E	Human	Esophagus	ESCC	2.79e-14	2.57e-01	0.108

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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

∗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:00069139	Cervix	CC	nucleocytoplasmic transport	71/2311	301/18723	4.04e-08	2.54e-06	71
GO:00511699	Cervix	CC	nuclear transport	71/2311	301/18723	4.04e-08	2.54e-06	71
GO:000838010	Cervix	CC	RNA splicing	76/2311	434/18723	9.79e-04	8.19e-03	76
GO:000037710	Cervix	CC	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	55/2311	320/18723	6.71e-03	3.70e-02	55
GO:000039810	Cervix	CC	mRNA splicing, via spliceosome	55/2311	320/18723	6.71e-03	3.70e-02	55
GO:000037510	Cervix	CC	RNA splicing, via transesterification reactions	55/2311	324/18723	8.61e-03	4.44e-02	55
GO:0008380	Colorectum	AD	RNA splicing	169/3918	434/18723	3.59e-18	2.04e-15	169
GO:0000377	Colorectum	AD	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	130/3918	320/18723	5.88e-16	2.16e-13	130
GO:0000398	Colorectum	AD	mRNA splicing, via spliceosome	130/3918	320/18723	5.88e-16	2.16e-13	130
GO:0000375	Colorectum	AD	RNA splicing, via transesterification reactions	131/3918	324/18723	7.11e-16	2.22e-13	131
GO:0006913	Colorectum	AD	nucleocytoplasmic transport	102/3918	301/18723	1.00e-07	4.85e-06	102
GO:0051169	Colorectum	AD	nuclear transport	102/3918	301/18723	1.00e-07	4.85e-06	102
GO:0000380	Colorectum	AD	alternative mRNA splicing, via spliceosome	33/3918	77/18723	1.13e-05	2.55e-04	33
GO:00083801	Colorectum	SER	RNA splicing	123/2897	434/18723	3.84e-12	8.41e-10	123
GO:00003751	Colorectum	SER	RNA splicing, via transesterification reactions	90/2897	324/18723	8.68e-09	7.50e-07	90
GO:00003771	Colorectum	SER	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	89/2897	320/18723	9.82e-09	8.14e-07	89
GO:00003981	Colorectum	SER	mRNA splicing, via spliceosome	89/2897	320/18723	9.82e-09	8.14e-07	89
GO:00069131	Colorectum	SER	nucleocytoplasmic transport	77/2897	301/18723	3.39e-06	1.32e-04	77
GO:00511691	Colorectum	SER	nuclear transport	77/2897	301/18723	3.39e-06	1.32e-04	77
GO:00003801	Colorectum	SER	alternative mRNA splicing, via spliceosome	24/2897	77/18723	4.08e-04	6.09e-03	24

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0513525	Oral cavity	LP	Yersinia infection	59/2418	137/8465	1.81e-04	1.04e-03	6.71e-04	59
hsa05417210	Oral cavity	LP	Lipid and atherosclerosis	84/2418	215/8465	5.02e-04	2.61e-03	1.68e-03	84
hsa0521923	Oral cavity	LP	Bladder cancer	22/2418	41/8465	6.22e-04	3.19e-03	2.06e-03	22
hsa0516122	Oral cavity	LP	Hepatitis B	65/2418	162/8465	9.31e-04	4.43e-03	2.86e-03	65
hsa0516329	Oral cavity	LP	Human cytomegalovirus infection	85/2418	225/8465	1.55e-03	6.89e-03	4.45e-03	85
hsa0520527	Oral cavity	LP	Proteoglycans in cancer	77/2418	205/8465	3.01e-03	1.29e-02	8.35e-03	77
hsa0462521	Oral cavity	LP	C-type lectin receptor signaling pathway	43/2418	104/8465	3.33e-03	1.41e-02	9.06e-03	43
hsa0515221	Oral cavity	LP	Tuberculosis	65/2418	180/8465	1.60e-02	4.92e-02	3.17e-02	65
hsa0520838	Oral cavity	LP	Chemical carcinogenesis - reactive oxygen species	119/2418	223/8465	3.00e-15	8.32e-14	5.37e-14	119
hsa0414436	Oral cavity	LP	Endocytosis	121/2418	251/8465	1.89e-11	3.70e-10	2.38e-10	121
hsa0520334	Oral cavity	LP	Viral carcinogenesis	90/2418	204/8465	1.20e-06	1.38e-05	8.89e-06	90
hsa0513038	Oral cavity	LP	Pathogenic Escherichia coli infection	87/2418	197/8465	1.71e-06	1.78e-05	1.15e-05	87
hsa0541838	Oral cavity	LP	Fluid shear stress and atherosclerosis	65/2418	139/8465	3.42e-06	3.26e-05	2.10e-05	65
hsa0513138	Oral cavity	LP	Shigellosis	103/2418	247/8465	4.98e-06	4.14e-05	2.67e-05	103
hsa0512034	Oral cavity	LP	Epithelial cell signaling in Helicobacter pylori infection	38/2418	70/8465	5.17e-06	4.20e-05	2.71e-05	38
hsa0516737	Oral cavity	LP	Kaposi sarcoma-associated herpesvirus infection	84/2418	194/8465	6.66e-06	5.16e-05	3.33e-05	84
hsa0413737	Oral cavity	LP	Mitophagy - animal	38/2418	72/8465	1.24e-05	8.63e-05	5.57e-05	38
hsa0510038	Oral cavity	LP	Bacterial invasion of epithelial cells	39/2418	77/8465	3.34e-05	2.22e-04	1.43e-04	39
hsa0513535	Oral cavity	LP	Yersinia infection	59/2418	137/8465	1.81e-04	1.04e-03	6.71e-04	59
hsa0541738	Oral cavity	LP	Lipid and atherosclerosis	84/2418	215/8465	5.02e-04	2.61e-03	1.68e-03	84

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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

SRC

SNV

Missense_Mutation

c.806C>T

p.Ser269Leu

p.S269L

P12931

protein_coding

deleterious(0)

probably_damaging(0.99)

TCGA-D8-A1J8-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

nolvadex

SRC

insertion

Frame_Shift_Ins

novel

c.1176_1177insCTCATCT

p.Ala393LeufsTer25

p.A393Lfs*25

P12931

protein_coding

TCGA-AO-A0JB-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

cyclophosphamide

SRC

insertion

Frame_Shift_Ins

novel

c.1177_1178insTGTCTGGGTCCGCTGGGGCCTCTTTC

p.Ala393ValfsTer72

p.A393Vfs*72

P12931

protein_coding

TCGA-AO-A0JB-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

cyclophosphamide

SRC

SNV

Missense_Mutation

novel

c.11N>G

p.Asn4Ser

p.N4S

P12931

protein_coding

tolerated_low_confidence(0.97)

benign(0)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

SRC

SNV

Missense_Mutation

novel

c.439C>A

p.Gln147Lys

p.Q147K

P12931

protein_coding

deleterious(0.04)

possibly_damaging(0.882)

TCGA-AA-3947-01

Colorectum

colon adenocarcinoma

Female

<65

I/II

Unknown

SRC

SNV

Missense_Mutation

c.1571N>T

p.Thr524Met

p.T524M

P12931

protein_coding

deleterious(0.01)

possibly_damaging(0.52)

TCGA-AD-6899-01

Colorectum

colon adenocarcinoma

Male

>=65

III/IV

Unknown

SRC

SNV

Missense_Mutation

c.1489N>A

p.Leu497Ile

p.L497I

P12931

protein_coding

tolerated(1)

probably_damaging(0.993)

TCGA-AD-A5EJ-01

Colorectum

colon adenocarcinoma

Female

>=65

I/II

Unknown

SRC

SNV

Missense_Mutation

novel

c.659N>A

p.Arg220His

p.R220H

P12931

protein_coding

deleterious(0.01)

benign(0.428)

TCGA-A5-A0G2-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Unknown

SRC

SNV

Missense_Mutation

rs533607141

c.812N>A

p.Arg271Gln

p.R271Q

P12931

protein_coding

tolerated(0.53)

benign(0.318)

TCGA-AJ-A3BG-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Chemotherapy

carboplatin

SRC

SNV

Missense_Mutation

c.272C>T

p.Ala91Val

p.A91V

P12931

protein_coding

deleterious(0.01)

benign(0.437)

TCGA-AP-A059-01

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
6714	SRC	CLINICALLY ACTIONABLE, KINASE, TYROSINE KINASE, DRUGGABLE GENOME, TRANSCRIPTION FACTOR, ENZYME		CEDIRANIB	CEDIRANIB
6714	SRC	CLINICALLY ACTIONABLE, KINASE, TYROSINE KINASE, DRUGGABLE GENOME, TRANSCRIPTION FACTOR, ENZYME	inhibitor	CHEMBL24828	VANDETANIB
6714	SRC	CLINICALLY ACTIONABLE, KINASE, TYROSINE KINASE, DRUGGABLE GENOME, TRANSCRIPTION FACTOR, ENZYME	inhibitor	CHEMBL3545196	PD-0166285
6714	SRC	CLINICALLY ACTIONABLE, KINASE, TYROSINE KINASE, DRUGGABLE GENOME, TRANSCRIPTION FACTOR, ENZYME		DOVITINIB	DOVITINIB
6714	SRC	CLINICALLY ACTIONABLE, KINASE, TYROSINE KINASE, DRUGGABLE GENOME, TRANSCRIPTION FACTOR, ENZYME		TYRPHOSTIN A9		11112699
6714	SRC	CLINICALLY ACTIONABLE, KINASE, TYROSINE KINASE, DRUGGABLE GENOME, TRANSCRIPTION FACTOR, ENZYME		KX2-361	KX2-361
6714	SRC	CLINICALLY ACTIONABLE, KINASE, TYROSINE KINASE, DRUGGABLE GENOME, TRANSCRIPTION FACTOR, ENZYME		AZD0530	SARACATINIB
6714	SRC	CLINICALLY ACTIONABLE, KINASE, TYROSINE KINASE, DRUGGABLE GENOME, TRANSCRIPTION FACTOR, ENZYME	inhibitor	178102599
6714	SRC	CLINICALLY ACTIONABLE, KINASE, TYROSINE KINASE, DRUGGABLE GENOME, TRANSCRIPTION FACTOR, ENZYME	inhibitor	CHEMBL1421	DASATINIB
6714	SRC	CLINICALLY ACTIONABLE, KINASE, TYROSINE KINASE, DRUGGABLE GENOME, TRANSCRIPTION FACTOR, ENZYME	inhibitor	354702286

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