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: SYNJ2BP

Gene summary for SYNJ2BP

Gene summary.

Gene information	Species	Human
	Gene symbol	SYNJ2BP
	Gene ID	55333
	Gene name	synaptojanin 2 binding protein
	Gene Alias	ARIP2
	Cytomap	14q24.2
	Gene Type	protein-coding
	GO ID	GO:0000165
	UniProtAcc	A0A024R670

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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
55333	SYNJ2BP	LZE7T	Human	Esophagus	ESCC	2.79e-08	5.05e-01	0.0667
55333	SYNJ2BP	LZE8T	Human	Esophagus	ESCC	4.99e-11	2.65e-01	0.067
55333	SYNJ2BP	LZE20T	Human	Esophagus	ESCC	2.34e-13	4.70e-01	0.0662
55333	SYNJ2BP	LZE21D1	Human	Esophagus	HGIN	8.90e-03	2.24e-01	0.0632
55333	SYNJ2BP	LZE22D1	Human	Esophagus	HGIN	7.04e-03	1.65e-01	0.0595
55333	SYNJ2BP	LZE22T	Human	Esophagus	ESCC	1.96e-11	4.66e-01	0.068
55333	SYNJ2BP	LZE24T	Human	Esophagus	ESCC	1.03e-24	6.11e-01	0.0596
55333	SYNJ2BP	LZE21T	Human	Esophagus	ESCC	4.39e-05	3.77e-01	0.0655
55333	SYNJ2BP	LZE6T	Human	Esophagus	ESCC	1.35e-03	2.96e-01	0.0845
55333	SYNJ2BP	P2T-E	Human	Esophagus	ESCC	8.80e-05	5.63e-02	0.1177
55333	SYNJ2BP	P4T-E	Human	Esophagus	ESCC	1.95e-07	6.36e-02	0.1323
55333	SYNJ2BP	P5T-E	Human	Esophagus	ESCC	2.27e-04	-9.49e-03	0.1327
55333	SYNJ2BP	P8T-E	Human	Esophagus	ESCC	1.73e-11	1.95e-01	0.0889
55333	SYNJ2BP	P9T-E	Human	Esophagus	ESCC	3.59e-02	2.85e-02	0.1131
55333	SYNJ2BP	P10T-E	Human	Esophagus	ESCC	1.34e-10	1.24e-01	0.116
55333	SYNJ2BP	P11T-E	Human	Esophagus	ESCC	1.21e-02	8.97e-02	0.1426
55333	SYNJ2BP	P12T-E	Human	Esophagus	ESCC	5.32e-09	7.71e-02	0.1122
55333	SYNJ2BP	P15T-E	Human	Esophagus	ESCC	3.36e-10	7.37e-02	0.1149
55333	SYNJ2BP	P16T-E	Human	Esophagus	ESCC	2.62e-05	3.76e-02	0.1153
55333	SYNJ2BP	P20T-E	Human	Esophagus	ESCC	1.20e-07	8.02e-02	0.1124

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Colorectum (GSE201348)		FAP: Familial adenomatous polyposis
		CRC: Colorectal cancer
Colorectum (HTA11)		AD: Adenomas
		SER: Sessile serrated lesions
		MSI-H: Microsatellite-high colorectal cancer
		MSS: Microsatellite stable colorectal cancer
Esophagus		ESCC: Esophageal squamous cell carcinoma
		HGIN: High-grade intraepithelial neoplasias
		LGIN: Low-grade intraepithelial neoplasias
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:0007163	Colorectum	AD	establishment or maintenance of cell polarity	77/3918	218/18723	5.72e-07	2.08e-05	77
GO:0001667	Colorectum	AD	ameboidal-type cell migration	137/3918	475/18723	2.17e-05	4.33e-04	137
GO:0090132	Colorectum	AD	epithelium migration	105/3918	360/18723	1.18e-04	1.73e-03	105
GO:0010632	Colorectum	AD	regulation of epithelial cell migration	88/3918	292/18723	1.19e-04	1.75e-03	88
GO:0010631	Colorectum	AD	epithelial cell migration	104/3918	357/18723	1.33e-04	1.90e-03	104
GO:0090130	Colorectum	AD	tissue migration	105/3918	365/18723	2.10e-04	2.77e-03	105
GO:0045197	Colorectum	AD	establishment or maintenance of epithelial cell apical/basal polarity	20/3918	44/18723	2.26e-04	2.94e-03	20
GO:0035088	Colorectum	AD	establishment or maintenance of apical/basal cell polarity	21/3918	49/18723	4.31e-04	4.82e-03	21
GO:0061245	Colorectum	AD	establishment or maintenance of bipolar cell polarity	21/3918	49/18723	4.31e-04	4.82e-03	21
GO:0043409	Colorectum	AD	negative regulation of MAPK cascade	57/3918	180/18723	4.61e-04	5.14e-03	57
GO:0050673	Colorectum	AD	epithelial cell proliferation	119/3918	437/18723	8.75e-04	8.51e-03	119
GO:0043542	Colorectum	AD	endothelial cell migration	78/3918	279/18723	2.97e-03	2.22e-02	78
GO:0007219	Colorectum	AD	Notch signaling pathway	50/3918	172/18723	6.92e-03	4.26e-02	50
GO:00071631	Colorectum	SER	establishment or maintenance of cell polarity	60/2897	218/18723	3.45e-06	1.33e-04	60
GO:00016671	Colorectum	SER	ameboidal-type cell migration	105/2897	475/18723	6.97e-05	1.59e-03	105
GO:00901321	Colorectum	SER	epithelium migration	82/2897	360/18723	1.50e-04	2.93e-03	82
GO:00106311	Colorectum	SER	epithelial cell migration	81/2897	357/18723	1.87e-04	3.44e-03	81
GO:00901301	Colorectum	SER	tissue migration	82/2897	365/18723	2.40e-04	4.12e-03	82
GO:00106321	Colorectum	SER	regulation of epithelial cell migration	68/2897	292/18723	2.72e-04	4.53e-03	68
GO:00451971	Colorectum	SER	establishment or maintenance of epithelial cell apical/basal polarity	16/2897	44/18723	5.64e-04	7.83e-03	16

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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

SYNJ2BP

insertion

In_Frame_Ins

novel

c.107_108insGAAGTTACTTGTTCAAAAAGCACAAGGCAGGAAGCAGCGAGG

p.Val36_Ser37insLysLeuLeuValGlnLysAlaGlnGlyArgLysGlnArgGly

p.V36_S37insKLLVQKAQGRKQRG

P57105

protein_coding

TCGA-A2-A0CQ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

SYNJ2BP

SNV

Missense_Mutation

novel

c.349N>A

p.Gly117Ser

p.G117S

P57105

protein_coding

tolerated(0.55)

benign(0.001)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

SYNJ2BP

SNV

Missense_Mutation

c.377N>T

p.Pro126Leu

p.P126L

P57105

protein_coding

tolerated(0.07)

benign(0.23)

TCGA-AA-3852-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

SYNJ2BP

SNV

Missense_Mutation

novel

c.379G>T

p.Val127Leu

p.V127L

P57105

protein_coding

tolerated(0.46)

benign(0.003)

TCGA-A5-A0G2-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Unknown

SYNJ2BP

SNV

Missense_Mutation

c.331G>T

p.Gly111Cys

p.G111C

P57105

protein_coding

tolerated(0.05)

benign(0.219)

TCGA-AP-A051-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

SYNJ2BP

SNV

Missense_Mutation

c.329N>A

p.Arg110Gln

p.R110Q

P57105

protein_coding

tolerated(0.24)

benign(0.015)

TCGA-AP-A0LM-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

cisplatin

SYNJ2BP

SNV

Missense_Mutation

novel

c.16G>A

p.Asp6Asn

p.D6N

P57105

protein_coding

tolerated(0.42)

benign(0.013)

TCGA-B5-A3FC-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

SYNJ2BP

SNV

Missense_Mutation

novel

c.85N>A

p.Gly29Ser

p.G29S

P57105

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-EO-A22U-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

SYNJ2BP

SNV

Missense_Mutation

rs201847524

c.256N>T

p.Arg86Cys

p.R86C

P57105

protein_coding

deleterious(0.04)

probably_damaging(0.967)

TCGA-53-7624-01

Lung

lung adenocarcinoma

Female

<65

III/IV

Chemotherapy

cisplatin

SYNJ2BP

SNV

Missense_Mutation

c.344N>A

p.Pro115Gln

p.P115Q

P57105

protein_coding

tolerated(0.05)

possibly_damaging(0.462)

TCGA-78-7163-01

Lung

lung adenocarcinoma

Male

<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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