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: SEC23B

Gene summary for SEC23B

Gene summary.

Gene information	Species	Human
	Gene symbol	SEC23B
	Gene ID	10483
	Gene name	SEC23 homolog B, COPII coat complex component
	Gene Alias	CDA-II
	Cytomap	20p11.23
	Gene Type	protein-coding
	GO ID	GO:0006810
	UniProtAcc	Q15437

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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
10483	SEC23B	LZE2T	Human	Esophagus	ESCC	4.70e-02	3.13e-01	0.082
10483	SEC23B	LZE4T	Human	Esophagus	ESCC	6.17e-12	2.69e-01	0.0811
10483	SEC23B	LZE7T	Human	Esophagus	ESCC	6.04e-04	1.99e-01	0.0667
10483	SEC23B	LZE8T	Human	Esophagus	ESCC	1.54e-03	1.09e-01	0.067
10483	SEC23B	LZE20T	Human	Esophagus	ESCC	2.02e-02	-6.01e-03	0.0662
10483	SEC23B	LZE22T	Human	Esophagus	ESCC	8.41e-04	2.06e-01	0.068
10483	SEC23B	LZE24T	Human	Esophagus	ESCC	3.47e-10	2.52e-01	0.0596
10483	SEC23B	LZE21T	Human	Esophagus	ESCC	3.56e-05	1.97e-01	0.0655
10483	SEC23B	P1T-E	Human	Esophagus	ESCC	4.00e-04	4.83e-01	0.0875
10483	SEC23B	P2T-E	Human	Esophagus	ESCC	5.44e-27	3.89e-01	0.1177
10483	SEC23B	P4T-E	Human	Esophagus	ESCC	2.50e-14	3.68e-01	0.1323
10483	SEC23B	P5T-E	Human	Esophagus	ESCC	1.18e-14	1.38e-01	0.1327
10483	SEC23B	P8T-E	Human	Esophagus	ESCC	7.07e-21	2.73e-01	0.0889
10483	SEC23B	P9T-E	Human	Esophagus	ESCC	1.45e-05	1.57e-01	0.1131
10483	SEC23B	P10T-E	Human	Esophagus	ESCC	1.35e-18	3.53e-01	0.116
10483	SEC23B	P11T-E	Human	Esophagus	ESCC	3.57e-12	3.88e-01	0.1426
10483	SEC23B	P12T-E	Human	Esophagus	ESCC	1.67e-23	5.03e-01	0.1122
10483	SEC23B	P15T-E	Human	Esophagus	ESCC	2.39e-23	3.22e-01	0.1149
10483	SEC23B	P16T-E	Human	Esophagus	ESCC	4.97e-26	5.44e-01	0.1153
10483	SEC23B	P17T-E	Human	Esophagus	ESCC	1.06e-04	4.58e-01	0.1278

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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

∗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:004819318	Esophagus	ESCC	Golgi vesicle transport	231/8552	296/18723	1.82e-30	9.63e-28	231
GO:001605014	Esophagus	ESCC	vesicle organization	211/8552	300/18723	2.85e-18	2.87e-16	211
GO:000688815	Esophagus	ESCC	endoplasmic reticulum to Golgi vesicle-mediated transport	102/8552	130/18723	1.73e-14	9.22e-13	102
GO:0006900111	Esophagus	ESCC	vesicle budding from membrane	54/8552	61/18723	2.66e-12	1.07e-10	54
GO:009011414	Esophagus	ESCC	COPII-coated vesicle budding	27/8552	29/18723	8.09e-08	1.39e-06	27
GO:00901104	Esophagus	ESCC	COPII-coated vesicle cargo loading	14/8552	15/18723	1.47e-04	9.85e-04	14
GO:00354595	Esophagus	ESCC	vesicle cargo loading	19/8552	27/18723	8.35e-03	2.95e-02	19
GO:004819321	Liver	HCC	Golgi vesicle transport	217/7958	296/18723	2.58e-27	1.02e-24	217
GO:000688821	Liver	HCC	endoplasmic reticulum to Golgi vesicle-mediated transport	100/7958	130/18723	1.15e-15	8.67e-14	100
GO:001605021	Liver	HCC	vesicle organization	194/7958	300/18723	5.58e-15	3.97e-13	194
GO:000690021	Liver	HCC	vesicle budding from membrane	53/7958	61/18723	7.38e-13	3.80e-11	53
GO:00901142	Liver	HCC	COPII-coated vesicle budding	27/7958	29/18723	1.28e-08	3.14e-07	27
GO:00901102	Liver	HCC	COPII-coated vesicle cargo loading	14/7958	15/18723	5.65e-05	5.26e-04	14
GO:003545921	Liver	HCC	vesicle cargo loading	19/7958	27/18723	3.18e-03	1.47e-02	19
GO:004819315	Oral cavity	OSCC	Golgi vesicle transport	209/7305	296/18723	1.39e-28	6.30e-26	209
GO:00160508	Oral cavity	OSCC	vesicle organization	189/7305	300/18723	2.40e-17	2.14e-15	189
GO:00068888	Oral cavity	OSCC	endoplasmic reticulum to Golgi vesicle-mediated transport	97/7305	130/18723	1.42e-16	1.15e-14	97
GO:000690019	Oral cavity	OSCC	vesicle budding from membrane	49/7305	61/18723	4.73e-11	1.50e-09	49
GO:00901145	Oral cavity	OSCC	COPII-coated vesicle budding	24/7305	29/18723	1.74e-06	2.26e-05	24
GO:00901103	Oral cavity	OSCC	COPII-coated vesicle cargo loading	11/7305	15/18723	7.49e-03	2.75e-02	11

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa04141211	Esophagus	ESCC	Protein processing in endoplasmic reticulum	147/4205	174/8465	3.29e-22	1.10e-19	5.64e-20	147
hsa04141310	Esophagus	ESCC	Protein processing in endoplasmic reticulum	147/4205	174/8465	3.29e-22	1.10e-19	5.64e-20	147
hsa0414122	Liver	HCC	Protein processing in endoplasmic reticulum	146/4020	174/8465	7.34e-24	2.46e-21	1.37e-21	146
hsa0414132	Liver	HCC	Protein processing in endoplasmic reticulum	146/4020	174/8465	7.34e-24	2.46e-21	1.37e-21	146
hsa0414130	Oral cavity	OSCC	Protein processing in endoplasmic reticulum	143/3704	174/8465	6.82e-26	2.28e-23	1.16e-23	143
hsa04141113	Oral cavity	OSCC	Protein processing in endoplasmic reticulum	143/3704	174/8465	6.82e-26	2.28e-23	1.16e-23	143
hsa04141210	Oral cavity	LP	Protein processing in endoplasmic reticulum	113/2418	174/8465	8.74e-24	5.82e-22	3.76e-22	113
hsa0414138	Oral cavity	LP	Protein processing in endoplasmic reticulum	113/2418	174/8465	8.74e-24	5.82e-22	3.76e-22	113
hsa0414145	Oral cavity	EOLP	Protein processing in endoplasmic reticulum	70/1218	174/8465	2.84e-17	3.06e-15	1.81e-15	70
hsa0414155	Oral cavity	EOLP	Protein processing in endoplasmic reticulum	70/1218	174/8465	2.84e-17	3.06e-15	1.81e-15	70

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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

SEC23B

SNV

Missense_Mutation

novel

c.1696N>C

p.Asp566His

p.D566H

Q15437

protein_coding

deleterious(0)

probably_damaging(0.934)

TCGA-AR-A2LH-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

adriamycin

SEC23B

SNV

Missense_Mutation

c.914N>C

p.Gly305Ala

p.G305A

Q15437

protein_coding

tolerated(0.07)

benign(0.403)

TCGA-BH-A0BW-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

adriamycin

SEC23B

SNV

Missense_Mutation

c.961N>C

p.Asp321His

p.D321H

Q15437

protein_coding

deleterious(0)

probably_damaging(0.977)

TCGA-E9-A1ND-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

aromasin

SEC23B

insertion

Frame_Shift_Ins

novel

c.1599_1600insCCCGAAAGTAAGCAGCCCCAGT

p.Phe534ProfsTer37

p.F534Pfs*37

Q15437

protein_coding

TCGA-AN-A0FX-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

SEC23B

deletion

Frame_Shift_Del

novel

c.307_343delGAGGTGAATCAACCTGCCGAATTGATGCCCCAGTTTT

p.Glu103LeufsTer6

p.E103Lfs*6

Q15437

protein_coding

TCGA-BH-A0DD-01

Breast

breast invasive carcinoma

Male

<65

I/II

Chemotherapy

docetaxel

SEC23B

insertion

Nonsense_Mutation

novel

c.196_197insGAACCCGGGAG

p.Cys66Ter

p.C66*

Q15437

protein_coding

TCGA-BH-A0DS-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Chemotherapy

cyclophosphamide

SEC23B

insertion

Frame_Shift_Ins

novel

c.198_199insGGAGGCTGCAGTGAGCTGAGATGGGAAAA

p.Lys67GlyfsTer48

p.K67Gfs*48

Q15437

protein_coding

TCGA-BH-A0DS-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Chemotherapy

cyclophosphamide

SEC23B

SNV

Missense_Mutation

novel

c.338N>G

p.Gln113Arg

p.Q113R

Q15437

protein_coding

deleterious(0.01)

benign(0.14)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

SEC23B

SNV

Missense_Mutation

c.526N>T

p.His176Tyr

p.H176Y

Q15437

protein_coding

tolerated(0.09)

benign(0.405)

TCGA-EK-A3GK-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

SEC23B

SNV

Missense_Mutation

novel

c.279N>C

p.Gln93His

p.Q93H

Q15437

protein_coding

tolerated(1)

benign(0.009)

TCGA-JW-A5VL-01

Cervix

cervical & endocervical cancer

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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