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: GYG1

Gene summary for GYG1

Gene summary.

Gene information	Species	Human
	Gene symbol	GYG1
	Gene ID	2992
	Gene name	glycogenin 1
	Gene Alias	GSD15
	Cytomap	3q24
	Gene Type	protein-coding
	GO ID	GO:0000271
	UniProtAcc	P46976

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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
2992	GYG1	LZE4T	Human	Esophagus	ESCC	5.06e-21	5.69e-01	0.0811
2992	GYG1	LZE5T	Human	Esophagus	ESCC	1.96e-02	2.53e-01	0.0514
2992	GYG1	LZE7T	Human	Esophagus	ESCC	7.02e-12	7.39e-01	0.0667
2992	GYG1	LZE8T	Human	Esophagus	ESCC	1.87e-11	4.42e-01	0.067
2992	GYG1	LZE22T	Human	Esophagus	ESCC	4.07e-04	3.32e-01	0.068
2992	GYG1	LZE24T	Human	Esophagus	ESCC	4.92e-16	5.10e-01	0.0596
2992	GYG1	LZE6T	Human	Esophagus	ESCC	1.19e-06	3.41e-01	0.0845
2992	GYG1	P2T-E	Human	Esophagus	ESCC	4.98e-63	1.13e+00	0.1177
2992	GYG1	P4T-E	Human	Esophagus	ESCC	9.41e-22	5.41e-01	0.1323
2992	GYG1	P5T-E	Human	Esophagus	ESCC	2.70e-31	7.03e-01	0.1327
2992	GYG1	P8T-E	Human	Esophagus	ESCC	9.21e-32	6.28e-01	0.0889
2992	GYG1	P9T-E	Human	Esophagus	ESCC	1.84e-13	3.52e-01	0.1131
2992	GYG1	P10T-E	Human	Esophagus	ESCC	4.99e-24	4.55e-01	0.116
2992	GYG1	P11T-E	Human	Esophagus	ESCC	6.47e-13	5.80e-01	0.1426
2992	GYG1	P12T-E	Human	Esophagus	ESCC	4.18e-12	3.24e-01	0.1122
2992	GYG1	P15T-E	Human	Esophagus	ESCC	1.76e-20	5.79e-01	0.1149
2992	GYG1	P16T-E	Human	Esophagus	ESCC	5.17e-35	7.52e-01	0.1153
2992	GYG1	P17T-E	Human	Esophagus	ESCC	7.16e-08	4.00e-01	0.1278
2992	GYG1	P19T-E	Human	Esophagus	ESCC	5.09e-07	7.30e-01	0.1662
2992	GYG1	P20T-E	Human	Esophagus	ESCC	2.84e-25	6.65e-01	0.1124

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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:0006091110	Esophagus	ESCC	generation of precursor metabolites and energy	331/8552	490/18723	3.86e-23	8.45e-21	331
GO:0015980110	Esophagus	ESCC	energy derivation by oxidation of organic compounds	220/8552	318/18723	1.20e-17	1.09e-15	220
GO:00442626	Esophagus	ESCC	cellular carbohydrate metabolic process	160/8552	283/18723	1.43e-04	9.66e-04	160
GO:00160514	Esophagus	ESCC	carbohydrate biosynthetic process	117/8552	202/18723	2.96e-04	1.79e-03	117
GO:00346372	Esophagus	ESCC	cellular carbohydrate biosynthetic process	46/8552	78/18723	1.24e-02	4.13e-02	46
GO:000609122	Liver	HCC	generation of precursor metabolites and energy	340/7958	490/18723	4.04e-34	2.85e-31	340
GO:001598022	Liver	HCC	energy derivation by oxidation of organic compounds	221/7958	318/18723	1.02e-22	1.86e-20	221
GO:004426221	Liver	HCC	cellular carbohydrate metabolic process	153/7958	283/18723	5.27e-05	5.00e-04	153
GO:00160512	Liver	HCC	carbohydrate biosynthetic process	113/7958	202/18723	7.64e-05	6.83e-04	113
GO:00059772	Liver	HCC	glycogen metabolic process	46/7958	72/18723	2.02e-04	1.56e-03	46
GO:00060732	Liver	HCC	cellular glucan metabolic process	46/7958	73/18723	3.23e-04	2.28e-03	46
GO:00440422	Liver	HCC	glucan metabolic process	46/7958	73/18723	3.23e-04	2.28e-03	46
GO:00059781	Liver	HCC	glycogen biosynthetic process	29/7958	44/18723	1.46e-03	7.75e-03	29
GO:00092501	Liver	HCC	glucan biosynthetic process	29/7958	44/18723	1.46e-03	7.75e-03	29
GO:00061122	Liver	HCC	energy reserve metabolic process	49/7958	84/18723	2.46e-03	1.19e-02	49
GO:00346371	Liver	HCC	cellular carbohydrate biosynthetic process	44/7958	78/18723	9.13e-03	3.51e-02	44
GO:00442641	Liver	HCC	cellular polysaccharide metabolic process	52/7958	96/18723	1.38e-02	4.91e-02	52
GO:000609118	Oral cavity	OSCC	generation of precursor metabolites and energy	286/7305	490/18723	1.45e-18	1.71e-16	286
GO:001598018	Oral cavity	OSCC	energy derivation by oxidation of organic compounds	190/7305	318/18723	4.10e-14	2.26e-12	190
GO:00160513	Oral cavity	OSCC	carbohydrate biosynthetic process	97/7305	202/18723	5.50e-03	2.13e-02	97

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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

GYG1

SNV

Missense_Mutation

c.539G>T

p.Arg180Ile

p.R180I

P46976

protein_coding

deleterious(0.05)

benign(0.206)

TCGA-A2-A0EY-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

GYG1

SNV

Missense_Mutation

rs781042039

c.875G>C

p.Arg292Thr

p.R292T

P46976

protein_coding

tolerated(0.5)

benign(0.236)

TCGA-BH-A0BP-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

GYG1

SNV

Missense_Mutation

novel

c.698N>A

p.Ser233Asn

p.S233N

P46976

protein_coding

tolerated(0.29)

benign(0)

TCGA-LL-A6FQ-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Unknown

GYG1

insertion

In_Frame_Ins

novel

c.736_737insAGCAGGGTTTGGAGCTAGGCTACAGGTTTGGTCCAGATCTGT

p.Leu246delinsGlnGlnGlyLeuGluLeuGlyTyrArgPheGlyProAspLeuPhe

p.L246delinsQQGLELGYRFGPDLF

P46976

protein_coding

TCGA-AN-A04A-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

GYG1

insertion

Nonsense_Mutation

novel

c.579_580insTTATTTCTTTTGAATGAATGGCCATGATCCCCGCTTTCTGAGGAAG

p.Ile194LeufsTer9

p.I194Lfs*9

P46976

protein_coding

TCGA-B6-A0RE-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

GYG1

SNV

Missense_Mutation

c.71N>T

p.Ser24Leu

p.S24L

P46976

protein_coding

tolerated(0.11)

benign(0.018)

TCGA-C5-A1BQ-01

Cervix

cervical & endocervical cancer

Female

>=65

III/IV

Chemotherapy

cisplatin

GYG1

SNV

Missense_Mutation

c.334G>A

p.Asp112Asn

p.D112N

P46976

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-Q1-A73O-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

GYG1

SNV

Missense_Mutation

novel

c.163N>C

p.Phe55Leu

p.F55L

P46976

protein_coding

deleterious(0)

probably_damaging(0.951)

TCGA-F5-6814-01

Colorectum

rectum adenocarcinoma

Male

<65

I/II

Unknown

GYG1

SNV

Missense_Mutation

novel

c.736N>A

p.Leu246Ile

p.L246I

P46976

protein_coding

tolerated(0.06)

possibly_damaging(0.818)

TCGA-F5-6814-01

Colorectum

rectum adenocarcinoma

Male

<65

I/II

Unknown

GYG1

SNV

Missense_Mutation

novel

c.953N>T

p.Ser318Leu

p.S318L

P46976

protein_coding

deleterious(0.03)

possibly_damaging(0.594)

TCGA-A5-A0G2-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

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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