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: GALNT2

Gene summary for GALNT2

Gene summary.

Gene information	Species	Human
	Gene symbol	GALNT2
	Gene ID	2590
	Gene name	polypeptide N-acetylgalactosaminyltransferase 2
	Gene Alias	CDG2T
	Cytomap	1q42.13
	Gene Type	protein-coding
	GO ID	GO:0006464
	UniProtAcc	B7Z6K2

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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
2590	GALNT2	CCI_1	Human	Cervix	CC	1.63e-03	6.17e-01	0.528
2590	GALNT2	CCI_2	Human	Cervix	CC	1.23e-04	6.88e-01	0.5249
2590	GALNT2	CCI_3	Human	Cervix	CC	6.13e-24	1.52e+00	0.516
2590	GALNT2	EEC-subject3	Human	Endometrium	EEC	2.37e-05	1.93e-01	-0.2525
2590	GALNT2	GSM6177620_NYU_UCEC1_lib1_lib1	Human	Endometrium	EEC	2.06e-14	3.08e-01	-0.1869
2590	GALNT2	GSM6177620_NYU_UCEC1_lib2_lib2	Human	Endometrium	EEC	1.40e-10	2.40e-01	-0.1875
2590	GALNT2	GSM6177620_NYU_UCEC1_lib3_lib3	Human	Endometrium	EEC	7.60e-11	1.26e-01	-0.1883
2590	GALNT2	GSM6177621_NYU_UCEC2_lib1_lib1	Human	Endometrium	EEC	4.18e-15	2.75e-01	-0.1934
2590	GALNT2	GSM6177622_NYU_UCEC3_lib1_lib1	Human	Endometrium	EEC	1.66e-16	2.62e-01	-0.1917
2590	GALNT2	GSM6177622_NYU_UCEC3_lib2_lib2	Human	Endometrium	EEC	1.92e-19	3.66e-01	-0.1916
2590	GALNT2	GSM6177623_NYU_UCEC3_Vis	Human	Endometrium	EEC	8.10e-03	2.84e-01	-0.1269
2590	GALNT2	LZE2D	Human	Esophagus	HGIN	1.15e-02	2.88e-01	0.0642
2590	GALNT2	LZE4T	Human	Esophagus	ESCC	3.26e-13	3.45e-01	0.0811
2590	GALNT2	LZE5T	Human	Esophagus	ESCC	2.60e-04	1.06e-01	0.0514
2590	GALNT2	LZE7T	Human	Esophagus	ESCC	4.66e-06	2.06e-01	0.0667
2590	GALNT2	LZE8T	Human	Esophagus	ESCC	1.07e-07	8.81e-02	0.067
2590	GALNT2	LZE20T	Human	Esophagus	ESCC	4.52e-02	2.26e-01	0.0662
2590	GALNT2	LZE22D1	Human	Esophagus	HGIN	1.19e-04	1.64e-01	0.0595
2590	GALNT2	LZE22T	Human	Esophagus	ESCC	1.67e-07	4.17e-01	0.068
2590	GALNT2	LZE24T	Human	Esophagus	ESCC	6.53e-17	5.14e-01	0.0596

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Cervix		CC: Cervix cancer
		HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions
		N_HPV: HPV-infected normal cervix
Endometrium		AEH: Atypical endometrial hyperplasia
		EEC: Endometrioid Cancer
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
Lung		AAH: Atypical adenomatous hyperplasia
		AIS: Adenocarcinoma in situ
		IAC: Invasive lung adenocarcinoma
		MIA: Minimally invasive adenocarcinoma
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:00182096	Cervix	CC	peptidyl-serine modification	66/2311	338/18723	9.58e-05	1.25e-03	66
GO:00516048	Cervix	CC	protein maturation	56/2311	294/18723	5.90e-04	5.59e-03	56
GO:00182106	Cervix	CC	peptidyl-threonine modification	26/2311	125/18723	4.98e-03	2.97e-02	26
GO:0018279	Colorectum	AD	protein N-linked glycosylation via asparagine	15/3918	23/18723	5.47e-06	1.40e-04	15
GO:0018196	Colorectum	AD	peptidyl-asparagine modification	15/3918	24/18723	1.18e-05	2.62e-04	15
GO:0030258	Colorectum	AD	lipid modification	67/3918	212/18723	1.66e-04	2.27e-03	67
GO:0006487	Colorectum	AD	protein N-linked glycosylation	25/3918	65/18723	9.12e-04	8.71e-03	25
GO:0009225	Colorectum	AD	nucleotide-sugar metabolic process	16/3918	36/18723	1.27e-03	1.12e-02	16
GO:0006486	Colorectum	AD	protein glycosylation	64/3918	226/18723	4.86e-03	3.27e-02	64
GO:0043413	Colorectum	AD	macromolecule glycosylation	64/3918	226/18723	4.86e-03	3.27e-02	64
GO:0070085	Colorectum	AD	glycosylation	67/3918	240/18723	5.78e-03	3.67e-02	67
GO:0007162	Colorectum	SER	negative regulation of cell adhesion	68/2897	303/18723	8.02e-04	1.01e-02	68
GO:00182791	Colorectum	SER	protein N-linked glycosylation via asparagine	9/2897	23/18723	5.20e-03	3.95e-02	9
GO:00302581	Colorectum	SER	lipid modification	47/2897	212/18723	6.01e-03	4.38e-02	47
GO:0022408	Colorectum	SER	negative regulation of cell-cell adhesion	44/2897	196/18723	6.08e-03	4.42e-02	44
GO:00092251	Colorectum	SER	nucleotide-sugar metabolic process	12/2897	36/18723	6.11e-03	4.42e-02	12
GO:00181961	Colorectum	SER	peptidyl-asparagine modification	9/2897	24/18723	7.19e-03	4.99e-02	9
GO:00182792	Colorectum	MSS	protein N-linked glycosylation via asparagine	13/3467	23/18723	5.21e-05	9.31e-04	13
GO:00181962	Colorectum	MSS	peptidyl-asparagine modification	13/3467	24/18723	9.44e-05	1.49e-03	13
GO:00064871	Colorectum	MSS	protein N-linked glycosylation	23/3467	65/18723	9.47e-04	9.54e-03	23

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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

GALNT2

SNV

Missense_Mutation

novel

c.615G>A

p.Met205Ile

p.M205I

Q10471

protein_coding

tolerated(1)

benign(0.025)

TCGA-A2-A3XY-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

GALNT2

SNV

Missense_Mutation

c.483N>C

p.Lys161Asn

p.K161N

Q10471

protein_coding

tolerated(1)

benign(0.003)

TCGA-A8-A07U-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Chemotherapy

5-fluorouracil

GALNT2

SNV

Missense_Mutation

rs763766688

c.1642N>A

p.Gly548Arg

p.G548R

Q10471

protein_coding

tolerated(0.34)

benign(0.015)

TCGA-AR-A5QQ-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Chemotherapy

carboplatin

GALNT2

SNV

Missense_Mutation

novel

c.610N>T

p.Leu204Phe

p.L204F

Q10471

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-BH-A8FY-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

GALNT2

SNV

Missense_Mutation

c.137A>G

p.Asn46Ser

p.N46S

Q10471

protein_coding

tolerated(0.41)

benign(0)

TCGA-E9-A22B-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

tamoxiphen

GALNT2

insertion

In_Frame_Ins

novel

c.1086_1087insCTTCACTTAATTTCCTGGGAATACTATCCAGCCAGAAAA

p.Arg362_Lys363insLeuHisLeuIleSerTrpGluTyrTyrProAlaArgLys

p.R362_K363insLHLISWEYYPARK

Q10471

protein_coding

TCGA-A2-A0EY-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

GALNT2

insertion

In_Frame_Ins

novel

c.1057_1058insTTGATGTTGAAAGCTTCTTTAGGCTCGATTACTATA

p.Pro353delinsLeuAspValGluSerPhePheArgLeuAspTyrTyrThr

p.P353delinsLDVESFFRLDYYT

Q10471

protein_coding

TCGA-AN-A049-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

GALNT2

SNV

Missense_Mutation

rs779465339

c.382C>T

p.Arg128Trp

p.R128W

Q10471

protein_coding

deleterious(0.02)

possibly_damaging(0.521)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

GALNT2

SNV

Missense_Mutation

rs147219046

c.1504C>T

p.Arg502Trp

p.R502W

Q10471

protein_coding

tolerated(0.18)

possibly_damaging(0.744)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

GALNT2

SNV

Missense_Mutation

c.703N>A

p.Glu235Lys

p.E235K

Q10471

protein_coding

deleterious(0.02)

probably_damaging(1)

TCGA-AA-3715-01

Colorectum

colon 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
2590	GALNT2	DRUGGABLE GENOME		atenolol	ATENOLOL

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