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: PGM2

Gene summary for PGM2

Gene summary.

Gene information	Species	Human
	Gene symbol	PGM2
	Gene ID	55276
	Gene name	phosphoglucomutase 2
	Gene Alias	MSTP006
	Cytomap	4p14
	Gene Type	protein-coding
	GO ID	GO:0005975
	UniProtAcc	Q96G03

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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
55276	PGM2	LZE4T	Human	Esophagus	ESCC	4.12e-05	2.34e-01	0.0811
55276	PGM2	LZE8T	Human	Esophagus	ESCC	9.14e-04	1.39e-01	0.067
55276	PGM2	LZE20T	Human	Esophagus	ESCC	1.32e-05	2.39e-01	0.0662
55276	PGM2	LZE24T	Human	Esophagus	ESCC	3.30e-08	1.96e-01	0.0596
55276	PGM2	LZE21T	Human	Esophagus	ESCC	4.46e-03	4.06e-01	0.0655
55276	PGM2	LZE6T	Human	Esophagus	ESCC	1.11e-02	2.57e-01	0.0845
55276	PGM2	P2T-E	Human	Esophagus	ESCC	4.07e-20	3.84e-01	0.1177
55276	PGM2	P4T-E	Human	Esophagus	ESCC	8.46e-14	3.43e-01	0.1323
55276	PGM2	P5T-E	Human	Esophagus	ESCC	1.54e-12	2.34e-01	0.1327
55276	PGM2	P8T-E	Human	Esophagus	ESCC	1.36e-08	1.13e-01	0.0889
55276	PGM2	P9T-E	Human	Esophagus	ESCC	3.81e-09	2.19e-01	0.1131
55276	PGM2	P10T-E	Human	Esophagus	ESCC	3.88e-14	9.44e-02	0.116
55276	PGM2	P11T-E	Human	Esophagus	ESCC	1.25e-09	4.31e-01	0.1426
55276	PGM2	P12T-E	Human	Esophagus	ESCC	5.59e-14	2.21e-01	0.1122
55276	PGM2	P15T-E	Human	Esophagus	ESCC	6.29e-11	3.32e-01	0.1149
55276	PGM2	P16T-E	Human	Esophagus	ESCC	3.66e-21	4.62e-01	0.1153
55276	PGM2	P17T-E	Human	Esophagus	ESCC	1.19e-05	5.26e-01	0.1278
55276	PGM2	P19T-E	Human	Esophagus	ESCC	9.25e-04	5.65e-01	0.1662
55276	PGM2	P20T-E	Human	Esophagus	ESCC	2.11e-08	1.67e-01	0.1124
55276	PGM2	P21T-E	Human	Esophagus	ESCC	7.53e-14	2.73e-01	0.1617

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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
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:00059969	Esophagus	ESCC	monosaccharide metabolic process	159/8552	257/18723	1.11e-07	1.81e-06	159
GO:00193189	Esophagus	ESCC	hexose metabolic process	147/8552	237/18723	2.63e-07	3.94e-06	147
GO:00060069	Esophagus	ESCC	glucose metabolic process	119/8552	196/18723	1.51e-05	1.36e-04	119
GO:19011362	Esophagus	ESCC	carbohydrate derivative catabolic process	99/8552	172/18723	1.11e-03	5.54e-03	99
GO:001969212	Esophagus	ESCC	deoxyribose phosphate metabolic process	29/8552	42/18723	1.87e-03	8.46e-03	29
GO:000599621	Liver	HCC	monosaccharide metabolic process	167/7958	257/18723	2.31e-13	1.25e-11	167
GO:001931821	Liver	HCC	hexose metabolic process	155/7958	237/18723	7.63e-13	3.90e-11	155
GO:000600621	Liver	HCC	glucose metabolic process	128/7958	196/18723	8.60e-11	3.06e-09	128
GO:00196923	Oral cavity	OSCC	deoxyribose phosphate metabolic process	30/7305	42/18723	2.06e-05	1.96e-04	30
GO:00059968	Oral cavity	OSCC	monosaccharide metabolic process	129/7305	257/18723	1.63e-04	1.13e-03	129
GO:19011361	Oral cavity	OSCC	carbohydrate derivative catabolic process	89/7305	172/18723	4.52e-04	2.73e-03	89
GO:00193188	Oral cavity	OSCC	hexose metabolic process	118/7305	237/18723	4.53e-04	2.73e-03	118
GO:00060068	Oral cavity	OSCC	glucose metabolic process	98/7305	196/18723	1.10e-03	5.63e-03	98
GO:00463862	Oral cavity	OSCC	deoxyribose phosphate catabolic process	21/7305	31/18723	1.13e-03	5.75e-03	21
GO:000599613	Oral cavity	LP	monosaccharide metabolic process	86/4623	257/18723	9.13e-04	7.79e-03	86
GO:001931813	Oral cavity	LP	hexose metabolic process	78/4623	237/18723	2.55e-03	1.80e-02	78
GO:000600614	Oral cavity	LP	glucose metabolic process	64/4623	196/18723	7.09e-03	3.98e-02	64
GO:00060067	Prostate	BPH	glucose metabolic process	49/3107	196/18723	1.65e-03	9.55e-03	49
GO:000600613	Prostate	Tumor	glucose metabolic process	55/3246	196/18723	1.22e-04	1.14e-03	55
GO:00193187	Prostate	Tumor	hexose metabolic process	59/3246	237/18723	1.96e-03	1.14e-02	59

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa012505	Esophagus	ESCC	Biosynthesis of nucleotide sugars	28/4205	37/8465	1.10e-03	3.42e-03	1.75e-03	28
hsa005202	Esophagus	ESCC	Amino sugar and nucleotide sugar metabolism	35/4205	49/8465	1.60e-03	4.88e-03	2.50e-03	35
hsa0001016	Esophagus	ESCC	Glycolysis / Gluconeogenesis	42/4205	67/8465	2.15e-02	4.78e-02	2.45e-02	42
hsa0125012	Esophagus	ESCC	Biosynthesis of nucleotide sugars	28/4205	37/8465	1.10e-03	3.42e-03	1.75e-03	28
hsa0052011	Esophagus	ESCC	Amino sugar and nucleotide sugar metabolism	35/4205	49/8465	1.60e-03	4.88e-03	2.50e-03	35
hsa0001017	Esophagus	ESCC	Glycolysis / Gluconeogenesis	42/4205	67/8465	2.15e-02	4.78e-02	2.45e-02	42
hsa00520	Oral cavity	OSCC	Amino sugar and nucleotide sugar metabolism	34/3704	49/8465	2.48e-04	8.08e-04	4.11e-04	34
hsa012504	Oral cavity	OSCC	Biosynthesis of nucleotide sugars	25/3704	37/8465	2.93e-03	7.49e-03	3.81e-03	25
hsa0001014	Oral cavity	OSCC	Glycolysis / Gluconeogenesis	40/3704	67/8465	6.08e-03	1.44e-02	7.31e-03	40
hsa005201	Oral cavity	OSCC	Amino sugar and nucleotide sugar metabolism	34/3704	49/8465	2.48e-04	8.08e-04	4.11e-04	34
hsa0125011	Oral cavity	OSCC	Biosynthesis of nucleotide sugars	25/3704	37/8465	2.93e-03	7.49e-03	3.81e-03	25
hsa0001015	Oral cavity	OSCC	Glycolysis / Gluconeogenesis	40/3704	67/8465	6.08e-03	1.44e-02	7.31e-03	40

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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

PGM2

SNV

Missense_Mutation

rs151106378

c.1096C>T

p.Arg366Cys

p.R366C

Q96G03

protein_coding

tolerated(0.08)

possibly_damaging(0.505)

TCGA-A2-A0T0-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

taxotere

PGM2

SNV

Missense_Mutation

novel

c.455N>T

p.Ser152Leu

p.S152L

Q96G03

protein_coding

tolerated(0.72)

benign(0)

TCGA-C8-A8HQ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

PGM2

SNV

Missense_Mutation

novel

c.562N>G

p.His188Asp

p.H188D

Q96G03

protein_coding

deleterious(0.01)

benign(0.141)

TCGA-C8-A8HQ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

PGM2

SNV

Missense_Mutation

c.601G>C

p.Glu201Gln

p.E201Q

Q96G03

protein_coding

tolerated(0.06)

benign(0.091)

TCGA-EW-A1J5-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

PGM2

insertion

In_Frame_Ins

novel

c.287_288insCATCCATTCATTCATTCATTTAACACACTTATTGAGTAC

p.Leu96delinsPheIleHisSerPheIleHisLeuThrHisLeuLeuSerThr

p.L96delinsFIHSFIHLTHLLST

Q96G03

protein_coding

TCGA-AN-A049-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

PGM2

SNV

Missense_Mutation

novel

c.1447A>T

p.Ile483Phe

p.I483F

Q96G03

protein_coding

tolerated(0.22)

benign(0.038)

TCGA-C5-A1M8-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

PGM2

SNV

Missense_Mutation

c.1436N>T

p.Ala479Val

p.A479V

Q96G03

protein_coding

tolerated(0.17)

benign(0.007)

TCGA-DS-A1OA-01

Cervix

cervical & endocervical cancer

Female

>=65

I/II

Chemotherapy

carboplatin

PGM2

SNV

Missense_Mutation

c.874N>G

p.Lys292Glu

p.K292E

Q96G03

protein_coding

deleterious(0.05)

benign(0.014)

TCGA-A6-6653-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

PGM2

SNV

Missense_Mutation

novel

c.964G>T

p.Asp322Tyr

p.D322Y

Q96G03

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-EI-6917-01

Colorectum

rectum adenocarcinoma

Male

<65

III/IV

Chemotherapy

5fluorouracil+oxaciplatina+l-folinian

PGM2

SNV

Missense_Mutation

novel

c.149G>A

p.Cys50Tyr

p.C50Y

Q96G03

protein_coding

tolerated(0.26)

benign(0.001)

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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