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: PMM2

Gene summary for PMM2

Gene summary.

Gene information	Species	Human
	Gene symbol	PMM2
	Gene ID	5373
	Gene name	phosphomannomutase 2
	Gene Alias	CDG1
	Cytomap	16p13.2
	Gene Type	protein-coding
	GO ID	GO:0005975
	UniProtAcc	A0A0S2Z4J6

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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
5373	PMM2	HTA11_3410_2000001011	Human	Colorectum	AD	1.00e-09	-4.84e-01	0.0155
5373	PMM2	HTA11_3361_2000001011	Human	Colorectum	AD	1.78e-05	-5.69e-01	-0.1207
5373	PMM2	HTA11_866_3004761011	Human	Colorectum	AD	3.95e-07	-4.82e-01	0.096
5373	PMM2	HTA11_99999970781_79442	Human	Colorectum	MSS	1.80e-16	-5.41e-01	0.294
5373	PMM2	HTA11_99999971662_82457	Human	Colorectum	MSS	6.21e-03	-2.91e-01	0.3859
5373	PMM2	HTA11_99999974143_84620	Human	Colorectum	MSS	1.88e-16	-5.95e-01	0.3005
5373	PMM2	F007	Human	Colorectum	FAP	2.30e-02	-2.57e-01	0.1176
5373	PMM2	A001-C-207	Human	Colorectum	FAP	1.92e-02	-1.71e-01	0.1278
5373	PMM2	A015-C-203	Human	Colorectum	FAP	1.20e-25	-5.48e-01	-0.1294
5373	PMM2	A015-C-204	Human	Colorectum	FAP	1.26e-05	-1.99e-01	-0.0228
5373	PMM2	A014-C-040	Human	Colorectum	FAP	3.79e-05	-4.65e-01	-0.1184
5373	PMM2	A002-C-201	Human	Colorectum	FAP	9.68e-17	-4.95e-01	0.0324
5373	PMM2	A002-C-203	Human	Colorectum	FAP	8.03e-04	-2.08e-01	0.2786
5373	PMM2	A001-C-119	Human	Colorectum	FAP	9.23e-11	-4.56e-01	-0.1557
5373	PMM2	A001-C-108	Human	Colorectum	FAP	9.79e-18	-4.76e-01	-0.0272
5373	PMM2	A002-C-205	Human	Colorectum	FAP	1.41e-24	-5.58e-01	-0.1236
5373	PMM2	A001-C-104	Human	Colorectum	FAP	1.75e-05	-3.88e-01	0.0184
5373	PMM2	A015-C-005	Human	Colorectum	FAP	9.09e-05	-3.54e-01	-0.0336
5373	PMM2	A015-C-006	Human	Colorectum	FAP	3.62e-18	-5.62e-01	-0.0994
5373	PMM2	A015-C-106	Human	Colorectum	FAP	1.19e-13	-3.61e-01	-0.0511

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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
Liver		HCC: Hepatocellular carcinoma
		NAFLD: Non-alcoholic fatty liver disease
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:0019318	Colorectum	AD	hexose metabolic process	77/3918	237/18723	1.96e-05	4.01e-04	77
GO:0005996	Colorectum	AD	monosaccharide metabolic process	80/3918	257/18723	7.31e-05	1.17e-03	80
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:00064871	Colorectum	MSS	protein N-linked glycosylation	23/3467	65/18723	9.47e-04	9.54e-03	23
GO:00193182	Colorectum	MSS	hexose metabolic process	63/3467	237/18723	1.32e-03	1.25e-02	63
GO:00059962	Colorectum	MSS	monosaccharide metabolic process	66/3467	257/18723	2.61e-03	2.06e-02	66
GO:00092252	Colorectum	MSS	nucleotide-sugar metabolic process	14/3467	36/18723	3.40e-03	2.56e-02	14
GO:00193183	Colorectum	FAP	hexose metabolic process	58/2622	237/18723	1.09e-05	3.08e-04	58
GO:00059963	Colorectum	FAP	monosaccharide metabolic process	59/2622	257/18723	6.79e-05	1.28e-03	59
GO:00064861	Colorectum	FAP	protein glycosylation	48/2622	226/18723	1.85e-03	1.57e-02	48
GO:00434131	Colorectum	FAP	macromolecule glycosylation	48/2622	226/18723	1.85e-03	1.57e-02	48
GO:00700851	Colorectum	FAP	glycosylation	50/2622	240/18723	2.30e-03	1.85e-02	50
GO:0009101	Colorectum	FAP	glycoprotein biosynthetic process	63/2622	317/18723	2.31e-03	1.86e-02	63
GO:00064872	Colorectum	FAP	protein N-linked glycosylation	18/2622	65/18723	2.85e-03	2.19e-02	18
GO:00092253	Colorectum	CRC	nucleotide-sugar metabolic process	10/2078	36/18723	4.68e-03	3.62e-02	10
GO:00064876	Esophagus	HGIN	protein N-linked glycosylation	17/2587	65/18723	6.04e-03	4.87e-02	17

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa00051	Colorectum	AD	Fructose and mannose metabolism	17/2092	34/8465	1.25e-03	8.02e-03	5.12e-03	17
hsa000511	Colorectum	AD	Fructose and mannose metabolism	17/2092	34/8465	1.25e-03	8.02e-03	5.12e-03	17
hsa01250	Colorectum	FAP	Biosynthesis of nucleotide sugars	13/1404	37/8465	4.79e-03	1.91e-02	1.16e-02	13
hsa012501	Colorectum	FAP	Biosynthesis of nucleotide sugars	13/1404	37/8465	4.79e-03	1.91e-02	1.16e-02	13
hsa012405	Esophagus	ESCC	Biosynthesis of cofactors	97/4205	153/8465	3.88e-04	1.35e-03	6.94e-04	97
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
hsa000512	Esophagus	ESCC	Fructose and mannose metabolism	24/4205	34/8465	1.09e-02	2.51e-02	1.29e-02	24
hsa0124012	Esophagus	ESCC	Biosynthesis of cofactors	97/4205	153/8465	3.88e-04	1.35e-03	6.94e-04	97
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
hsa0005111	Esophagus	ESCC	Fructose and mannose metabolism	24/4205	34/8465	1.09e-02	2.51e-02	1.29e-02	24
hsa012402	Liver	HCC	Biosynthesis of cofactors	103/4020	153/8465	4.67e-07	5.05e-06	2.81e-06	103
hsa012403	Liver	HCC	Biosynthesis of cofactors	103/4020	153/8465	4.67e-07	5.05e-06	2.81e-06	103

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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

PMM2

SNV

Missense_Mutation

c.569N>A

p.Arg190Lys

p.R190K

O15305

protein_coding

tolerated(0.16)

possibly_damaging(0.84)

TCGA-BI-A0VS-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

PMM2

SNV

Missense_Mutation

novel

c.283N>A

p.Leu95Ile

p.L95I

O15305

protein_coding

tolerated(0.19)

benign(0.007)

TCGA-MA-AA41-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

PMM2

SNV

Missense_Mutation

c.618C>A

p.Phe206Leu

p.F206L

O15305

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-A5-A2K5-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

PMM2

SNV

Missense_Mutation

rs746610168

c.421C>T

p.Arg141Cys

p.R141C

O15305

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-AP-A051-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

PMM2

SNV

Missense_Mutation

rs200503569

c.323N>T

p.Ala108Val

p.A108V

O15305

protein_coding

deleterious(0.01)

benign(0.107)

TCGA-AP-A0LM-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

cisplatin

PMM2

SNV

Missense_Mutation

novel

c.269A>G

p.His90Arg

p.H90R

O15305

protein_coding

tolerated(0.18)

possibly_damaging(0.489)

TCGA-AP-A1DK-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

PMM2

SNV

Missense_Mutation

novel

c.281N>T

p.Ala94Val

p.A94V

O15305

protein_coding

deleterious(0.01)

benign(0.003)

TCGA-AX-A2HD-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

III/IV

Unknown

PMM2

SNV

Missense_Mutation

c.229N>G

p.Lys77Glu

p.K77E

O15305

protein_coding

tolerated(0.08)

benign(0.007)

TCGA-B5-A11H-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

III/IV

Hormone Therapy

megace

PMM2

SNV

Missense_Mutation

c.254N>G

p.Gln85Arg

p.Q85R

O15305

protein_coding

deleterious(0.03)

benign(0.072)

TCGA-BS-A0UJ-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

PMM2

SNV

Missense_Mutation

c.618C>A

p.Phe206Leu

p.F206L

O15305

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-BS-A0UV-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
5373	PMM2	ENZYME		EBSELEN	EBSELEN

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