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: UGGT1

Gene summary for UGGT1

Gene summary.

Gene information	Species	Human
	Gene symbol	UGGT1
	Gene ID	56886
	Gene name	UDP-glucose glycoprotein glucosyltransferase 1
	Gene Alias	HUGT1
	Cytomap	2q14.3
	Gene Type	protein-coding
	GO ID	GO:0006011
	UniProtAcc	Q9NYU2

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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
56886	UGGT1	LZE2T	Human	Esophagus	ESCC	1.54e-03	4.41e-01	0.082
56886	UGGT1	LZE4T	Human	Esophagus	ESCC	1.98e-05	2.55e-01	0.0811
56886	UGGT1	LZE5T	Human	Esophagus	ESCC	1.37e-04	4.16e-01	0.0514
56886	UGGT1	LZE7T	Human	Esophagus	ESCC	5.93e-05	3.74e-01	0.0667
56886	UGGT1	LZE20T	Human	Esophagus	ESCC	6.23e-03	1.39e-01	0.0662
56886	UGGT1	LZE22T	Human	Esophagus	ESCC	1.67e-02	2.55e-01	0.068
56886	UGGT1	LZE24T	Human	Esophagus	ESCC	1.07e-06	1.80e-01	0.0596
56886	UGGT1	P1T-E	Human	Esophagus	ESCC	4.77e-03	2.88e-01	0.0875
56886	UGGT1	P2T-E	Human	Esophagus	ESCC	9.02e-09	2.31e-01	0.1177
56886	UGGT1	P4T-E	Human	Esophagus	ESCC	3.32e-07	2.42e-01	0.1323
56886	UGGT1	P5T-E	Human	Esophagus	ESCC	1.63e-11	1.66e-01	0.1327
56886	UGGT1	P8T-E	Human	Esophagus	ESCC	2.47e-08	2.09e-01	0.0889
56886	UGGT1	P9T-E	Human	Esophagus	ESCC	5.70e-21	2.34e-01	0.1131
56886	UGGT1	P10T-E	Human	Esophagus	ESCC	3.62e-09	2.33e-01	0.116
56886	UGGT1	P11T-E	Human	Esophagus	ESCC	4.02e-10	3.64e-01	0.1426
56886	UGGT1	P12T-E	Human	Esophagus	ESCC	8.54e-14	2.32e-01	0.1122
56886	UGGT1	P15T-E	Human	Esophagus	ESCC	1.53e-14	3.46e-01	0.1149
56886	UGGT1	P16T-E	Human	Esophagus	ESCC	8.34e-18	2.40e-01	0.1153
56886	UGGT1	P17T-E	Human	Esophagus	ESCC	1.09e-02	2.29e-01	0.1278
56886	UGGT1	P20T-E	Human	Esophagus	ESCC	5.32e-04	1.34e-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
Prostate		BPH: Benign Prostatic Hyperplasia
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:0010498111	Esophagus	ESCC	proteasomal protein catabolic process	369/8552	490/18723	1.13e-41	1.80e-38	369
GO:0034976111	Esophagus	ESCC	response to endoplasmic reticulum stress	192/8552	256/18723	7.15e-22	1.30e-19	192
GO:0006457110	Esophagus	ESCC	protein folding	163/8552	212/18723	1.13e-20	1.74e-18	163
GO:0035966111	Esophagus	ESCC	response to topologically incorrect protein	125/8552	159/18723	1.44e-17	1.27e-15	125
GO:0035967111	Esophagus	ESCC	cellular response to topologically incorrect protein	90/8552	116/18723	1.94e-12	8.11e-11	90
GO:003650315	Esophagus	ESCC	ERAD pathway	82/8552	107/18723	5.80e-11	1.84e-09	82
GO:000648714	Esophagus	ESCC	protein N-linked glycosylation	51/8552	65/18723	6.41e-08	1.13e-06	51
GO:00091002	Esophagus	ESCC	glycoprotein metabolic process	226/8552	387/18723	2.64e-07	3.94e-06	226
GO:0006458110	Esophagus	ESCC	'de novo' protein folding	36/8552	43/18723	2.90e-07	4.20e-06	36
GO:00181969	Esophagus	ESCC	peptidyl-asparagine modification	22/8552	24/18723	2.82e-06	3.21e-05	22
GO:0051084110	Esophagus	ESCC	'de novo' posttranslational protein folding	32/8552	39/18723	3.27e-06	3.65e-05	32
GO:00700854	Esophagus	ESCC	glycosylation	144/8552	240/18723	5.12e-06	5.38e-05	144
GO:00182799	Esophagus	ESCC	protein N-linked glycosylation via asparagine	21/8552	23/18723	5.69e-06	5.90e-05	21
GO:00064865	Esophagus	ESCC	protein glycosylation	135/8552	226/18723	1.36e-05	1.24e-04	135
GO:00434135	Esophagus	ESCC	macromolecule glycosylation	135/8552	226/18723	1.36e-05	1.24e-04	135
GO:00092256	Esophagus	ESCC	nucleotide-sugar metabolic process	29/8552	36/18723	1.91e-05	1.67e-04	29
GO:00091012	Esophagus	ESCC	glycoprotein biosynthetic process	181/8552	317/18723	2.54e-05	2.15e-04	181
GO:007171211	Esophagus	ESCC	ER-associated misfolded protein catabolic process	12/8552	12/18723	8.21e-05	6.01e-04	12
GO:00517884	Esophagus	ESCC	response to misfolded protein	21/8552	25/18723	9.12e-05	6.54e-04	21
GO:00712184	Esophagus	ESCC	cellular response to misfolded protein	19/8552	23/18723	3.12e-04	1.85e-03	19

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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
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
hsa0414128	Prostate	BPH	Protein processing in endoplasmic reticulum	97/1718	174/8465	2.37e-25	1.30e-23	8.07e-24	97
hsa04141112	Prostate	BPH	Protein processing in endoplasmic reticulum	97/1718	174/8465	2.37e-25	1.30e-23	8.07e-24	97
hsa0414129	Prostate	Tumor	Protein processing in endoplasmic reticulum	99/1791	174/8465	2.58e-25	1.71e-23	1.06e-23	99
hsa0414137	Prostate	Tumor	Protein processing in endoplasmic reticulum	99/1791	174/8465	2.58e-25	1.71e-23	1.06e-23	99

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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

UGGT1

SNV

Missense_Mutation

c.1187A>G

p.Asn396Ser

p.N396S

Q9NYU2

protein_coding

deleterious(0)

probably_damaging(0.997)

TCGA-A8-A0A4-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

tamoxiphen

UGGT1

SNV

Missense_Mutation

c.4426N>C

p.Glu1476Gln

p.E1476Q

Q9NYU2

protein_coding

deleterious(0.02)

probably_damaging(0.996)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

UGGT1

SNV

Missense_Mutation

c.4657N>A

p.Glu1553Lys

p.E1553K

Q9NYU2

protein_coding

tolerated(0.07)

benign(0.025)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

UGGT1

SNV

Missense_Mutation

rs766018217

c.1114N>A

p.Glu372Lys

p.E372K

Q9NYU2

protein_coding

deleterious(0)

probably_damaging(0.975)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

UGGT1

SNV

Missense_Mutation

c.2081N>A

p.Arg694Gln

p.R694Q

Q9NYU2

protein_coding

deleterious(0)

probably_damaging(0.984)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

UGGT1

SNV

Missense_Mutation

rs764969270

c.4166N>A

p.Arg1389Gln

p.R1389Q

Q9NYU2

protein_coding

deleterious(0)

probably_damaging(0.97)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

UGGT1

SNV

Missense_Mutation

c.4078N>T

p.Asp1360Tyr

p.D1360Y

Q9NYU2

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-D8-A1JA-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

adriamycin

UGGT1

SNV

Missense_Mutation

c.4105G>C

p.Glu1369Gln

p.E1369Q

Q9NYU2

protein_coding

deleterious(0)

probably_damaging(0.994)

TCGA-D8-A27G-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

UGGT1

SNV

Missense_Mutation

rs764250020

c.1468C>T

p.Arg490Trp

p.R490W

Q9NYU2

protein_coding

deleterious(0)

probably_damaging(0.987)

TCGA-E2-A574-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

UGGT1

SNV

Missense_Mutation

rs774831190

c.1621N>A

p.Val541Ile

p.V541I

Q9NYU2

protein_coding

tolerated(0.42)

benign(0.001)

TCGA-GM-A2DD-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

fluorouracil

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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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