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: STT3A

Gene summary for STT3A

Gene summary.

Gene information	Species	Human
	Gene symbol	STT3A
	Gene ID	3703
	Gene name	STT3 oligosaccharyltransferase complex catalytic subunit A
	Gene Alias	ITM1
	Cytomap	11q24.2
	Gene Type	protein-coding
	GO ID	GO:0006464
	UniProtAcc	P46977

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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
3703	STT3A	HTA11_347_2000001011	Human	Colorectum	AD	3.34e-12	4.35e-01	-0.1954
3703	STT3A	HTA11_1391_2000001011	Human	Colorectum	AD	4.11e-03	3.36e-01	-0.059
3703	STT3A	HTA11_5212_2000001011	Human	Colorectum	AD	1.57e-02	2.19e-01	-0.2061
3703	STT3A	HTA11_866_3004761011	Human	Colorectum	AD	1.11e-02	2.47e-01	0.096
3703	STT3A	HTA11_99999970781_79442	Human	Colorectum	MSS	1.07e-08	4.23e-01	0.294
3703	STT3A	HTA11_99999965062_69753	Human	Colorectum	MSI-H	1.95e-03	9.41e-01	0.3487
3703	STT3A	HTA11_99999971662_82457	Human	Colorectum	MSS	9.98e-11	5.46e-01	0.3859
3703	STT3A	LZE4T	Human	Esophagus	ESCC	3.56e-12	3.35e-01	0.0811
3703	STT3A	LZE8T	Human	Esophagus	ESCC	3.49e-08	1.22e-01	0.067
3703	STT3A	LZE20T	Human	Esophagus	ESCC	3.68e-04	2.54e-01	0.0662
3703	STT3A	LZE24T	Human	Esophagus	ESCC	1.99e-17	4.65e-01	0.0596
3703	STT3A	LZE21T	Human	Esophagus	ESCC	3.52e-03	1.58e-01	0.0655
3703	STT3A	P1T-E	Human	Esophagus	ESCC	2.87e-04	2.67e-01	0.0875
3703	STT3A	P2T-E	Human	Esophagus	ESCC	2.62e-16	3.43e-01	0.1177
3703	STT3A	P4T-E	Human	Esophagus	ESCC	8.68e-43	1.02e+00	0.1323
3703	STT3A	P5T-E	Human	Esophagus	ESCC	2.14e-11	2.66e-01	0.1327
3703	STT3A	P8T-E	Human	Esophagus	ESCC	9.18e-27	5.75e-01	0.0889
3703	STT3A	P9T-E	Human	Esophagus	ESCC	1.10e-16	2.93e-01	0.1131
3703	STT3A	P10T-E	Human	Esophagus	ESCC	1.20e-30	4.66e-01	0.116
3703	STT3A	P11T-E	Human	Esophagus	ESCC	1.09e-24	9.36e-01	0.1426

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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
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
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: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:0006487	Colorectum	AD	protein N-linked glycosylation	25/3918	65/18723	9.12e-04	8.71e-03	25
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: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
GO:00182793	Colorectum	MSI-H	protein N-linked glycosylation via asparagine	7/1319	23/18723	7.62e-04	1.42e-02	7
GO:00181963	Colorectum	MSI-H	peptidyl-asparagine modification	7/1319	24/18723	1.01e-03	1.73e-02	7
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:00181969	Esophagus	ESCC	peptidyl-asparagine modification	22/8552	24/18723	2.82e-06	3.21e-05	22
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:00091012	Esophagus	ESCC	glycoprotein biosynthetic process	181/8552	317/18723	2.54e-05	2.15e-04	181
GO:00182795	Liver	Cirrhotic	protein N-linked glycosylation via asparagine	16/4634	23/18723	7.54e-06	1.15e-04	16

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa005134	Liver	Cirrhotic	Various types of N-glycan biosynthesis	26/2530	42/8465	1.65e-05	1.41e-04	8.69e-05	26
hsa0414115	Liver	Cirrhotic	Protein processing in endoplasmic reticulum	114/2530	174/8465	1.16e-22	9.67e-21	5.96e-21	114
hsa0051011	Liver	Cirrhotic	N-Glycan biosynthesis	32/2530	53/8465	3.82e-06	4.10e-05	2.53e-05	32
hsa0051311	Liver	Cirrhotic	Various types of N-glycan biosynthesis	26/2530	42/8465	1.65e-05	1.41e-04	8.69e-05	26
hsa0414122	Liver	HCC	Protein processing in endoplasmic reticulum	146/4020	174/8465	7.34e-24	2.46e-21	1.37e-21	146
hsa0051021	Liver	HCC	N-Glycan biosynthesis	40/4020	53/8465	2.95e-05	1.87e-04	1.04e-04	40
hsa005132	Liver	HCC	Various types of N-glycan biosynthesis	30/4020	42/8465	1.41e-03	5.07e-03	2.82e-03	30
hsa0414132	Liver	HCC	Protein processing in endoplasmic reticulum	146/4020	174/8465	7.34e-24	2.46e-21	1.37e-21	146
hsa0051031	Liver	HCC	N-Glycan biosynthesis	40/4020	53/8465	2.95e-05	1.87e-04	1.04e-04	40
hsa005133	Liver	HCC	Various types of N-glycan biosynthesis	30/4020	42/8465	1.41e-03	5.07e-03	2.82e-03	30
hsa0414130	Oral cavity	OSCC	Protein processing in endoplasmic reticulum	143/3704	174/8465	6.82e-26	2.28e-23	1.16e-23	143
hsa005105	Oral cavity	OSCC	N-Glycan biosynthesis	39/3704	53/8465	9.77e-06	4.36e-05	2.22e-05	39
hsa005135	Oral cavity	OSCC	Various types of N-glycan biosynthesis	29/3704	42/8465	8.03e-04	2.32e-03	1.18e-03	29
hsa04141113	Oral cavity	OSCC	Protein processing in endoplasmic reticulum	143/3704	174/8465	6.82e-26	2.28e-23	1.16e-23	143
hsa0051012	Oral cavity	OSCC	N-Glycan biosynthesis	39/3704	53/8465	9.77e-06	4.36e-05	2.22e-05	39
hsa0051312	Oral cavity	OSCC	Various types of N-glycan biosynthesis	29/3704	42/8465	8.03e-04	2.32e-03	1.18e-03	29
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

STT3A

SNV

Missense_Mutation

rs752248846

c.2066N>G

p.Val689Gly

p.V689G

P46977

protein_coding

deleterious(0)

probably_damaging(0.99)

TCGA-A2-A1G0-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

taxotere

STT3A

SNV

Missense_Mutation

rs752248846

c.2066T>G

p.Val689Gly

p.V689G

P46977

protein_coding

deleterious(0)

probably_damaging(0.99)

TCGA-A2-A25A-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unspecific

Cytoxan

STT3A

SNV

Missense_Mutation

rs752248846

c.2066N>G

p.Val689Gly

p.V689G

P46977

protein_coding

deleterious(0)

probably_damaging(0.99)

TCGA-AC-A23C-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

chemo

STT3A

SNV

Missense_Mutation

rs752248846

c.2066N>G

p.Val689Gly

p.V689G

P46977

protein_coding

deleterious(0)

probably_damaging(0.99)

TCGA-AR-A255-01

Breast

breast invasive carcinoma

Female

<65

I/II

Targeted Molecular therapy

trastuzumab

STT3A

SNV

Missense_Mutation

rs752248846

c.2066N>G

p.Val689Gly

p.V689G

P46977

protein_coding

deleterious(0)

probably_damaging(0.99)

TCGA-C8-A273-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

tamoxiphen

STT3A

SNV

Missense_Mutation

rs752248846

c.2066N>G

p.Val689Gly

p.V689G

P46977

protein_coding

deleterious(0)

probably_damaging(0.99)

TCGA-D8-A1Y1-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Hormone Therapy

tamoxiphen

STT3A

SNV

Missense_Mutation

rs752248846

c.2066N>G

p.Val689Gly

p.V689G

P46977

protein_coding

deleterious(0)

probably_damaging(0.99)

TCGA-E9-A1RE-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Hormone Therapy

tamoxiphen

STT3A

SNV

Missense_Mutation

rs764341467

c.898N>T

p.Arg300Trp

p.R300W

P46977

protein_coding

tolerated(0.19)

possibly_damaging(0.901)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

STT3A

SNV

Missense_Mutation

rs540684198

c.224N>A

p.Arg75Gln

p.R75Q

P46977

protein_coding

deleterious(0.01)

benign(0.206)

TCGA-FU-A23K-01

Cervix

cervical & endocervical cancer

Female

<65

III/IV

Unknown

STT3A

SNV

Missense_Mutation

novel

c.671T>C

p.Leu224Pro

p.L224P

P46977

protein_coding

deleterious(0)

probably_damaging(0.988)

TCGA-AA-3520-01

Colorectum

colon adenocarcinoma

Female

>=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

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