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: OSTC

Gene summary for OSTC

Gene summary.

Gene information	Species	Human
	Gene symbol	OSTC
	Gene ID	58505
	Gene name	oligosaccharyltransferase complex non-catalytic subunit
	Gene Alias	DC2
	Cytomap	4q25
	Gene Type	protein-coding
	GO ID	GO:0006464
	UniProtAcc	A0A087WUD3

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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
58505	OSTC	CA_HPV_1	Human	Cervix	CC	3.46e-11	-9.82e-02	0.0264
58505	OSTC	CA_HPV_3	Human	Cervix	CC	2.30e-03	2.90e-02	0.0414
58505	OSTC	CCI_3	Human	Cervix	CC	4.04e-02	-5.01e-01	0.516
58505	OSTC	CCII_1	Human	Cervix	CC	1.12e-15	-6.83e-01	0.3249
58505	OSTC	L1	Human	Cervix	CC	3.05e-06	-3.56e-01	0.0802
58505	OSTC	HTA11_866_3004761011	Human	Colorectum	AD	9.16e-04	3.70e-01	0.096
58505	OSTC	HTA11_6801_2000001011	Human	Colorectum	SER	3.32e-02	5.79e-01	0.0171
58505	OSTC	HTA11_99999970781_79442	Human	Colorectum	MSS	4.18e-12	5.39e-01	0.294
58505	OSTC	HTA11_99999965062_69753	Human	Colorectum	MSI-H	1.40e-04	1.38e+00	0.3487
58505	OSTC	HTA11_99999965104_69814	Human	Colorectum	MSS	1.36e-07	6.58e-01	0.281
58505	OSTC	HTA11_99999971662_82457	Human	Colorectum	MSS	2.37e-10	6.18e-01	0.3859
58505	OSTC	A015-C-203	Human	Colorectum	FAP	1.90e-03	-1.25e-01	-0.1294
58505	OSTC	A001-C-108	Human	Colorectum	FAP	1.33e-02	-9.16e-02	-0.0272
58505	OSTC	A015-C-106	Human	Colorectum	FAP	5.77e-04	-1.26e-01	-0.0511
58505	OSTC	A015-C-104	Human	Colorectum	FAP	2.97e-03	-6.34e-02	-0.1899
58505	OSTC	A002-C-116	Human	Colorectum	FAP	3.42e-04	-1.08e-01	-0.0452
58505	OSTC	AEH-subject1	Human	Endometrium	AEH	4.56e-36	-7.31e-01	-0.3059
58505	OSTC	AEH-subject2	Human	Endometrium	AEH	9.30e-30	-6.74e-01	-0.2525
58505	OSTC	AEH-subject3	Human	Endometrium	AEH	6.30e-17	-4.56e-01	-0.2576
58505	OSTC	AEH-subject4	Human	Endometrium	AEH	2.53e-21	-6.05e-01	-0.2657

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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
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
Endometrium		AEH: Atypical endometrial hyperplasia
		EEC: Endometrioid Cancer
Esophagus		ESCC: Esophageal squamous cell carcinoma
		HGIN: High-grade intraepithelial neoplasias
		LGIN: Low-grade intraepithelial neoplasias
GC		CAG: Chronic atrophic gastritis
		CAG with IM: Chronic atrophic gastritis with intestinal metaplasia
		CSG: Chronic superficial gastritis
		GC: Gastric cancer
		SIM: Severe intestinal metaplasia
		WIM: Wild intestinal metaplasia
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
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:00182791	Colorectum	SER	protein N-linked glycosylation via asparagine	9/2897	23/18723	5.20e-03	3.95e-02	9
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
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:00182794	Colorectum	FAP	protein N-linked glycosylation via asparagine	10/2622	23/18723	5.68e-04	6.33e-03	10
GO:00181964	Colorectum	FAP	peptidyl-asparagine modification	10/2622	24/18723	8.53e-04	8.79e-03	10
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

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0414120	Cervix	CC	Protein processing in endoplasmic reticulum	55/1267	174/8465	1.74e-08	2.68e-07	1.58e-07	55
hsa04141110	Cervix	CC	Protein processing in endoplasmic reticulum	55/1267	174/8465	1.74e-08	2.68e-07	1.58e-07	55
hsa00510	Colorectum	AD	N-Glycan biosynthesis	21/2092	53/8465	1.15e-02	4.24e-02	2.71e-02	21
hsa005101	Colorectum	AD	N-Glycan biosynthesis	21/2092	53/8465	1.15e-02	4.24e-02	2.71e-02	21
hsa041414	Colorectum	MSS	Protein processing in endoplasmic reticulum	75/1875	174/8465	3.78e-10	8.44e-09	5.17e-09	75
hsa005102	Colorectum	MSS	N-Glycan biosynthesis	20/1875	53/8465	7.17e-03	2.83e-02	1.73e-02	20
hsa00513	Colorectum	MSS	Various types of N-glycan biosynthesis	16/1875	42/8465	1.39e-02	4.53e-02	2.77e-02	16
hsa041415	Colorectum	MSS	Protein processing in endoplasmic reticulum	75/1875	174/8465	3.78e-10	8.44e-09	5.17e-09	75
hsa005103	Colorectum	MSS	N-Glycan biosynthesis	20/1875	53/8465	7.17e-03	2.83e-02	1.73e-02	20
hsa005131	Colorectum	MSS	Various types of N-glycan biosynthesis	16/1875	42/8465	1.39e-02	4.53e-02	2.77e-02	16
hsa041416	Colorectum	MSI-H	Protein processing in endoplasmic reticulum	46/797	174/8465	4.53e-11	9.78e-10	8.19e-10	46
hsa041417	Colorectum	MSI-H	Protein processing in endoplasmic reticulum	46/797	174/8465	4.53e-11	9.78e-10	8.19e-10	46
hsa041418	Colorectum	FAP	Protein processing in endoplasmic reticulum	50/1404	174/8465	3.64e-05	3.68e-04	2.24e-04	50
hsa041419	Colorectum	FAP	Protein processing in endoplasmic reticulum	50/1404	174/8465	3.64e-05	3.68e-04	2.24e-04	50
hsa0414126	Endometrium	AEH	Protein processing in endoplasmic reticulum	62/1197	174/8465	5.97e-13	1.39e-11	1.01e-11	62
hsa04141111	Endometrium	AEH	Protein processing in endoplasmic reticulum	62/1197	174/8465	5.97e-13	1.39e-11	1.01e-11	62
hsa0414127	Endometrium	EEC	Protein processing in endoplasmic reticulum	64/1237	174/8465	2.17e-13	5.09e-12	3.80e-12	64
hsa0414136	Endometrium	EEC	Protein processing in endoplasmic reticulum	64/1237	174/8465	2.17e-13	5.09e-12	3.80e-12	64
hsa0414139	Esophagus	HGIN	Protein processing in endoplasmic reticulum	67/1383	174/8465	1.06e-12	2.16e-11	1.72e-11	67
hsa04141114	Esophagus	HGIN	Protein processing in endoplasmic reticulum	67/1383	174/8465	1.06e-12	2.16e-11	1.72e-11	67

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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

OSTC

SNV

Missense_Mutation

c.383N>C

p.Val128Ala

p.V128A

Q9NRP0

protein_coding

deleterious(0.01)

possibly_damaging(0.777)

TCGA-AA-A010-01

Colorectum

colon adenocarcinoma

Female

<65

I/II

Chemotherapy

folinic

OSTC

SNV

Missense_Mutation

novel

c.511N>G

p.Ile171Val

p.I171V

Q9NRP0

protein_coding

deleterious_low_confidence(0)

benign(0)

TCGA-DY-A1DG-01

Colorectum

rectum adenocarcinoma

Male

>=65

I/II

Unknown

OSTC

SNV

Missense_Mutation

novel

c.82C>T

p.Pro28Ser

p.P28S

Q9NRP0

protein_coding

deleterious(0.03)

benign(0.176)

TCGA-A5-A0G2-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Unknown

OSTC

SNV

Missense_Mutation

c.431N>G

p.Pro144Arg

p.P144R

Q9NRP0

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-A5-A0R7-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

OSTC

SNV

Missense_Mutation

novel

c.89N>T

p.Ala30Val

p.A30V

Q9NRP0

protein_coding

deleterious(0.02)

possibly_damaging(0.817)

TCGA-AP-A1DV-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

OSTC

SNV

Missense_Mutation

novel

c.235G>A

p.Val79Ile

p.V79I

Q9NRP0

protein_coding

tolerated(0.2)

probably_damaging(0.946)

TCGA-AX-A06F-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

carboplatin

OSTC

SNV

Missense_Mutation

novel

c.272N>A

p.Ser91Asn

p.S91N

Q9NRP0

protein_coding

deleterious(0.01)

probably_damaging(0.989)

TCGA-D1-A103-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

OSTC

SNV

Missense_Mutation

novel

c.50N>C

p.Leu17Pro

p.L17P

Q9NRP0

protein_coding

deleterious(0.02)

probably_damaging(0.976)

TCGA-EC-A1QX-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Chemotherapy

cyclophosphamide

OSTC

SNV

Missense_Mutation

novel

c.358C>A

p.Leu120Ile

p.L120I

Q9NRP0

protein_coding

tolerated(0.06)

probably_damaging(0.923)

TCGA-EO-A3AV-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

carboplatin

OSTC

SNV

Missense_Mutation

novel

c.371N>C

p.Gly124Ala

p.G124A

Q9NRP0

protein_coding

deleterious(0.04)

possibly_damaging(0.814)

TCGA-34-2609-01

Lung

lung squamous cell carcinoma

Male

>=65

I/II

Chemotherapy

gemcitabine

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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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