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: SEC24C

Gene summary for SEC24C

Gene summary.

Gene information	Species	Human
	Gene symbol	SEC24C
	Gene ID	9632
	Gene name	SEC24 homolog C, COPII coat complex component
	Gene Alias	SEC24C
	Cytomap	10q22.2
	Gene Type	protein-coding
	GO ID	GO:0001701
	UniProtAcc	A0A024QZM6

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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
9632	SEC24C	LZE20T	Human	Esophagus	ESCC	4.80e-02	3.98e-02	0.0662
9632	SEC24C	LZE22T	Human	Esophagus	ESCC	2.91e-05	2.83e-01	0.068
9632	SEC24C	LZE24T	Human	Esophagus	ESCC	6.68e-16	4.16e-01	0.0596
9632	SEC24C	P1T-E	Human	Esophagus	ESCC	1.62e-04	2.16e-01	0.0875
9632	SEC24C	P2T-E	Human	Esophagus	ESCC	2.71e-16	2.74e-01	0.1177
9632	SEC24C	P4T-E	Human	Esophagus	ESCC	3.71e-14	2.30e-01	0.1323
9632	SEC24C	P5T-E	Human	Esophagus	ESCC	6.11e-12	9.56e-02	0.1327
9632	SEC24C	P8T-E	Human	Esophagus	ESCC	2.69e-14	2.41e-01	0.0889
9632	SEC24C	P10T-E	Human	Esophagus	ESCC	1.37e-11	2.03e-01	0.116
9632	SEC24C	P11T-E	Human	Esophagus	ESCC	5.04e-07	1.86e-01	0.1426
9632	SEC24C	P12T-E	Human	Esophagus	ESCC	9.93e-15	3.17e-01	0.1122
9632	SEC24C	P15T-E	Human	Esophagus	ESCC	6.64e-16	2.82e-01	0.1149
9632	SEC24C	P16T-E	Human	Esophagus	ESCC	7.87e-15	2.89e-01	0.1153
9632	SEC24C	P17T-E	Human	Esophagus	ESCC	2.63e-08	3.08e-01	0.1278
9632	SEC24C	P19T-E	Human	Esophagus	ESCC	2.05e-06	3.84e-01	0.1662
9632	SEC24C	P20T-E	Human	Esophagus	ESCC	1.31e-09	2.28e-01	0.1124
9632	SEC24C	P21T-E	Human	Esophagus	ESCC	5.02e-20	4.37e-01	0.1617
9632	SEC24C	P22T-E	Human	Esophagus	ESCC	7.41e-06	1.02e-01	0.1236
9632	SEC24C	P23T-E	Human	Esophagus	ESCC	3.34e-15	3.09e-01	0.108
9632	SEC24C	P24T-E	Human	Esophagus	ESCC	1.75e-13	2.56e-01	0.1287

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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

∗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:004819318	Esophagus	ESCC	Golgi vesicle transport	231/8552	296/18723	1.82e-30	9.63e-28	231
GO:001605014	Esophagus	ESCC	vesicle organization	211/8552	300/18723	2.85e-18	2.87e-16	211
GO:000170119	Esophagus	ESCC	in utero embryonic development	243/8552	367/18723	1.00e-15	6.86e-14	243
GO:000688815	Esophagus	ESCC	endoplasmic reticulum to Golgi vesicle-mediated transport	102/8552	130/18723	1.73e-14	9.22e-13	102
GO:0006900111	Esophagus	ESCC	vesicle budding from membrane	54/8552	61/18723	2.66e-12	1.07e-10	54
GO:009011414	Esophagus	ESCC	COPII-coated vesicle budding	27/8552	29/18723	8.09e-08	1.39e-06	27
GO:00901104	Esophagus	ESCC	COPII-coated vesicle cargo loading	14/8552	15/18723	1.47e-04	9.85e-04	14
GO:00354595	Esophagus	ESCC	vesicle cargo loading	19/8552	27/18723	8.35e-03	2.95e-02	19
GO:004819321	Liver	HCC	Golgi vesicle transport	217/7958	296/18723	2.58e-27	1.02e-24	217
GO:000688821	Liver	HCC	endoplasmic reticulum to Golgi vesicle-mediated transport	100/7958	130/18723	1.15e-15	8.67e-14	100
GO:001605021	Liver	HCC	vesicle organization	194/7958	300/18723	5.58e-15	3.97e-13	194
GO:000690021	Liver	HCC	vesicle budding from membrane	53/7958	61/18723	7.38e-13	3.80e-11	53
GO:00901142	Liver	HCC	COPII-coated vesicle budding	27/7958	29/18723	1.28e-08	3.14e-07	27
GO:000170111	Liver	HCC	in utero embryonic development	204/7958	367/18723	2.44e-07	4.30e-06	204
GO:00901102	Liver	HCC	COPII-coated vesicle cargo loading	14/7958	15/18723	5.65e-05	5.26e-04	14
GO:003545921	Liver	HCC	vesicle cargo loading	19/7958	27/18723	3.18e-03	1.47e-02	19
GO:004819315	Oral cavity	OSCC	Golgi vesicle transport	209/7305	296/18723	1.39e-28	6.30e-26	209
GO:00160508	Oral cavity	OSCC	vesicle organization	189/7305	300/18723	2.40e-17	2.14e-15	189
GO:00068888	Oral cavity	OSCC	endoplasmic reticulum to Golgi vesicle-mediated transport	97/7305	130/18723	1.42e-16	1.15e-14	97
GO:000170116	Oral cavity	OSCC	in utero embryonic development	207/7305	367/18723	7.92e-12	2.95e-10	207

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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
hsa05130211	Esophagus	ESCC	Pathogenic Escherichia coli infection	142/4205	197/8465	8.21e-11	1.06e-09	5.42e-10	142
hsa04141310	Esophagus	ESCC	Protein processing in endoplasmic reticulum	147/4205	174/8465	3.29e-22	1.10e-19	5.64e-20	147
hsa05130310	Esophagus	ESCC	Pathogenic Escherichia coli infection	142/4205	197/8465	8.21e-11	1.06e-09	5.42e-10	142
hsa0414122	Liver	HCC	Protein processing in endoplasmic reticulum	146/4020	174/8465	7.34e-24	2.46e-21	1.37e-21	146
hsa0513042	Liver	HCC	Pathogenic Escherichia coli infection	129/4020	197/8465	2.02e-07	2.50e-06	1.39e-06	129
hsa0414132	Liver	HCC	Protein processing in endoplasmic reticulum	146/4020	174/8465	7.34e-24	2.46e-21	1.37e-21	146
hsa0513052	Liver	HCC	Pathogenic Escherichia coli infection	129/4020	197/8465	2.02e-07	2.50e-06	1.39e-06	129
hsa0414130	Oral cavity	OSCC	Protein processing in endoplasmic reticulum	143/3704	174/8465	6.82e-26	2.28e-23	1.16e-23	143
hsa0513030	Oral cavity	OSCC	Pathogenic Escherichia coli infection	129/3704	197/8465	4.32e-10	5.17e-09	2.63e-09	129
hsa04141113	Oral cavity	OSCC	Protein processing in endoplasmic reticulum	143/3704	174/8465	6.82e-26	2.28e-23	1.16e-23	143
hsa05130114	Oral cavity	OSCC	Pathogenic Escherichia coli infection	129/3704	197/8465	4.32e-10	5.17e-09	2.63e-09	129
hsa04141210	Oral cavity	LP	Protein processing in endoplasmic reticulum	113/2418	174/8465	8.74e-24	5.82e-22	3.76e-22	113
hsa05130210	Oral cavity	LP	Pathogenic Escherichia coli infection	87/2418	197/8465	1.71e-06	1.78e-05	1.15e-05	87
hsa0414138	Oral cavity	LP	Protein processing in endoplasmic reticulum	113/2418	174/8465	8.74e-24	5.82e-22	3.76e-22	113
hsa0513038	Oral cavity	LP	Pathogenic Escherichia coli infection	87/2418	197/8465	1.71e-06	1.78e-05	1.15e-05	87

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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

SEC24C

SNV

Missense_Mutation

rs755761928

c.614N>T

p.Ser205Phe

p.S205F

P53992

protein_coding

deleterious(0.04)

benign(0.05)

TCGA-A8-A08H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SEC24C

SNV

Missense_Mutation

c.1521N>C

p.Met507Ile

p.M507I

P53992

protein_coding

tolerated(0.08)

benign(0.073)

TCGA-AN-A0XW-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

SEC24C

SNV

Missense_Mutation

c.3230N>T

p.Ser1077Phe

p.S1077F

P53992

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-AR-A1AK-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

anastrozole

SEC24C

SNV

Missense_Mutation

c.2113N>A

p.Asp705Asn

p.D705N

P53992

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-BH-A0DH-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cyclophosphamide

SEC24C

SNV

Missense_Mutation

c.1330C>A

p.Arg444Ser

p.R444S

P53992

protein_coding

deleterious(0)

possibly_damaging(0.495)

TCGA-BH-A18G-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SEC24C

SNV

Missense_Mutation

c.1359N>G

p.Ile453Met

p.I453M

P53992

protein_coding

deleterious(0.01)

benign(0.238)

TCGA-C8-A12T-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

SEC24C

SNV

Missense_Mutation

c.263N>G

p.Gln88Arg

p.Q88R

P53992

protein_coding

deleterious(0.01)

benign(0.165)

TCGA-EW-A1IZ-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

taxotere

SEC24C

SNV

Missense_Mutation

rs780721252

c.2201N>A

p.Arg734Gln

p.R734Q

P53992

protein_coding

tolerated(0.36)

benign(0.205)

TCGA-S3-AA10-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

cytoxan

SEC24C

insertion

Frame_Shift_Ins

rs764652839

c.1368_1369insC

p.Gln459ProfsTer17

p.Q459Pfs*17

P53992

protein_coding

TCGA-A2-A0T2-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Chemotherapy

xeloda

SEC24C

insertion

Frame_Shift_Ins

novel

c.324_325insGGAGA

p.Pro109GlyfsTer120

p.P109Gfs*120

P53992

protein_coding

TCGA-A8-A07R-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Ancillary

zoledronic

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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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