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: DEF8

Gene summary for DEF8

Gene summary.

Gene information	Species	Human
	Gene symbol	DEF8
	Gene ID	54849
	Gene name	differentially expressed in FDCP 8 homolog
	Gene Alias	DEF8
	Cytomap	16q24.3
	Gene Type	protein-coding
	GO ID	GO:0001894
	UniProtAcc	Q6ZN54

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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
54849	DEF8	LZE4T	Human	Esophagus	ESCC	2.56e-14	3.59e-01	0.0811
54849	DEF8	LZE7T	Human	Esophagus	ESCC	1.74e-20	6.67e-01	0.0667
54849	DEF8	LZE8T	Human	Esophagus	ESCC	3.61e-03	2.04e-01	0.067
54849	DEF8	LZE20T	Human	Esophagus	ESCC	3.74e-06	6.00e-02	0.0662
54849	DEF8	LZE22D1	Human	Esophagus	HGIN	3.88e-05	1.92e-01	0.0595
54849	DEF8	LZE22T	Human	Esophagus	ESCC	9.16e-03	1.70e-01	0.068
54849	DEF8	LZE24T	Human	Esophagus	ESCC	4.00e-21	2.16e-01	0.0596
54849	DEF8	LZE21T	Human	Esophagus	ESCC	2.11e-05	3.47e-01	0.0655
54849	DEF8	LZE6T	Human	Esophagus	ESCC	4.23e-03	1.22e-01	0.0845
54849	DEF8	P1T-E	Human	Esophagus	ESCC	1.45e-13	3.81e-01	0.0875
54849	DEF8	P2T-E	Human	Esophagus	ESCC	1.19e-22	3.88e-01	0.1177
54849	DEF8	P4T-E	Human	Esophagus	ESCC	1.37e-23	6.00e-01	0.1323
54849	DEF8	P5T-E	Human	Esophagus	ESCC	1.09e-22	4.61e-01	0.1327
54849	DEF8	P8T-E	Human	Esophagus	ESCC	3.21e-19	3.86e-01	0.0889
54849	DEF8	P9T-E	Human	Esophagus	ESCC	1.74e-14	2.56e-01	0.1131
54849	DEF8	P10T-E	Human	Esophagus	ESCC	1.06e-17	2.28e-01	0.116
54849	DEF8	P11T-E	Human	Esophagus	ESCC	2.08e-15	4.80e-01	0.1426
54849	DEF8	P12T-E	Human	Esophagus	ESCC	1.85e-19	3.48e-01	0.1122
54849	DEF8	P15T-E	Human	Esophagus	ESCC	8.65e-19	2.99e-01	0.1149
54849	DEF8	P16T-E	Human	Esophagus	ESCC	9.42e-10	1.44e-01	0.1153

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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
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:006049117	Esophagus	HGIN	regulation of cell projection assembly	39/2587	188/18723	5.61e-03	4.57e-02	39
GO:003134616	Esophagus	ESCC	positive regulation of cell projection organization	201/8552	353/18723	1.19e-05	1.11e-04	201
GO:00315299	Esophagus	ESCC	ruffle organization	39/8552	56/18723	2.44e-04	1.51e-03	39
GO:00971789	Esophagus	ESCC	ruffle assembly	32/8552	44/18723	2.50e-04	1.54e-03	32
GO:006049118	Esophagus	ESCC	regulation of cell projection assembly	110/8552	188/18723	2.60e-04	1.58e-03	110
GO:012003218	Esophagus	ESCC	regulation of plasma membrane bounded cell projection assembly	108/8552	186/18723	4.37e-04	2.46e-03	108
GO:01200347	Esophagus	ESCC	positive regulation of plasma membrane bounded cell projection assembly	64/8552	105/18723	1.15e-03	5.70e-03	64
GO:19000277	Esophagus	ESCC	regulation of ruffle assembly	21/8552	31/18723	1.10e-02	3.70e-02	21
GO:00315294	Liver	Cirrhotic	ruffle organization	26/4634	56/18723	3.40e-04	2.91e-03	26
GO:00971783	Liver	Cirrhotic	ruffle assembly	21/4634	44/18723	7.88e-04	5.79e-03	21
GO:00487711	Liver	Cirrhotic	tissue remodeling	60/4634	175/18723	2.86e-03	1.65e-02	60
GO:01200326	Liver	Cirrhotic	regulation of plasma membrane bounded cell projection assembly	63/4634	186/18723	3.16e-03	1.78e-02	63
GO:19000273	Liver	Cirrhotic	regulation of ruffle assembly	15/4634	31/18723	3.68e-03	2.02e-02	15
GO:00604915	Liver	Cirrhotic	regulation of cell projection assembly	63/4634	188/18723	4.17e-03	2.22e-02	63
GO:003134611	Liver	HCC	positive regulation of cell projection organization	193/7958	353/18723	2.28e-06	3.08e-05	193
GO:006049112	Liver	HCC	regulation of cell projection assembly	101/7958	188/18723	1.20e-03	6.69e-03	101
GO:012003212	Liver	HCC	regulation of plasma membrane bounded cell projection assembly	100/7958	186/18723	1.23e-03	6.81e-03	100
GO:003152911	Liver	HCC	ruffle organization	34/7958	56/18723	4.54e-03	1.96e-02	34
GO:01200344	Liver	HCC	positive regulation of plasma membrane bounded cell projection assembly	58/7958	105/18723	5.66e-03	2.36e-02	58
GO:003134610	Oral cavity	OSCC	positive regulation of cell projection organization	176/7305	353/18723	1.94e-05	1.87e-04	176

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Enriched KEGG pathways.

Pathway ID

Tissue

Disease Stage

Description

Gene Ratio

Bg Ratio

pvalue

p.adjust

qvalue

Count

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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

DEF8

SNV

Missense_Mutation

novel

c.836N>T

p.Ala279Val

p.A279V

Q6ZN54

protein_coding

deleterious(0.01)

benign(0.209)

TCGA-A7-A0CJ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

DEF8

SNV

Missense_Mutation

novel

c.1364G>A

p.Arg455Lys

p.R455K

Q6ZN54

protein_coding

tolerated(1)

benign(0.005)

TCGA-GM-A3XL-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

fluorouracil

DEF8

SNV

Missense_Mutation

novel

c.164N>T

p.Arg55Leu

p.R55L

Q6ZN54

protein_coding

deleterious_low_confidence(0.02)

benign(0)

TCGA-LL-A7SZ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

DEF8

SNV

Missense_Mutation

rs146004686

c.602G>A

p.Arg201His

p.R201H

Q6ZN54

protein_coding

tolerated(0.68)

probably_damaging(0.974)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

DEF8

SNV

Missense_Mutation

novel

c.1200G>T

p.Gln400His

p.Q400H

Q6ZN54

protein_coding

deleterious(0.04)

probably_damaging(0.995)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

DEF8

SNV

Missense_Mutation

c.636G>C

p.Gln212His

p.Q212H

Q6ZN54

protein_coding

tolerated(0.24)

benign(0.015)

TCGA-DR-A0ZM-01

Cervix

cervical & endocervical cancer

Female

<65

III/IV

Unspecific

Cisplatin

DEF8

SNV

Missense_Mutation

novel

c.196N>A

p.Glu66Lys

p.E66K

Q6ZN54

protein_coding

deleterious_low_confidence(0.01)

benign(0.214)

TCGA-HM-A4S6-01

Cervix

cervical & endocervical cancer

Female

<65

III/IV

Chemotherapy

cisplatin

DEF8

SNV

Missense_Mutation

novel

c.103C>T

p.Leu35Phe

p.L35F

Q6ZN54

protein_coding

deleterious_low_confidence(0.05)

benign(0)

TCGA-VS-A9UB-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

DEF8

SNV

Missense_Mutation

c.65N>T

p.Thr22Met

p.T22M

Q6ZN54

protein_coding

deleterious_low_confidence(0)

benign(0)

TCGA-AA-3495-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

DEF8

SNV

Missense_Mutation

novel

c.1436N>A

p.Arg479Lys

p.R479K

Q6ZN54

protein_coding

tolerated(0.14)

benign(0.194)

TCGA-AA-3949-01

Colorectum

colon adenocarcinoma

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

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