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: ZNF292

Gene summary for ZNF292

Gene summary.

Gene information	Species	Human
	Gene symbol	ZNF292
	Gene ID	23036
	Gene name	zinc finger protein 292
	Gene Alias	MRD63
	Cytomap	6q14.3
	Gene Type	protein-coding
	GO ID	GO:0006139
	UniProtAcc	O60281

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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
23036	ZNF292	052097_1595-all-cells	Human	Prostate	BPH	4.70e-04	2.67e-01	0.0972
23036	ZNF292	052099_1652-all-cells	Human	Prostate	BPH	8.76e-08	3.40e-01	0.1038
23036	ZNF292	Dong_P1	Human	Prostate	Tumor	3.10e-11	4.08e-02	0.035
23036	ZNF292	Dong_P3	Human	Prostate	Tumor	5.10e-12	1.97e-01	0.0278
23036	ZNF292	Dong_P4	Human	Prostate	Tumor	6.60e-07	3.21e-01	0.0292
23036	ZNF292	Dong_P5	Human	Prostate	Tumor	1.68e-19	3.91e-02	0.053
23036	ZNF292	GSM5353215_PA_AUG_PB_1B_S2	Human	Prostate	Tumor	8.16e-08	7.91e-01	0.1557
23036	ZNF292	GSM5353216_PA_PB1A_Pool_1_3_S50_L002	Human	Prostate	Tumor	6.19e-03	6.30e-01	0.159
23036	ZNF292	GSM5353220_PA_PB1B_Pool_3_S51_L002	Human	Prostate	Tumor	2.22e-02	4.59e-01	0.1531
23036	ZNF292	GSM5353221_PA_PB2A_Pool_1_3_S25_L001	Human	Prostate	Tumor	4.31e-22	8.61e-01	0.1633
23036	ZNF292	GSM5353222_PA_PB2B_Pool_1_3_S52_L002	Human	Prostate	Tumor	4.03e-19	7.76e-01	0.1608
23036	ZNF292	GSM5353223_PA_PB2B_Pool_2_S26_L001	Human	Prostate	Tumor	3.09e-07	5.86e-01	0.1604
23036	ZNF292	GSM5353224_PA_PR5186_Pool_1_2_3_S27_L001	Human	Prostate	Tumor	3.19e-14	7.85e-01	0.1621
23036	ZNF292	GSM5353225_PA_PR5196-1_Pool_1_2_3_S53_L002	Human	Prostate	Tumor	3.85e-11	8.35e-01	0.1619
23036	ZNF292	GSM5353227_PA_PR5199-193K_Pool_1_2_3_S55_L002	Human	Prostate	Tumor	3.89e-16	8.18e-01	0.1602
23036	ZNF292	GSM5353228_PA_PR5199-640K_Pool_1_3_S108_L004	Human	Prostate	Tumor	5.37e-08	8.98e-01	0.1537
23036	ZNF292	GSM5353236_PA_PR5251_T1_S7_L001	Human	Prostate	Tumor	7.24e-05	5.46e-01	0.1608
23036	ZNF292	GSM5353237_PA_PR5251_T2_S8_L001	Human	Prostate	Tumor	6.54e-05	7.18e-01	0.1622
23036	ZNF292	GSM5353240_PA_PR5254_T1_S15_L001	Human	Prostate	Tumor	9.30e-05	3.65e-01	0.1575
23036	ZNF292	GSM5353243_PA_PR5261_T1_S23_L002	Human	Prostate	Tumor	4.53e-08	3.65e-01	0.1545

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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
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
Lung		AAH: Atypical adenomatous hyperplasia
		AIS: Adenocarcinoma in situ
		IAC: Invasive lung adenocarcinoma
		MIA: Minimally invasive adenocarcinoma
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

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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

ZNF292

SNV

Missense_Mutation

novel

c.6965N>A

p.Arg2322Lys

p.R2322K

O60281

protein_coding

tolerated(0.37)

benign(0.003)

TCGA-5L-AAT1-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Hormone Therapy

letrozol

ZNF292

SNV

Missense_Mutation

novel

c.8085N>T

p.Lys2695Asn

p.K2695N

O60281

protein_coding

tolerated(0.08)

benign(0.05)

TCGA-A2-A0ER-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

ZNF292

SNV

Missense_Mutation

novel

c.4842N>A

p.Asn1614Lys

p.N1614K

O60281

protein_coding

deleterious_low_confidence(0.01)

benign(0.076)

TCGA-A2-A25C-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

taxotere

ZNF292

SNV

Missense_Mutation

c.1202A>T

p.Asp401Val

p.D401V

O60281

protein_coding

deleterious(0)

probably_damaging(0.991)

TCGA-A8-A09M-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Chemotherapy

paclitaxel

ZNF292

SNV

Missense_Mutation

c.3904G>C

p.Glu1302Gln

p.E1302Q

O60281

protein_coding

tolerated(0.25)

benign(0.261)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

ZNF292

SNV

Missense_Mutation

c.5485G>A

p.Glu1829Lys

p.E1829K

O60281

protein_coding

tolerated(0.06)

benign(0.003)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

ZNF292

SNV

Missense_Mutation

novel

c.471G>T

p.Glu157Asp

p.E157D

O60281

protein_coding

deleterious(0.04)

benign(0.189)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

ZNF292

SNV

Missense_Mutation

novel

c.1493C>A

p.Ser498Tyr

p.S498Y

O60281

protein_coding

deleterious(0.02)

possibly_damaging(0.804)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

ZNF292

SNV

Missense_Mutation

novel

c.5817G>T

p.Lys1939Asn

p.K1939N

O60281

protein_coding

deleterious(0)

probably_damaging(0.994)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

ZNF292

SNV

Missense_Mutation

rs756555025

c.2552N>T

p.Ser851Phe

p.S851F

O60281

protein_coding

tolerated(0.06)

benign(0.046)

TCGA-AN-A04C-01

Breast

breast invasive carcinoma

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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