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: CNBP

Gene summary for CNBP

Gene summary.

Gene information	Species	Human
	Gene symbol	CNBP
	Gene ID	7555
	Gene name	CCHC-type zinc finger nucleic acid binding protein
	Gene Alias	CNBP1
	Cytomap	3q21.3
	Gene Type	protein-coding
	GO ID	GO:0000122
	UniProtAcc	P62633

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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
7555	CNBP	GSM4909282	Human	Breast	IDC	1.33e-03	2.87e-01	-0.0288
7555	CNBP	GSM4909286	Human	Breast	IDC	3.33e-08	-9.06e-02	0.1081
7555	CNBP	GSM4909288	Human	Breast	IDC	8.99e-03	-1.59e-01	0.0988
7555	CNBP	GSM4909291	Human	Breast	IDC	3.13e-02	-3.34e-01	0.1753
7555	CNBP	GSM4909293	Human	Breast	IDC	1.60e-03	6.71e-02	0.1581
7555	CNBP	GSM4909294	Human	Breast	IDC	8.34e-07	-3.27e-01	0.2022
7555	CNBP	GSM4909296	Human	Breast	IDC	1.25e-25	-5.75e-01	0.1524
7555	CNBP	GSM4909297	Human	Breast	IDC	1.18e-22	-2.50e-01	0.1517
7555	CNBP	GSM4909301	Human	Breast	IDC	9.60e-26	-6.54e-01	0.1577
7555	CNBP	GSM4909302	Human	Breast	IDC	2.63e-16	-5.23e-01	0.1545
7555	CNBP	GSM4909309	Human	Breast	IDC	8.42e-05	-2.62e-01	0.0483
7555	CNBP	GSM4909311	Human	Breast	IDC	2.85e-48	-6.34e-01	0.1534
7555	CNBP	GSM4909312	Human	Breast	IDC	1.74e-10	-3.53e-02	0.1552
7555	CNBP	GSM4909313	Human	Breast	IDC	1.76e-04	-2.89e-01	0.0391
7555	CNBP	GSM4909316	Human	Breast	IDC	2.87e-05	9.12e-02	0.21
7555	CNBP	GSM4909318	Human	Breast	IDC	1.76e-06	1.87e-01	0.2031
7555	CNBP	GSM4909319	Human	Breast	IDC	9.78e-62	-5.46e-01	0.1563
7555	CNBP	GSM4909320	Human	Breast	IDC	1.27e-15	-6.58e-01	0.1575
7555	CNBP	GSM4909321	Human	Breast	IDC	7.15e-21	-3.27e-01	0.1559
7555	CNBP	brca1	Human	Breast	Precancer	2.02e-11	4.07e-01	-0.0338

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Breast		IDC: Invasive ductal carcinoma
		DCIS: Ductal carcinoma in situ
		Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers
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
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
Oral cavity	OSCC
Oral cavity	LP
Oral cavity	EOLP
Oral cavity	NEOLP
Esophagus	HGIN

∗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:00021819	Breast	Precancer	cytoplasmic translation	80/1080	148/18723	1.59e-59	8.54e-56	80
GO:00064179	Breast	Precancer	regulation of translation	67/1080	468/18723	4.71e-12	7.64e-10	67
GO:00457279	Breast	Precancer	positive regulation of translation	32/1080	136/18723	5.89e-12	9.27e-10	32
GO:00342509	Breast	Precancer	positive regulation of cellular amide metabolic process	33/1080	162/18723	1.72e-10	1.77e-08	33
GO:000218114	Breast	IDC	cytoplasmic translation	82/1434	148/18723	2.60e-52	1.48e-48	82
GO:000641714	Breast	IDC	regulation of translation	74/1434	468/18723	1.67e-09	1.53e-07	74
GO:004572714	Breast	IDC	positive regulation of translation	33/1434	136/18723	1.92e-09	1.73e-07	33
GO:003425014	Breast	IDC	positive regulation of cellular amide metabolic process	35/1434	162/18723	1.63e-08	1.16e-06	35
GO:000218124	Breast	DCIS	cytoplasmic translation	82/1390	148/18723	2.21e-53	1.25e-49	82
GO:000641724	Breast	DCIS	regulation of translation	72/1390	468/18723	2.46e-09	2.17e-07	72
GO:004572724	Breast	DCIS	positive regulation of translation	32/1390	136/18723	3.56e-09	3.10e-07	32
GO:003425023	Breast	DCIS	positive regulation of cellular amide metabolic process	34/1390	162/18723	2.60e-08	1.73e-06	34
GO:000218116	Endometrium	AEH	cytoplasmic translation	104/2100	148/18723	1.01e-64	6.07e-61	104
GO:000641716	Endometrium	AEH	regulation of translation	94/2100	468/18723	1.14e-08	7.62e-07	94
GO:004572715	Endometrium	AEH	positive regulation of translation	38/2100	136/18723	6.37e-08	3.38e-06	38
GO:003425015	Endometrium	AEH	positive regulation of cellular amide metabolic process	42/2100	162/18723	1.35e-07	6.12e-06	42
GO:000218117	Endometrium	EEC	cytoplasmic translation	104/2168	148/18723	2.53e-63	1.52e-59	104
GO:000641717	Endometrium	EEC	regulation of translation	94/2168	468/18723	5.37e-08	2.88e-06	94
GO:004572716	Endometrium	EEC	positive regulation of translation	38/2168	136/18723	1.47e-07	6.89e-06	38
GO:003425016	Endometrium	EEC	positive regulation of cellular amide metabolic process	42/2168	162/18723	3.24e-07	1.32e-05	42

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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

CNBP

insertion

In_Frame_Ins

novel

c.20_21insAGAAGAAAACTCATTGCAGAGATTCTTCCAGAGATG

p.Phe7delinsLeuGluGluAsnSerLeuGlnArgPhePheGlnArgCys

p.F7delinsLEENSLQRFFQRC

P62633

protein_coding

TCGA-A2-A0T2-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Chemotherapy

xeloda

CNBP

SNV

Missense_Mutation

c.245N>A

p.Gly82Asp

p.G82D

P62633

protein_coding

tolerated(0.07)

benign(0.345)

TCGA-AZ-6601-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

CNBP

SNV

Missense_Mutation

novel

c.304N>G

p.Asn102Asp

p.N102D

P62633

protein_coding

tolerated(0.19)

benign(0.331)

TCGA-A5-A0G1-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

CNBP

SNV

Missense_Mutation

c.518N>T

p.Cys173Phe

p.C173F

P62633

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-A5-A0G9-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

CNBP

SNV

Missense_Mutation

novel

c.80G>A

p.Arg27His

p.R27H

P62633

protein_coding

tolerated(0.34)

benign(0.022)

TCGA-AJ-A3OK-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Chemotherapy

carboplatin

CNBP

SNV

Missense_Mutation

c.223N>T

p.Ala75Ser

p.A75S

P62633

protein_coding

tolerated(0.39)

benign(0.047)

TCGA-AP-A051-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

CNBP

SNV

Missense_Mutation

novel

c.103G>A

p.Gly35Ser

p.G35S

P62633

protein_coding

tolerated(0.14)

benign(0.074)

TCGA-AP-A1DK-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

CNBP

SNV

Missense_Mutation

novel

c.52N>A

p.Glu18Lys

p.E18K

P62633

protein_coding

tolerated(0.54)

benign(0.186)

TCGA-AP-A1DV-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

CNBP

SNV

Missense_Mutation

novel

c.103N>T

p.Gly35Cys

p.G35C

P62633

protein_coding

deleterious(0.01)

benign(0.354)

TCGA-EO-A22R-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

CNBP

SNV

Missense_Mutation

c.419A>G

p.Tyr140Cys

p.Y140C

P62633

protein_coding

deleterious(0)

possibly_damaging(0.449)

TCGA-55-A490-01

Lung

lung adenocarcinoma

Male

>=65

I/II

Chemotherapy

carboplatin

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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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