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: CBFA2T2

Gene summary for CBFA2T2

Gene summary.

Gene information	Species	Human
	Gene symbol	CBFA2T2
	Gene ID	9139
	Gene name	CBFA2/RUNX1 partner transcriptional co-repressor 2
	Gene Alias	EHT
	Cytomap	20q11.21-q11.22
	Gene Type	protein-coding
	GO ID	GO:0000122
	UniProtAcc	O43439

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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
9139	CBFA2T2	CCI_1	Human	Cervix	CC	9.93e-15	1.03e+00	0.528
9139	CBFA2T2	CCI_2	Human	Cervix	CC	8.31e-13	1.35e+00	0.5249
9139	CBFA2T2	CCI_3	Human	Cervix	CC	1.15e-17	1.07e+00	0.516
9139	CBFA2T2	CCII_1	Human	Cervix	CC	2.83e-02	2.91e-01	0.3249
9139	CBFA2T2	HTA11_3410_2000001011	Human	Colorectum	AD	7.50e-04	-3.24e-01	0.0155
9139	CBFA2T2	HTA11_347_2000001011	Human	Colorectum	AD	4.53e-06	6.18e-01	-0.1954
9139	CBFA2T2	HTA11_696_2000001011	Human	Colorectum	AD	2.07e-02	4.82e-01	-0.1464
9139	CBFA2T2	HTA11_5212_2000001011	Human	Colorectum	AD	5.81e-03	-4.39e-01	-0.2061
9139	CBFA2T2	HTA11_99999965104_69814	Human	Colorectum	MSS	2.04e-05	5.97e-01	0.281
9139	CBFA2T2	HTA11_99999971662_82457	Human	Colorectum	MSS	1.07e-04	7.26e-01	0.3859
9139	CBFA2T2	F007	Human	Colorectum	FAP	8.11e-05	-1.06e-01	0.1176
9139	CBFA2T2	A001-C-207	Human	Colorectum	FAP	2.13e-05	-2.45e-01	0.1278
9139	CBFA2T2	A015-C-203	Human	Colorectum	FAP	5.61e-45	-5.27e-01	-0.1294
9139	CBFA2T2	A015-C-204	Human	Colorectum	FAP	1.07e-11	-4.36e-01	-0.0228
9139	CBFA2T2	A014-C-040	Human	Colorectum	FAP	1.47e-05	-2.51e-01	-0.1184
9139	CBFA2T2	A002-C-201	Human	Colorectum	FAP	1.16e-17	-3.32e-01	0.0324
9139	CBFA2T2	A002-C-203	Human	Colorectum	FAP	3.50e-05	-2.11e-01	0.2786
9139	CBFA2T2	A001-C-119	Human	Colorectum	FAP	2.28e-07	-1.40e-01	-0.1557
9139	CBFA2T2	A001-C-108	Human	Colorectum	FAP	1.22e-23	-3.89e-01	-0.0272
9139	CBFA2T2	A002-C-205	Human	Colorectum	FAP	7.71e-30	-3.73e-01	-0.1236

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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
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
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
Breast	Precancer
Breast	IDC
Breast	DCIS
Cervix	CC
Cervix	HSIL_HPV

∗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:00109757	Cervix	CC	regulation of neuron projection development	88/2311	445/18723	4.26e-06	1.09e-04	88
GO:00313467	Cervix	CC	positive regulation of cell projection organization	72/2311	353/18723	1.04e-05	2.32e-04	72
GO:00072194	Cervix	CC	Notch signaling pathway	39/2311	172/18723	1.08e-04	1.38e-03	39
GO:00085933	Cervix	CC	regulation of Notch signaling pathway	25/2311	95/18723	1.61e-04	1.93e-03	25
GO:00313456	Cervix	CC	negative regulation of cell projection organization	39/2311	186/18723	5.86e-04	5.57e-03	39
GO:00109775	Cervix	CC	negative regulation of neuron projection development	28/2311	137/18723	4.74e-03	2.83e-02	28
GO:0010975	Colorectum	AD	regulation of neuron projection development	129/3918	445/18723	2.88e-05	5.37e-04	129
GO:0031346	Colorectum	AD	positive regulation of cell projection organization	104/3918	353/18723	8.26e-05	1.30e-03	104
GO:0031345	Colorectum	AD	negative regulation of cell projection organization	58/3918	186/18723	6.37e-04	6.58e-03	58
GO:0010977	Colorectum	AD	negative regulation of neuron projection development	43/3918	137/18723	2.60e-03	1.97e-02	43
GO:0007219	Colorectum	AD	Notch signaling pathway	50/3918	172/18723	6.92e-03	4.26e-02	50
GO:00313462	Colorectum	MSS	positive regulation of cell projection organization	96/3467	353/18723	3.44e-05	6.70e-04	96
GO:00109752	Colorectum	MSS	regulation of neuron projection development	115/3467	445/18723	6.91e-05	1.20e-03	115
GO:00313452	Colorectum	MSS	negative regulation of cell projection organization	54/3467	186/18723	3.03e-04	3.96e-03	54
GO:00109771	Colorectum	MSS	negative regulation of neuron projection development	39/3467	137/18723	2.86e-03	2.22e-02	39
GO:00109753	Colorectum	FAP	regulation of neuron projection development	102/2622	445/18723	2.04e-07	1.24e-05	102
GO:00313463	Colorectum	FAP	positive regulation of cell projection organization	82/2622	353/18723	1.78e-06	7.35e-05	82
GO:00313453	Colorectum	FAP	negative regulation of cell projection organization	44/2622	186/18723	2.69e-04	3.64e-03	44
GO:00109772	Colorectum	FAP	negative regulation of neuron projection development	33/2622	137/18723	1.07e-03	1.04e-02	33
GO:00072191	Colorectum	FAP	Notch signaling pathway	38/2622	172/18723	2.56e-03	2.01e-02	38

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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

CBFA2T2

SNV

Missense_Mutation

c.406N>A

p.Glu136Lys

p.E136K

O43439

protein_coding

deleterious(0)

probably_damaging(0.992)

TCGA-A2-A0CX-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

CBFA2T2

SNV

Missense_Mutation

novel

c.1434G>A

p.Met478Ile

p.M478I

O43439

protein_coding

deleterious(0.02)

possibly_damaging(0.885)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

CBFA2T2

SNV

Missense_Mutation

novel

c.1774N>G

p.Thr592Ala

p.T592A

O43439

protein_coding

deleterious_low_confidence(0.01)

benign(0.031)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

CBFA2T2

SNV

Missense_Mutation

novel

c.1384G>A

p.Glu462Lys

p.E462K

O43439

protein_coding

tolerated(0.11)

possibly_damaging(0.76)

TCGA-BH-A2L8-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

CBFA2T2

SNV

Missense_Mutation

c.1114C>G

p.Leu372Val

p.L372V

O43439

protein_coding

deleterious(0)

probably_damaging(0.994)

TCGA-GM-A2D9-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

CBFA2T2

SNV

Missense_Mutation

novel

c.1570N>A

p.Ala524Thr

p.A524T

O43439

protein_coding

deleterious(0)

probably_damaging(0.997)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

CBFA2T2

SNV

Missense_Mutation

novel

c.760N>A

p.Glu254Lys

p.E254K

O43439

protein_coding

tolerated(0.06)

probably_damaging(0.98)

TCGA-C5-A8XJ-01

Cervix

cervical & endocervical cancer

Female

>=65

I/II

Chemotherapy

cisplatin

CBFA2T2

SNV

Missense_Mutation

c.1255N>A

p.Asp419Asn

p.D419N

O43439

protein_coding

deleterious(0.04)

benign(0.001)

TCGA-JW-A5VL-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

CBFA2T2

SNV

Missense_Mutation

c.425N>T

p.Arg142Leu

p.R142L

O43439

protein_coding

deleterious(0)

probably_damaging(0.992)

TCGA-VS-A94Z-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

CBFA2T2

SNV

Missense_Mutation

c.1687N>A

p.Gly563Ser

p.G563S

O43439

protein_coding

tolerated(0.36)

benign(0.033)

TCGA-A6-6648-01

Colorectum

colon adenocarcinoma

Male

<65

I/II

Chemotherapy

oxaliplatin

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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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