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: MYCBP2

Gene summary for MYCBP2

Gene summary.

Gene information	Species	Human
	Gene symbol	MYCBP2
	Gene ID	23077
	Gene name	MYC binding protein 2
	Gene Alias	Myc-bp2
	Cytomap	13q22.3
	Gene Type	protein-coding
	GO ID	GO:0000902
	UniProtAcc	O75592

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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
23077	MYCBP2	CA_HPV_1	Human	Cervix	CC	7.00e-03	-3.50e-02	0.0264
23077	MYCBP2	N_HPV_2	Human	Cervix	N_HPV	1.09e-02	8.43e-02	-0.0131
23077	MYCBP2	CCI_1	Human	Cervix	CC	5.43e-07	1.10e+00	0.528
23077	MYCBP2	CCI_2	Human	Cervix	CC	3.05e-16	1.55e+00	0.5249
23077	MYCBP2	CCI_3	Human	Cervix	CC	3.17e-11	1.17e+00	0.516
23077	MYCBP2	sample3	Human	Cervix	CC	2.45e-02	9.83e-02	0.1387
23077	MYCBP2	T3	Human	Cervix	CC	4.05e-03	9.99e-02	0.1389
23077	MYCBP2	HTA11_3410_2000001011	Human	Colorectum	AD	5.10e-17	-6.24e-01	0.0155
23077	MYCBP2	HTA11_2487_2000001011	Human	Colorectum	SER	3.63e-06	-5.58e-01	-0.1808
23077	MYCBP2	HTA11_3361_2000001011	Human	Colorectum	AD	3.18e-09	-6.96e-01	-0.1207
23077	MYCBP2	HTA11_83_2000001011	Human	Colorectum	SER	1.85e-03	-5.11e-01	-0.1526
23077	MYCBP2	HTA11_696_2000001011	Human	Colorectum	AD	1.12e-13	-5.17e-01	-0.1464
23077	MYCBP2	HTA11_866_2000001011	Human	Colorectum	AD	1.59e-08	-4.74e-01	-0.1001
23077	MYCBP2	HTA11_5212_2000001011	Human	Colorectum	AD	1.16e-02	-6.35e-01	-0.2061
23077	MYCBP2	HTA11_7862_2000001011	Human	Colorectum	AD	1.48e-02	-4.10e-01	-0.0179
23077	MYCBP2	HTA11_866_3004761011	Human	Colorectum	AD	6.83e-09	-4.58e-01	0.096
23077	MYCBP2	HTA11_10711_2000001011	Human	Colorectum	AD	3.23e-05	-4.54e-01	0.0338
23077	MYCBP2	HTA11_7696_3000711011	Human	Colorectum	AD	9.40e-04	-2.70e-01	0.0674
23077	MYCBP2	HTA11_6818_2000001021	Human	Colorectum	AD	9.20e-04	-4.38e-01	0.0588
23077	MYCBP2	HTA11_99999970781_79442	Human	Colorectum	MSS	4.28e-02	-2.95e-01	0.294

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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
GO:004217610	Cervix	CC	regulation of protein catabolic process	104/2311	391/18723	9.39e-15	9.36e-12	104
GO:190332010	Cervix	CC	regulation of protein modification by small protein conjugation or removal	66/2311	242/18723	2.31e-10	3.46e-08	66
GO:003139610	Cervix	CC	regulation of protein ubiquitination	59/2311	210/18723	5.90e-10	7.51e-08	59
GO:000989510	Cervix	CC	negative regulation of catabolic process	69/2311	320/18723	2.15e-06	6.55e-05	69
GO:00485118	Cervix	CC	rhythmic process	65/2311	298/18723	2.79e-06	8.04e-05	65
GO:00509203	Cervix	CC	regulation of chemotaxis	51/2311	223/18723	8.03e-06	1.86e-04	51
GO:00615647	Cervix	CC	axon development	89/2311	467/18723	1.71e-05	3.27e-04	89
GO:00076238	Cervix	CC	circadian rhythm	46/2311	210/18723	6.76e-05	9.60e-04	46
GO:00074097	Cervix	CC	axonogenesis	78/2311	418/18723	1.14e-04	1.43e-03	78
GO:004217710	Cervix	CC	negative regulation of protein catabolic process	30/2311	121/18723	1.23e-04	1.53e-03	30
GO:00329226	Cervix	CC	circadian regulation of gene expression	18/2311	68/18723	1.18e-03	9.56e-03	18
GO:00219541	Cervix	CC	central nervous system neuron development	19/2311	81/18723	3.96e-03	2.48e-02	19
GO:00313983	Cervix	CC	positive regulation of protein ubiquitination	25/2311	119/18723	5.09e-03	3.01e-02	25
GO:19033224	Cervix	CC	positive regulation of protein modification by small protein conjugation or removal	28/2311	138/18723	5.26e-03	3.08e-02	28
GO:003139625	Cervix	N_HPV	regulation of protein ubiquitination	24/534	210/18723	8.06e-09	1.60e-06	24
GO:190332025	Cervix	N_HPV	regulation of protein modification by small protein conjugation or removal	25/534	242/18723	3.05e-08	3.66e-06	25
GO:004217625	Cervix	N_HPV	regulation of protein catabolic process	28/534	391/18723	8.41e-06	2.92e-04	28
GO:00509202	Cervix	N_HPV	regulation of chemotaxis	19/534	223/18723	2.29e-05	6.37e-04	19
GO:00219531	Cervix	N_HPV	central nervous system neuron differentiation	11/534	162/18723	6.86e-03	4.55e-02	11
GO:0042176	Colorectum	AD	regulation of protein catabolic process	160/3918	391/18723	1.06e-19	7.34e-17	160

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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

MYCBP2

SNV

Missense_Mutation

c.8219A>T

p.Lys2740Met

p.K2740M

O75592

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.99)

TCGA-A1-A0SO-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

MYCBP2

SNV

Missense_Mutation

c.11849N>T

p.Trp3950Leu

p.W3950L

O75592

protein_coding

deleterious(0)

probably_damaging(0.932)

TCGA-A2-A0CP-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

MYCBP2

SNV

Missense_Mutation

rs150834693

c.9229N>G

p.Ile3077Val

p.I3077V

O75592

protein_coding

tolerated(0.57)

possibly_damaging(0.558)

TCGA-A8-A06P-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unspecific

MYCBP2

SNV

Missense_Mutation

c.10846C>T

p.His3616Tyr

p.H3616Y

O75592

protein_coding

deleterious(0)

possibly_damaging(0.838)

TCGA-A8-A095-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

5-fluorouracil

MYCBP2

SNV

Missense_Mutation

c.11147C>T

p.Pro3716Leu

p.P3716L

O75592

protein_coding

deleterious(0.01)

probably_damaging(0.987)

TCGA-A8-A09Z-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

MYCBP2

SNV

Missense_Mutation

c.8154N>C

p.Lys2718Asn

p.K2718N

O75592

protein_coding

tolerated(0.25)

benign(0.04)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

MYCBP2

SNV

Missense_Mutation

c.7918N>C

p.Asp2640His

p.D2640H

O75592

protein_coding

deleterious(0.01)

possibly_damaging(0.674)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

MYCBP2

SNV

Missense_Mutation

c.3984N>C

p.Lys1328Asn

p.K1328N

O75592

protein_coding

deleterious(0.02)

probably_damaging(0.99)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

MYCBP2

SNV

Missense_Mutation

rs770147270

c.6037N>A

p.Glu2013Lys

p.E2013K

O75592

protein_coding

deleterious(0)

probably_damaging(0.935)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

MYCBP2

SNV

Missense_Mutation

novel

c.2920N>A

p.Val974Ile

p.V974I

O75592

protein_coding

tolerated(0.1)

possibly_damaging(0.846)

TCGA-AN-A046-01

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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