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: BRD4

Gene summary for BRD4

Gene summary.

Gene information	Species	Human
	Gene symbol	BRD4
	Gene ID	23476
	Gene name	bromodomain containing 4
	Gene Alias	CAP
	Cytomap	19p13.12
	Gene Type	protein-coding
	GO ID	GO:0000082
	UniProtAcc	A0A024R7H8

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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
23476	BRD4	CA_HPV_1	Human	Cervix	CC	2.43e-04	6.42e-02	0.0264
23476	BRD4	CCI_2	Human	Cervix	CC	2.96e-07	6.52e-01	0.5249
23476	BRD4	CCI_3	Human	Cervix	CC	1.34e-03	5.92e-01	0.516
23476	BRD4	sample1	Human	Cervix	CC	2.68e-02	4.60e-01	0.0959
23476	BRD4	sample3	Human	Cervix	CC	2.31e-02	7.18e-02	0.1387
23476	BRD4	T1	Human	Cervix	CC	2.24e-08	5.04e-01	0.0918
23476	BRD4	HTA11_3410_2000001011	Human	Colorectum	AD	3.09e-05	-3.27e-01	0.0155
23476	BRD4	HTA11_7696_3000711011	Human	Colorectum	AD	1.49e-10	5.38e-01	0.0674
23476	BRD4	A015-C-203	Human	Colorectum	FAP	1.01e-18	-1.24e-01	-0.1294
23476	BRD4	A015-C-204	Human	Colorectum	FAP	8.49e-03	-1.08e-01	-0.0228
23476	BRD4	A002-C-201	Human	Colorectum	FAP	2.74e-08	8.28e-02	0.0324
23476	BRD4	A001-C-119	Human	Colorectum	FAP	1.02e-03	4.82e-02	-0.1557
23476	BRD4	A001-C-108	Human	Colorectum	FAP	4.48e-10	-2.12e-02	-0.0272
23476	BRD4	A002-C-205	Human	Colorectum	FAP	1.53e-18	-1.13e-01	-0.1236
23476	BRD4	A015-C-005	Human	Colorectum	FAP	2.41e-02	-1.43e-01	-0.0336
23476	BRD4	A015-C-006	Human	Colorectum	FAP	1.02e-12	-1.92e-02	-0.0994
23476	BRD4	A015-C-106	Human	Colorectum	FAP	1.02e-06	-4.20e-02	-0.0511
23476	BRD4	A002-C-114	Human	Colorectum	FAP	3.29e-15	-2.09e-01	-0.1561
23476	BRD4	A015-C-104	Human	Colorectum	FAP	2.39e-20	-4.64e-02	-0.1899
23476	BRD4	A001-C-014	Human	Colorectum	FAP	1.61e-05	-8.49e-02	0.0135

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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
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:00434141	Liver	HCC	macromolecule methylation	183/7958	316/18723	2.00e-08	4.72e-07	183
GO:0032259	Liver	HCC	methylation	206/7958	364/18723	3.35e-08	7.53e-07	206
GO:000635411	Liver	HCC	DNA-templated transcription, elongation	64/7958	91/18723	7.00e-08	1.44e-06	64
GO:00064792	Liver	HCC	protein methylation	111/7958	181/18723	2.36e-07	4.18e-06	111
GO:00082132	Liver	HCC	protein alkylation	111/7958	181/18723	2.36e-07	4.18e-06	111
GO:000636811	Liver	HCC	transcription elongation from RNA polymerase II promoter	50/7958	69/18723	4.32e-07	7.22e-06	50
GO:00165712	Liver	HCC	histone methylation	88/7958	141/18723	1.41e-06	2.02e-05	88
GO:19019901	Liver	HCC	regulation of mitotic cell cycle phase transition	167/7958	299/18723	1.96e-06	2.71e-05	167
GO:19019871	Liver	HCC	regulation of cell cycle phase transition	211/7958	390/18723	2.11e-06	2.89e-05	211
GO:0032784	Liver	HCC	regulation of DNA-templated transcription, elongation	39/7958	53/18723	4.34e-06	5.53e-05	39
GO:004578711	Liver	HCC	positive regulation of cell cycle	172/7958	313/18723	5.29e-06	6.58e-05	172
GO:000724912	Liver	HCC	I-kappaB kinase/NF-kappaB signaling	156/7958	281/18723	6.66e-06	8.00e-05	156
GO:004312312	Liver	HCC	positive regulation of I-kappaB kinase/NF-kappaB signaling	108/7958	186/18723	1.28e-05	1.43e-04	108
GO:004312212	Liver	HCC	regulation of I-kappaB kinase/NF-kappaB signaling	138/7958	249/18723	2.47e-05	2.58e-04	138
GO:00448432	Liver	HCC	cell cycle G1/S phase transition	134/7958	241/18723	2.60e-05	2.70e-04	134
GO:00310601	Liver	HCC	regulation of histone methylation	46/7958	69/18723	4.30e-05	4.20e-04	46
GO:0034243	Liver	HCC	regulation of transcription elongation from RNA polymerase II promoter	25/7958	32/18723	4.38e-05	4.26e-04	25
GO:00349681	Liver	HCC	histone lysine methylation	70/7958	115/18723	5.32e-05	5.04e-04	70
GO:0031058	Liver	HCC	positive regulation of histone modification	58/7958	92/18723	5.55e-05	5.21e-04	58
GO:00000822	Liver	HCC	G1/S transition of mitotic cell cycle	119/7958	214/18723	7.11e-05	6.39e-04	119

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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

BRD4

SNV

Missense_Mutation

novel

c.2808N>T

p.Gln936His

p.Q936H

O60885

protein_coding

tolerated(0.08)

benign(0)

TCGA-A2-A4RY-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

taxotere

BRD4

SNV

Missense_Mutation

rs761158744

c.1638N>C

p.Lys546Asn

p.K546N

O60885

protein_coding

tolerated(0.1)

probably_damaging(0.922)

TCGA-A7-A26H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

anastrozole

BRD4

SNV

Missense_Mutation

rs369254108

c.44N>T

p.Pro15Leu

p.P15L

O60885

protein_coding

deleterious_low_confidence(0.02)

possibly_damaging(0.656)

TCGA-AR-A1AX-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

BRD4

SNV

Missense_Mutation

novel

c.1801T>A

p.Ser601Thr

p.S601T

O60885

protein_coding

deleterious(0.03)

benign(0.262)

TCGA-E9-A1NC-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

BRD4

SNV

Missense_Mutation

c.3219N>C

p.Met1073Ile

p.M1073I

O60885

protein_coding

tolerated_low_confidence(0.08)

benign(0)

TCGA-EW-A1PB-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Unknown

BRD4

insertion

In_Frame_Ins

novel

c.1798_1799insTCTGGGGCCTCTCTGCACCTTGTTGCCTGCAGCTGTGTTCTA

p.Glu600delinsValTrpGlyLeuSerAlaProCysCysLeuGlnLeuCysSerLys

p.E600delinsVWGLSAPCCLQLCSK

O60885

protein_coding

TCGA-A8-A095-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

5-fluorouracil

BRD4

insertion

Frame_Shift_Ins

novel

c.3504_3505insACCAGTCCCCAGGCTGACTGGGACCCTCT

p.Ala1169ThrfsTer36

p.A1169Tfs*36

O60885

protein_coding

TCGA-A8-A0A4-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

tamoxiphen

BRD4

insertion

Nonsense_Mutation

novel

c.4055_4056insACATAGTTGGCATATCTTTGTTTGAAGTTTGTTGGTGGA

p.Ser1351_Asp1352insGluHisSerTrpHisIlePheValTerSerLeuLeuVal

p.S1351_D1352insEHSWHIFV*SLLV

O60885

protein_coding

TCGA-B6-A0I8-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

BRD4

insertion

In_Frame_Ins

novel

c.3737_3738insCACAATGGCACTGCTTATCTC

p.Glu1246delinsAspThrMetAlaLeuLeuIleSer

p.E1246delinsDTMALLIS

O60885

protein_coding

TCGA-BH-A0H7-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Chemotherapy

doxorubicin

BRD4

SNV

Missense_Mutation

novel

c.3767N>A

p.Arg1256Gln

p.R1256Q

O60885

protein_coding

tolerated(0.18)

benign(0.196)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

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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
23476	BRD4	CLINICALLY ACTIONABLE, KINASE, SERINE THREONINE KINASE, ENZYME, DRUGGABLE GENOME		Aminocyclopentenone compound 1
23476	BRD4	CLINICALLY ACTIONABLE, KINASE, SERINE THREONINE KINASE, ENZYME, DRUGGABLE GENOME	inhibitor	178102626
23476	BRD4	CLINICALLY ACTIONABLE, KINASE, SERINE THREONINE KINASE, ENZYME, DRUGGABLE GENOME		Aminocyclopentenone compound 6
23476	BRD4	CLINICALLY ACTIONABLE, KINASE, SERINE THREONINE KINASE, ENZYME, DRUGGABLE GENOME	inhibitor	405067321
23476	BRD4	CLINICALLY ACTIONABLE, KINASE, SERINE THREONINE KINASE, ENZYME, DRUGGABLE GENOME		BIRABRESIB	BIRABRESIB	26976114
23476	BRD4	CLINICALLY ACTIONABLE, KINASE, SERINE THREONINE KINASE, ENZYME, DRUGGABLE GENOME		CPI-0610
23476	BRD4	CLINICALLY ACTIONABLE, KINASE, SERINE THREONINE KINASE, ENZYME, DRUGGABLE GENOME		RVX-208	APABETALONE
23476	BRD4	CLINICALLY ACTIONABLE, KINASE, SERINE THREONINE KINASE, ENZYME, DRUGGABLE GENOME		ALPRAZOLAM	ALPRAZOLAM	22137933
23476	BRD4	CLINICALLY ACTIONABLE, KINASE, SERINE THREONINE KINASE, ENZYME, DRUGGABLE GENOME	inhibitor	187051820
23476	BRD4	CLINICALLY ACTIONABLE, KINASE, SERINE THREONINE KINASE, ENZYME, DRUGGABLE GENOME	inhibitor	252166516

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