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: BPTF

Gene summary for BPTF

Gene summary.

Gene information	Species	Human
	Gene symbol	BPTF
	Gene ID	2186
	Gene name	bromodomain PHD finger transcription factor
	Gene Alias	FAC1
	Cytomap	17q24.2
	Gene Type	protein-coding
	GO ID	GO:0000003
	UniProtAcc	Q12830

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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
2186	BPTF	GSM4909285	Human	Breast	IDC	8.99e-10	1.40e-01	0.21
2186	BPTF	GSM4909286	Human	Breast	IDC	4.59e-11	1.91e-01	0.1081
2186	BPTF	GSM4909293	Human	Breast	IDC	6.42e-19	3.55e-01	0.1581
2186	BPTF	GSM4909298	Human	Breast	IDC	1.52e-22	4.04e-01	0.1551
2186	BPTF	GSM4909308	Human	Breast	IDC	2.58e-05	2.51e-01	0.158
2186	BPTF	GSM4909311	Human	Breast	IDC	3.45e-07	-1.87e-01	0.1534
2186	BPTF	GSM4909317	Human	Breast	IDC	3.42e-08	4.10e-01	0.1355
2186	BPTF	GSM4909319	Human	Breast	IDC	5.19e-09	-1.95e-01	0.1563
2186	BPTF	brca10	Human	Breast	Precancer	1.15e-04	-2.64e-01	-0.0029
2186	BPTF	M1	Human	Breast	IDC	9.42e-29	8.76e-01	0.1577
2186	BPTF	NCCBC14	Human	Breast	DCIS	2.78e-05	2.66e-01	0.2021
2186	BPTF	NCCBC2	Human	Breast	DCIS	9.95e-12	8.70e-01	0.1554
2186	BPTF	NCCBC3	Human	Breast	DCIS	3.49e-02	2.49e-01	0.1198
2186	BPTF	NCCBC5	Human	Breast	DCIS	2.98e-03	-1.05e-01	0.2046
2186	BPTF	P1	Human	Breast	IDC	6.13e-17	5.89e-01	0.1527
2186	BPTF	DCIS2	Human	Breast	DCIS	4.79e-65	5.62e-01	0.0085
2186	BPTF	CA_HPV_1	Human	Cervix	CC	6.40e-11	-2.27e-01	0.0264
2186	BPTF	N_HPV_1	Human	Cervix	N_HPV	1.54e-04	-1.25e-01	0.0079
2186	BPTF	CCI_2	Human	Cervix	CC	1.59e-08	6.40e-01	0.5249
2186	BPTF	CCI_3	Human	Cervix	CC	8.51e-04	6.56e-01	0.516

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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
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:004860816	Oral cavity	OSCC	reproductive structure development	214/7305	424/18723	8.58e-07	1.18e-05	214
GO:000189216	Oral cavity	OSCC	embryonic placenta development	50/7305	82/18723	4.58e-05	3.90e-04	50
GO:199009014	Oral cavity	OSCC	cellular response to nerve growth factor stimulus	35/7305	53/18723	6.14e-05	5.02e-04	35
GO:00074925	Oral cavity	OSCC	endoderm development	47/7305	77/18723	7.40e-05	5.81e-04	47
GO:19900899	Oral cavity	OSCC	response to nerve growth factor	36/7305	56/18723	1.12e-04	8.24e-04	36
GO:000632510	Oral cavity	OSCC	chromatin organization	190/7305	409/18723	1.17e-03	5.97e-03	190
GO:000632515	Oral cavity	EOLP	chromatin organization	84/2218	409/18723	2.68e-07	8.16e-06	84
GO:000189023	Oral cavity	EOLP	placenta development	39/2218	144/18723	4.49e-07	1.25e-05	39
GO:000189222	Oral cavity	EOLP	embryonic placenta development	26/2218	82/18723	1.50e-06	3.55e-05	26
GO:000170123	Oral cavity	EOLP	in utero embryonic development	72/2218	367/18723	1.02e-05	1.83e-04	72
GO:006145824	Oral cavity	EOLP	reproductive system development	81/2218	427/18723	1.09e-05	1.93e-04	81
GO:004860823	Oral cavity	EOLP	reproductive structure development	80/2218	424/18723	1.51e-05	2.50e-04	80
GO:199009015	Oral cavity	EOLP	cellular response to nerve growth factor stimulus	15/2218	53/18723	9.35e-04	7.11e-03	15
GO:000749212	Oral cavity	EOLP	endoderm development	19/2218	77/18723	1.32e-03	9.33e-03	19
GO:199008915	Oral cavity	EOLP	response to nerve growth factor	15/2218	56/18723	1.73e-03	1.14e-02	15
GO:00063383	Oral cavity	EOLP	chromatin remodeling	46/2218	255/18723	2.34e-03	1.44e-02	46
GO:006145831	Oral cavity	NEOLP	reproductive system development	91/2005	427/18723	8.18e-11	9.00e-09	91
GO:004860831	Oral cavity	NEOLP	reproductive structure development	90/2005	424/18723	1.30e-10	1.33e-08	90
GO:000189031	Oral cavity	NEOLP	placenta development	42/2005	144/18723	8.01e-10	6.02e-08	42
GO:000170132	Oral cavity	NEOLP	in utero embryonic development	76/2005	367/18723	1.11e-08	5.44e-07	76

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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

TF	Cell Type	Tissue	Disease Stage	Target Gene	RSS	Regulon Activity
BPTF	CD8TEFF	Breast	IDC	PLCG2,DDX17,SYNE2, etc.	7.55e-02
BPTF	ASC	Colorectum	SER	ARL17B,HNF1A-AS1,MT-ATP8, etc.	1.20e-01
BPTF	CD8TEXINT	Stomach	CAG	GRAMD2B,MCTP2,PACS1, etc.	1.82e-02
BPTF	CD4TN	Stomach	CAG	GRAMD2B,MCTP2,PACS1, etc.	1.17e-02
BPTF	CD4TN	Stomach	CSG	GRAMD2B,MCTP2,PACS1, etc.	8.54e-02
BPTF	MAIT	Stomach	SIM	GRAMD2B,MCTP2,PACS1, etc.	4.20e-02
BPTF	LYMEND	Stomach	ADJ	PHF14,PLA2G2A,MT-ND2, etc.	1.50e-02
BPTF	MVA	Stomach	CAG	PHF14,PLA2G2A,MT-ND2, etc.	6.16e-02
BPTF	CAF	Stomach	CSG	PHF14,PLA2G2A,MT-ND2, etc.	1.16e-01
BPTF	MVA	Stomach	Healthy	PHF14,PLA2G2A,MT-ND2, etc.	3.92e-02

∗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

BPTF

SNV

Missense_Mutation

novel

c.4221N>G

p.Ile1407Met

p.I1407M

Q12830

protein_coding

tolerated_low_confidence(0.28)

benign(0.295)

TCGA-A7-A4SE-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

BPTF

SNV

Missense_Mutation

novel

c.587N>A

p.Ser196Asn

p.S196N

Q12830

protein_coding

deleterious(0)

probably_damaging(0.943)

TCGA-A8-A07W-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Hormone Therapy

exemestane

BPTF

SNV

Missense_Mutation

c.6194N>C

p.Arg2065Thr

p.R2065T

Q12830

protein_coding

deleterious(0)

probably_damaging(0.919)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

BPTF

SNV

Missense_Mutation

c.5514N>G

p.Ile1838Met

p.I1838M

Q12830

protein_coding

deleterious(0.01)

possibly_damaging(0.847)

TCGA-BH-A0DZ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

docetaxel

BPTF

SNV

Missense_Mutation

c.6368N>T

p.Ser2123Leu

p.S2123L

Q12830

protein_coding

deleterious(0.02)

benign(0.164)

TCGA-BH-A2L8-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

BPTF

SNV

Missense_Mutation

c.5401C>A

p.Pro1801Thr

p.P1801T

Q12830

protein_coding

deleterious(0.01)

possibly_damaging(0.908)

TCGA-C8-A132-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

BPTF

SNV

Missense_Mutation

c.2908N>C

p.Asp970His

p.D970H

Q12830

protein_coding

tolerated(0.07)

possibly_damaging(0.548)

TCGA-C8-A26Y-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

BPTF

SNV

Missense_Mutation

c.4442N>G

p.Ser1481Cys

p.S1481C

Q12830

protein_coding

tolerated_low_confidence(0.14)

possibly_damaging(0.634)

TCGA-D8-A1JA-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

adriamycin

BPTF

SNV

Missense_Mutation

c.2053N>C

p.Glu685Gln

p.E685Q

Q12830

protein_coding

deleterious(0.02)

benign(0.076)

TCGA-D8-A1JC-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

adriamycin

BPTF

SNV

Missense_Mutation

c.751G>A

p.Glu251Lys

p.E251K

Q12830

protein_coding

deleterious(0)

probably_damaging(0.997)

TCGA-D8-A27G-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
2186	BPTF	TRANSCRIPTION FACTOR	inhibitor	252827533

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