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: BRCA1

Gene summary for BRCA1

Gene summary.

Gene information	Species	Human
	Gene symbol	BRCA1
	Gene ID	672
	Gene name	BRCA1 DNA repair associated
	Gene Alias	BRCAI
	Cytomap	17q21.31
	Gene Type	protein-coding
	GO ID	GO:0000075
	UniProtAcc	P38398

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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
672	BRCA1	HTA11_78_2000001011	Human	Colorectum	AD	1.76e-02	3.19e-01	-0.1088
672	BRCA1	HTA11_347_2000001011	Human	Colorectum	AD	2.03e-16	4.99e-01	-0.1954
672	BRCA1	HTA11_83_2000001011	Human	Colorectum	SER	3.85e-02	3.24e-01	-0.1526
672	BRCA1	HTA11_696_2000001011	Human	Colorectum	AD	8.52e-07	4.31e-01	-0.1464
672	BRCA1	HTA11_866_2000001011	Human	Colorectum	AD	9.67e-07	4.20e-01	-0.1001
672	BRCA1	HTA11_1391_2000001011	Human	Colorectum	AD	4.64e-06	4.58e-01	-0.059
672	BRCA1	HTA11_7696_3000711011	Human	Colorectum	AD	8.36e-07	3.89e-01	0.0674
672	BRCA1	HTA11_99999970781_79442	Human	Colorectum	MSS	6.31e-13	5.48e-01	0.294
672	BRCA1	HTA11_99999965104_69814	Human	Colorectum	MSS	2.63e-08	4.51e-01	0.281
672	BRCA1	HTA11_99999971662_82457	Human	Colorectum	MSS	5.77e-11	5.33e-01	0.3859
672	BRCA1	LZE2T	Human	Esophagus	ESCC	3.94e-07	6.42e-01	0.082
672	BRCA1	LZE7T	Human	Esophagus	ESCC	1.02e-03	2.39e-01	0.0667
672	BRCA1	LZE21T	Human	Esophagus	ESCC	6.52e-03	2.43e-01	0.0655
672	BRCA1	P1T-E	Human	Esophagus	ESCC	1.64e-05	3.37e-01	0.0875
672	BRCA1	P2T-E	Human	Esophagus	ESCC	2.33e-12	4.11e-01	0.1177
672	BRCA1	P4T-E	Human	Esophagus	ESCC	1.78e-10	2.75e-01	0.1323
672	BRCA1	P5T-E	Human	Esophagus	ESCC	2.65e-08	2.36e-01	0.1327
672	BRCA1	P8T-E	Human	Esophagus	ESCC	1.49e-03	1.40e-01	0.0889
672	BRCA1	P9T-E	Human	Esophagus	ESCC	8.38e-03	1.18e-01	0.1131
672	BRCA1	P10T-E	Human	Esophagus	ESCC	3.00e-03	6.98e-02	0.116

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
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
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:0097193	Colorectum	AD	intrinsic apoptotic signaling pathway	108/3918	288/18723	6.25e-11	6.41e-09	108
GO:2001233	Colorectum	AD	regulation of apoptotic signaling pathway	119/3918	356/18723	2.14e-08	1.21e-06	119
GO:1903320	Colorectum	AD	regulation of protein modification by small protein conjugation or removal	86/3918	242/18723	9.43e-08	4.65e-06	86
GO:0010639	Colorectum	AD	negative regulation of organelle organization	114/3918	348/18723	1.41e-07	6.49e-06	114
GO:0051052	Colorectum	AD	regulation of DNA metabolic process	116/3918	359/18723	2.47e-07	1.00e-05	116
GO:0051054	Colorectum	AD	positive regulation of DNA metabolic process	73/3918	201/18723	3.27e-07	1.29e-05	73
GO:0071383	Colorectum	AD	cellular response to steroid hormone stimulus	73/3918	204/18723	6.31e-07	2.24e-05	73
GO:0030522	Colorectum	AD	intracellular receptor signaling pathway	87/3918	265/18723	3.69e-06	1.03e-04	87
GO:0031396	Colorectum	AD	regulation of protein ubiquitination	72/3918	210/18723	4.50e-06	1.21e-04	72
GO:0043401	Colorectum	AD	steroid hormone mediated signaling pathway	51/3918	136/18723	6.52e-06	1.63e-04	51
GO:0000209	Colorectum	AD	protein polyubiquitination	78/3918	236/18723	8.71e-06	2.06e-04	78
GO:0051494	Colorectum	AD	negative regulation of cytoskeleton organization	58/3918	163/18723	1.04e-05	2.40e-04	58
GO:0048545	Colorectum	AD	response to steroid hormone	104/3918	339/18723	1.33e-05	2.90e-04	104
GO:2001234	Colorectum	AD	negative regulation of apoptotic signaling pathway	74/3918	224/18723	1.49e-05	3.18e-04	74
GO:0009755	Colorectum	AD	hormone-mediated signaling pathway	64/3918	190/18723	2.78e-05	5.24e-04	64
GO:2001020	Colorectum	AD	regulation of response to DNA damage stimulus	71/3918	219/18723	4.38e-05	7.65e-04	71
GO:0030518	Colorectum	AD	intracellular steroid hormone receptor signaling pathway	43/3918	116/18723	4.61e-05	7.97e-04	43
GO:0006631	Colorectum	AD	fatty acid metabolic process	114/3918	390/18723	5.58e-05	9.44e-04	114
GO:0097191	Colorectum	AD	extrinsic apoptotic signaling pathway	68/3918	219/18723	2.64e-04	3.27e-03	68
GO:0072593	Colorectum	AD	reactive oxygen species metabolic process	73/3918	239/18723	2.79e-04	3.42e-03	73

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa04120	Colorectum	AD	Ubiquitin mediated proteolysis	58/2092	142/8465	1.46e-05	1.53e-04	9.76e-05	58
hsa041201	Colorectum	AD	Ubiquitin mediated proteolysis	58/2092	142/8465	1.46e-05	1.53e-04	9.76e-05	58
hsa041202	Colorectum	SER	Ubiquitin mediated proteolysis	39/1580	142/8465	6.18e-03	3.66e-02	2.66e-02	39
hsa041203	Colorectum	SER	Ubiquitin mediated proteolysis	39/1580	142/8465	6.18e-03	3.66e-02	2.66e-02	39
hsa041204	Colorectum	MSS	Ubiquitin mediated proteolysis	55/1875	142/8465	5.02e-06	6.00e-05	3.68e-05	55
hsa01524	Colorectum	MSS	Platinum drug resistance	25/1875	73/8465	1.17e-02	3.99e-02	2.44e-02	25
hsa041205	Colorectum	MSS	Ubiquitin mediated proteolysis	55/1875	142/8465	5.02e-06	6.00e-05	3.68e-05	55
hsa015241	Colorectum	MSS	Platinum drug resistance	25/1875	73/8465	1.17e-02	3.99e-02	2.44e-02	25
hsa0412027	Esophagus	ESCC	Ubiquitin mediated proteolysis	122/4205	142/8465	6.53e-20	7.29e-18	3.74e-18	122
hsa015247	Esophagus	ESCC	Platinum drug resistance	56/4205	73/8465	1.85e-06	1.13e-05	5.78e-06	56
hsa041517	Esophagus	ESCC	PI3K-Akt signaling pathway	197/4205	354/8465	1.24e-02	2.83e-02	1.45e-02	197
hsa0412036	Esophagus	ESCC	Ubiquitin mediated proteolysis	122/4205	142/8465	6.53e-20	7.29e-18	3.74e-18	122
hsa0152414	Esophagus	ESCC	Platinum drug resistance	56/4205	73/8465	1.85e-06	1.13e-05	5.78e-06	56
hsa0415114	Esophagus	ESCC	PI3K-Akt signaling pathway	197/4205	354/8465	1.24e-02	2.83e-02	1.45e-02	197
hsa0412041	Liver	HCC	Ubiquitin mediated proteolysis	110/4020	142/8465	1.67e-13	3.74e-12	2.08e-12	110
hsa015242	Liver	HCC	Platinum drug resistance	52/4020	73/8465	3.14e-05	1.88e-04	1.04e-04	52
hsa0412051	Liver	HCC	Ubiquitin mediated proteolysis	110/4020	142/8465	1.67e-13	3.74e-12	2.08e-12	110
hsa015243	Liver	HCC	Platinum drug resistance	52/4020	73/8465	3.14e-05	1.88e-04	1.04e-04	52
hsa0412020	Oral cavity	OSCC	Ubiquitin mediated proteolysis	105/3704	142/8465	1.83e-13	4.37e-12	2.23e-12	105
hsa015246	Oral cavity	OSCC	Platinum drug resistance	51/3704	73/8465	5.41e-06	2.75e-05	1.40e-05	51

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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
BRCA1	TAC	Colorectum	ADJ	KNTC1,FANCA,RAD51AP1, etc.	1.82e-01
BRCA1	ASC	Colorectum	SER	BRIP1,FANCA,DTL, etc.	1.14e-01
BRCA1	CD8TEX	Endometrium	Healthy	ATAD5,FAM208A,CASP8AP2, etc.	1.40e-01
BRCA1	PRO	Esophagus	ESCC	DTL,HELLS,BRCA2, etc.	1.45e-01
BRCA1	PRO	Esophagus	HGIN	DTL,HELLS,BRCA2, etc.	3.68e-01
BRCA1	BMEM	Liver	Healthy	KMO,COA7,HMGB1, etc.	6.26e-02
BRCA1	BAS	Oral cavity	Healthy	MCM3,DUT,MCM5, etc.	2.11e-01
BRCA1	STM	Pancreas	PanIN	HNRNPUL1,SLX4IP,BRIP1, etc.	2.91e-01
BRCA1	NKT	Pancreas	ADJ	NBR2,ATAD5,BRIP1, etc.	3.66e-01
BRCA1	MDSC	Prostate	ADJ	LIG1,MCM4,MCM7, etc.	8.17e-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

BRCA1

SNV

Missense_Mutation

c.25N>C

p.Glu9Gln

p.E9Q

P38398

protein_coding

tolerated(0.1)

possibly_damaging(0.749)

TCGA-A1-A0SI-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

BRCA1

SNV

Missense_Mutation

novel

c.149N>C

p.Lys50Thr

p.K50T

P38398

protein_coding

deleterious(0)

probably_damaging(0.984)

TCGA-A2-A4S0-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

BRCA1

SNV

Missense_Mutation

c.3292N>A

p.Leu1098Ile

p.L1098I

P38398

protein_coding

deleterious(0.01)

benign(0.373)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

BRCA1

SNV

Missense_Mutation

rs80357069

c.5426G>T

p.Gly1809Val

p.G1809V

P38398

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-AN-A0XU-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

BRCA1

SNV

Missense_Mutation

c.247N>T

p.Val83Phe

p.V83F

P38398

protein_coding

deleterious(0)

probably_damaging(0.949)

TCGA-AO-A0J4-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

BRCA1

SNV

Missense_Mutation

c.5495A>T

p.Gln1832Leu

p.Q1832L

P38398

protein_coding

deleterious(0)

possibly_damaging(0.849)

TCGA-BH-A0DS-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Chemotherapy

cyclophosphamide

BRCA1

SNV

Missense_Mutation

novel

c.4795N>C

p.Asp1599His

p.D1599H

P38398

protein_coding

deleterious(0.01)

possibly_damaging(0.891)

TCGA-BH-A2L8-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

BRCA1

SNV

Missense_Mutation

c.4030N>C

p.Asp1344His

p.D1344H

P38398

protein_coding

deleterious(0.04)

benign(0.065)

TCGA-C8-A12T-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

BRCA1

SNV

Missense_Mutation

c.6N>A

p.Asp2Glu

p.D2E

P38398

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-E2-A1BD-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

arimidex

BRCA1

SNV

Missense_Mutation

c.3080N>T

p.Ser1027Ile

p.S1027I

P38398

protein_coding

tolerated(0.08)

benign(0.202)

TCGA-E2-A1L9-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

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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
672	BRCA1	CLINICALLY ACTIONABLE, TUMOR SUPPRESSOR, ENZYME, DRUGGABLE GENOME, DRUG RESISTANCE		DOXORUBICIN HYDROCHLORIDE	DOXORUBICIN HYDROCHLORIDE
672	BRCA1	CLINICALLY ACTIONABLE, TUMOR SUPPRESSOR, ENZYME, DRUGGABLE GENOME, DRUG RESISTANCE		ACRIFLAVINE CHLORIDE	ACRIFLAVINE
672	BRCA1	CLINICALLY ACTIONABLE, TUMOR SUPPRESSOR, ENZYME, DRUGGABLE GENOME, DRUG RESISTANCE		7-O-ACETYLAFROMOSIN	CHEMBL446567
672	BRCA1	CLINICALLY ACTIONABLE, TUMOR SUPPRESSOR, ENZYME, DRUGGABLE GENOME, DRUG RESISTANCE		PIFEXOLE	PIFEXOLE
672	BRCA1	CLINICALLY ACTIONABLE, TUMOR SUPPRESSOR, ENZYME, DRUGGABLE GENOME, DRUG RESISTANCE		DOXORUBICIN	DOXORUBICIN	12698198
672	BRCA1	CLINICALLY ACTIONABLE, TUMOR SUPPRESSOR, ENZYME, DRUGGABLE GENOME, DRUG RESISTANCE		DNDI1417078	CHEMBL1320798
672	BRCA1	CLINICALLY ACTIONABLE, TUMOR SUPPRESSOR, ENZYME, DRUGGABLE GENOME, DRUG RESISTANCE		Cyclophosphamide	CYCLOPHOSPHAMIDE	25589624
672	BRCA1	CLINICALLY ACTIONABLE, TUMOR SUPPRESSOR, ENZYME, DRUGGABLE GENOME, DRUG RESISTANCE		HORMONES		9133444
672	BRCA1	CLINICALLY ACTIONABLE, TUMOR SUPPRESSOR, ENZYME, DRUGGABLE GENOME, DRUG RESISTANCE		MITOMYCIN C		15782115
672	BRCA1	CLINICALLY ACTIONABLE, TUMOR SUPPRESSOR, ENZYME, DRUGGABLE GENOME, DRUG RESISTANCE		ABT-767

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