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: FANCA

Gene summary for FANCA

Gene summary.

Gene information	Species	Human
	Gene symbol	FANCA
	Gene ID	2175
	Gene name	FA complementation group A
	Gene Alias	FA
	Cytomap	16q24.3
	Gene Type	protein-coding
	GO ID	GO:0000003
	UniProtAcc	O15360

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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
2175	FANCA	HSIL_HPV_2	Human	Cervix	HSIL_HPV	5.11e-03	1.82e-01	0.0208
2175	FANCA	CCI_1	Human	Cervix	CC	1.45e-11	6.31e-01	0.528
2175	FANCA	CCI_2	Human	Cervix	CC	9.85e-07	4.98e-01	0.5249
2175	FANCA	CCI_3	Human	Cervix	CC	5.99e-10	5.98e-01	0.516
2175	FANCA	CCII_1	Human	Cervix	CC	1.80e-03	2.37e-01	0.3249
2175	FANCA	HTA11_99999965062_69753	Human	Colorectum	MSI-H	1.06e-02	9.45e-01	0.3487
2175	FANCA	A001-C-119	Human	Colorectum	FAP	6.05e-06	5.42e-01	-0.1557
2175	FANCA	GSM6177623_NYU_UCEC3_Vis	Human	Endometrium	EEC	7.76e-03	2.05e-01	-0.1269
2175	FANCA	HCC1_Meng	Human	Liver	HCC	3.81e-09	2.18e-02	0.0246
2175	FANCA	HCC2	Human	Liver	HCC	6.36e-04	1.91e+00	0.5341
2175	FANCA	S014	Human	Liver	HCC	5.35e-14	5.96e-01	0.2254
2175	FANCA	S015	Human	Liver	HCC	8.83e-04	2.82e-01	0.2375
2175	FANCA	S016	Human	Liver	HCC	7.99e-10	3.32e-01	0.2243
2175	FANCA	S027	Human	Liver	HCC	4.43e-03	3.05e-01	0.2446
2175	FANCA	S028	Human	Liver	HCC	1.82e-03	2.37e-01	0.2503
2175	FANCA	S029	Human	Liver	HCC	1.90e-03	2.07e-01	0.2581
2175	FANCA	C04	Human	Oral cavity	OSCC	5.49e-09	3.66e-01	0.2633
2175	FANCA	C21	Human	Oral cavity	OSCC	5.81e-29	8.35e-01	0.2678
2175	FANCA	C30	Human	Oral cavity	OSCC	8.26e-09	3.52e-01	0.3055
2175	FANCA	C38	Human	Oral cavity	OSCC	9.35e-07	4.10e-01	0.172

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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
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:190210512	Cervix	HSIL_HPV	regulation of leukocyte differentiation	28/737	279/18723	5.84e-06	2.13e-04	28
GO:005109012	Cervix	HSIL_HPV	regulation of DNA-binding transcription factor activity	35/737	440/18723	6.77e-05	1.58e-03	35
GO:004860813	Cervix	HSIL_HPV	reproductive structure development	32/737	424/18723	3.52e-04	5.54e-03	32
GO:006145814	Cervix	HSIL_HPV	reproductive system development	32/737	427/18723	3.98e-04	6.14e-03	32
GO:00455891	Cervix	HSIL_HPV	regulation of regulatory T cell differentiation	6/737	28/18723	6.53e-04	8.92e-03	6
GO:00450661	Cervix	HSIL_HPV	regulatory T cell differentiation	6/737	31/18723	1.16e-03	1.38e-02	6
GO:00302171	Cervix	HSIL_HPV	T cell differentiation	20/737	257/18723	3.01e-03	2.78e-02	20
GO:190313112	Cervix	HSIL_HPV	mononuclear cell differentiation	29/737	426/18723	3.10e-03	2.84e-02	29
GO:00455801	Cervix	HSIL_HPV	regulation of T cell differentiation	13/737	146/18723	5.11e-03	4.14e-02	13
GO:19037062	Colorectum	MSI-H	regulation of hemopoiesis	41/1319	367/18723	2.31e-03	3.09e-02	41
GO:00614583	Colorectum	FAP	reproductive system development	85/2622	427/18723	4.30e-04	5.13e-03	85
GO:00486083	Colorectum	FAP	reproductive structure development	84/2622	424/18723	5.40e-04	6.10e-03	84
GO:1903131	Colorectum	FAP	mononuclear cell differentiation	79/2622	426/18723	5.00e-03	3.33e-02	79
GO:19037063	Colorectum	FAP	regulation of hemopoiesis	69/2622	367/18723	6.01e-03	3.78e-02	69
GO:00510901	Colorectum	FAP	regulation of DNA-binding transcription factor activity	80/2622	440/18723	7.90e-03	4.67e-02	80
GO:006145815	Endometrium	EEC	reproductive system development	91/2168	427/18723	4.54e-09	3.13e-07	91
GO:004860814	Endometrium	EEC	reproductive structure development	90/2168	424/18723	6.77e-09	4.41e-07	90
GO:004211014	Endometrium	EEC	T cell activation	85/2168	487/18723	6.81e-05	1.01e-03	85
GO:190370615	Endometrium	EEC	regulation of hemopoiesis	67/2168	367/18723	1.01e-04	1.40e-03	67
GO:005086313	Endometrium	EEC	regulation of T cell activation	60/2168	329/18723	2.33e-04	2.75e-03	60

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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

FANCA

SNV

Missense_Mutation

c.502C>G

p.Gln168Glu

p.Q168E

O15360

protein_coding

deleterious(0.03)

benign(0.006)

TCGA-A8-A09I-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

anastrozole

FANCA

SNV

Missense_Mutation

c.2791N>C

p.Asp931His

p.D931H

O15360

protein_coding

deleterious(0)

probably_damaging(0.963)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

FANCA

SNV

Missense_Mutation

c.112N>A

p.Glu38Lys

p.E38K

O15360

protein_coding

tolerated(0.15)

benign(0.272)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

FANCA

SNV

Missense_Mutation

rs376103033

c.3157N>T

p.Arg1053Cys

p.R1053C

O15360

protein_coding

tolerated(0.23)

benign(0.015)

TCGA-AN-A04A-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

FANCA

SNV

Missense_Mutation

rs764206631

c.3250N>T

p.Arg1084Cys

p.R1084C

O15360

protein_coding

tolerated(0.07)

benign(0.003)

TCGA-AR-A0TR-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

tamoxiphen

FANCA

SNV

Missense_Mutation

c.3043G>A

p.Glu1015Lys

p.E1015K

O15360

protein_coding

tolerated(0.74)

benign(0.003)

TCGA-BH-A1EO-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

FANCA

SNV

Missense_Mutation

c.2080N>T

p.Asp694Tyr

p.D694Y

O15360

protein_coding

tolerated(0.06)

possibly_damaging(0.819)

TCGA-C8-A26Y-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

FANCA

SNV

Missense_Mutation

c.155N>T

p.Arg52Leu

p.R52L

O15360

protein_coding

tolerated(0.06)

possibly_damaging(0.468)

TCGA-D8-A1J9-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

FANCA

insertion

Nonsense_Mutation

novel

c.3409_3410insTCTTCCATGAGTGTGGGTAATAAAT

p.Gly1137ValfsTer7

p.G1137Vfs*7

O15360

protein_coding

TCGA-A2-A04Y-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

FANCA

insertion

Nonsense_Mutation

novel

c.3130_3131insTGAGAGTCTGAGCCCTTGGGA

p.Gln1044delinsLeuArgValTerAlaLeuGlyLys

p.Q1044delinsLRV*ALGK

O15360

protein_coding

TCGA-A2-A0CM-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

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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
2175	FANCA	CLINICALLY ACTIONABLE, DNA REPAIR		CISPLATIN	CISPLATIN	26181256

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