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: RIF1

Gene summary for RIF1

Gene summary.

Gene information	Species	Human
	Gene symbol	RIF1
	Gene ID	55183
	Gene name	replication timing regulatory factor 1
	Gene Alias	RIF1
	Cytomap	2q23.3
	Gene Type	protein-coding
	GO ID	GO:0000018
	UniProtAcc	Q5UIP0

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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
55183	RIF1	CA_HPV_1	Human	Cervix	CC	3.72e-03	-4.79e-02	0.0264
55183	RIF1	CCI_1	Human	Cervix	CC	4.42e-02	5.65e-01	0.528
55183	RIF1	CCI_2	Human	Cervix	CC	6.25e-12	1.06e+00	0.5249
55183	RIF1	CCI_3	Human	Cervix	CC	1.20e-05	6.27e-01	0.516
55183	RIF1	HTA11_3410_2000001011	Human	Colorectum	AD	2.29e-13	-4.77e-01	0.0155
55183	RIF1	HTA11_2487_2000001011	Human	Colorectum	SER	2.92e-03	-3.72e-01	-0.1808
55183	RIF1	HTA11_3361_2000001011	Human	Colorectum	AD	2.71e-02	-4.06e-01	-0.1207
55183	RIF1	HTA11_696_2000001011	Human	Colorectum	AD	3.55e-05	-3.80e-01	-0.1464
55183	RIF1	HTA11_866_2000001011	Human	Colorectum	AD	1.36e-04	-3.60e-01	-0.1001
55183	RIF1	HTA11_1391_2000001011	Human	Colorectum	AD	2.55e-02	-3.04e-01	-0.059
55183	RIF1	HTA11_5212_2000001011	Human	Colorectum	AD	1.24e-02	-5.55e-01	-0.2061
55183	RIF1	HTA11_866_3004761011	Human	Colorectum	AD	2.92e-08	-4.19e-01	0.096
55183	RIF1	HTA11_10711_2000001011	Human	Colorectum	AD	1.39e-02	-3.46e-01	0.0338
55183	RIF1	HTA11_7696_3000711011	Human	Colorectum	AD	9.30e-07	-4.00e-01	0.0674
55183	RIF1	HTA11_6818_2000001021	Human	Colorectum	AD	2.45e-03	-4.24e-01	0.0588
55183	RIF1	A001-C-207	Human	Colorectum	FAP	4.79e-02	-6.15e-02	0.1278
55183	RIF1	A015-C-203	Human	Colorectum	FAP	8.66e-18	3.55e-02	-0.1294
55183	RIF1	A015-C-204	Human	Colorectum	FAP	1.61e-04	1.60e-02	-0.0228
55183	RIF1	A014-C-040	Human	Colorectum	FAP	2.21e-02	-2.85e-03	-0.1184
55183	RIF1	A002-C-201	Human	Colorectum	FAP	6.13e-11	-1.31e-01	0.0324

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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
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:00512517	Oral cavity	EOLP	positive regulation of lymphocyte activation	72/2218	362/18723	6.21e-06	1.22e-04	72
GO:005105421	Oral cavity	EOLP	positive regulation of DNA metabolic process	45/2218	201/18723	1.68e-05	2.77e-04	45
GO:00508677	Oral cavity	EOLP	positive regulation of cell activation	79/2218	420/18723	1.91e-05	3.02e-04	79
GO:00026968	Oral cavity	EOLP	positive regulation of leukocyte activation	77/2218	409/18723	2.34e-05	3.52e-04	77
GO:001820521	Oral cavity	EOLP	peptidyl-lysine modification	72/2218	376/18723	2.38e-05	3.56e-04	72
GO:199082315	Oral cavity	EOLP	response to leukemia inhibitory factor	26/2218	95/18723	2.91e-05	4.20e-04	26
GO:200102024	Oral cavity	EOLP	regulation of response to DNA damage stimulus	47/2218	219/18723	3.47e-05	4.85e-04	47
GO:00022633	Oral cavity	EOLP	cell activation involved in immune response	56/2218	279/18723	4.91e-05	6.47e-04	56
GO:00023662	Oral cavity	EOLP	leukocyte activation involved in immune response	55/2218	275/18723	6.32e-05	7.90e-04	55
GO:199083014	Oral cavity	EOLP	cellular response to leukemia inhibitory factor	25/2218	94/18723	6.89e-05	8.53e-04	25
GO:00022852	Oral cavity	EOLP	lymphocyte activation involved in immune response	42/2218	194/18723	7.17e-05	8.82e-04	42
GO:003220021	Oral cavity	EOLP	telomere organization	36/2218	159/18723	8.79e-05	1.04e-03	36
GO:003106012	Oral cavity	EOLP	regulation of histone methylation	19/2218	69/18723	3.05e-04	2.85e-03	19
GO:00421132	Oral cavity	EOLP	B cell activation	61/2218	334/18723	3.68e-04	3.35e-03	61
GO:00028193	Oral cavity	EOLP	regulation of adaptive immune response	38/2218	183/18723	3.75e-04	3.40e-03	38
GO:00026974	Oral cavity	EOLP	regulation of immune effector process	61/2218	339/18723	5.48e-04	4.68e-03	61
GO:003496813	Oral cavity	EOLP	histone lysine methylation	26/2218	115/18723	8.11e-04	6.35e-03	26
GO:001657113	Oral cavity	EOLP	histone methylation	30/2218	141/18723	9.78e-04	7.39e-03	30
GO:00400292	Oral cavity	EOLP	regulation of gene expression, epigenetic	24/2218	105/18723	1.07e-03	7.87e-03	24
GO:00090481	Oral cavity	EOLP	dosage compensation by inactivation of X chromosome	7/2218	16/18723	1.40e-03	9.58e-03	7

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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

RIF1

SNV

Missense_Mutation

novel

c.2705N>A

p.Gly902Glu

p.G902E

Q5UIP0

protein_coding

deleterious(0.03)

benign(0.275)

TCGA-5L-AAT0-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

tamoxiphen

RIF1

SNV

Missense_Mutation

c.1744N>A

p.Ala582Thr

p.A582T

Q5UIP0

protein_coding

deleterious(0)

probably_damaging(0.997)

TCGA-BH-A0AZ-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

doxorubicin

RIF1

SNV

Missense_Mutation

c.4006N>A

p.Glu1336Lys

p.E1336K

Q5UIP0

protein_coding

deleterious(0.03)

benign(0.053)

TCGA-BH-A0B5-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

adriamycin

RIF1

SNV

Missense_Mutation

c.4111N>T

p.Asn1371Tyr

p.N1371Y

Q5UIP0

protein_coding

deleterious(0.02)

benign(0.26)

TCGA-BH-A0HU-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

docetaxel

RIF1

SNV

Missense_Mutation

novel

c.7033N>T

p.Pro2345Ser

p.P2345S

Q5UIP0

protein_coding

deleterious(0)

probably_damaging(0.998)

TCGA-C8-A8HQ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

RIF1

SNV

Missense_Mutation

novel

c.7196N>C

p.Leu2399Pro

p.L2399P

Q5UIP0

protein_coding

deleterious(0)

possibly_damaging(0.543)

TCGA-C8-A8HR-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

5-fluorouracil

RIF1

SNV

Missense_Mutation

c.7030N>T

p.Leu2344Phe

p.L2344F

Q5UIP0

protein_coding

deleterious(0)

probably_damaging(0.966)

TCGA-D8-A1JA-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

adriamycin

RIF1

SNV

Missense_Mutation

novel

c.6699N>G

p.Ser2233Arg

p.S2233R

Q5UIP0

protein_coding

tolerated(0.12)

benign(0.235)

TCGA-D8-A1XK-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicine+cyclophosphamide

RIF1

SNV

Missense_Mutation

c.3977N>G

p.Asn1326Ser

p.N1326S

Q5UIP0

protein_coding

tolerated(0.15)

possibly_damaging(0.815)

TCGA-D8-A1XS-01

Breast

breast invasive carcinoma

Male

<65

III/IV

Chemotherapy

adriamycin+cyclophosphamide

RIF1

SNV

Missense_Mutation

novel

c.6515C>T

p.Ser2172Phe

p.S2172F

Q5UIP0

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-E2-A152-01

Breast

breast invasive carcinoma

Female

<65

I/II

Targeted Molecular therapy

trastuzumab

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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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