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: CPSF7

Gene summary for CPSF7

Gene summary.

Gene information	Species	Human
	Gene symbol	CPSF7
	Gene ID	79869
	Gene name	cleavage and polyadenylation specific factor 7
	Gene Alias	CFIm59
	Cytomap	11q12.2
	Gene Type	protein-coding
	GO ID	GO:0006139
	UniProtAcc	Q8N684

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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
79869	CPSF7	LZE4T	Human	Esophagus	ESCC	6.67e-08	3.38e-01	0.0811
79869	CPSF7	LZE7T	Human	Esophagus	ESCC	2.83e-03	2.72e-01	0.0667
79869	CPSF7	LZE8T	Human	Esophagus	ESCC	2.19e-05	2.75e-01	0.067
79869	CPSF7	LZE24T	Human	Esophagus	ESCC	2.20e-15	4.87e-01	0.0596
79869	CPSF7	LZE21T	Human	Esophagus	ESCC	7.97e-03	2.55e-01	0.0655
79869	CPSF7	LZE6T	Human	Esophagus	ESCC	1.39e-02	1.40e-01	0.0845
79869	CPSF7	P1T-E	Human	Esophagus	ESCC	4.53e-06	2.71e-01	0.0875
79869	CPSF7	P2T-E	Human	Esophagus	ESCC	8.77e-32	5.29e-01	0.1177
79869	CPSF7	P4T-E	Human	Esophagus	ESCC	3.28e-22	5.80e-01	0.1323
79869	CPSF7	P5T-E	Human	Esophagus	ESCC	7.26e-22	2.51e-01	0.1327
79869	CPSF7	P8T-E	Human	Esophagus	ESCC	1.02e-29	6.12e-01	0.0889
79869	CPSF7	P9T-E	Human	Esophagus	ESCC	5.36e-09	2.74e-01	0.1131
79869	CPSF7	P10T-E	Human	Esophagus	ESCC	2.73e-25	4.52e-01	0.116
79869	CPSF7	P11T-E	Human	Esophagus	ESCC	4.60e-11	5.73e-01	0.1426
79869	CPSF7	P12T-E	Human	Esophagus	ESCC	6.71e-29	5.50e-01	0.1122
79869	CPSF7	P15T-E	Human	Esophagus	ESCC	6.17e-11	1.78e-01	0.1149
79869	CPSF7	P16T-E	Human	Esophagus	ESCC	2.54e-32	6.50e-01	0.1153
79869	CPSF7	P17T-E	Human	Esophagus	ESCC	1.17e-07	2.90e-01	0.1278
79869	CPSF7	P20T-E	Human	Esophagus	ESCC	8.92e-17	3.87e-01	0.1124
79869	CPSF7	P21T-E	Human	Esophagus	ESCC	7.33e-21	2.98e-01	0.1617

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
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

∗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:0022613111	Esophagus	ESCC	ribonucleoprotein complex biogenesis	365/8552	463/18723	1.74e-49	1.11e-45	365
GO:1903311110	Esophagus	ESCC	regulation of mRNA metabolic process	210/8552	288/18723	3.25e-21	5.56e-19	210
GO:0071826111	Esophagus	ESCC	ribonucleoprotein complex subunit organization	166/8552	227/18723	2.94e-17	2.42e-15	166
GO:0050684110	Esophagus	ESCC	regulation of mRNA processing	109/8552	137/18723	3.51e-16	2.59e-14	109
GO:0022618111	Esophagus	ESCC	ribonucleoprotein complex assembly	159/8552	220/18723	8.19e-16	5.71e-14	159
GO:00905013	Esophagus	ESCC	RNA phosphodiester bond hydrolysis	110/8552	152/18723	1.95e-11	6.81e-10	110
GO:00903053	Esophagus	ESCC	nucleic acid phosphodiester bond hydrolysis	163/8552	261/18723	3.07e-08	5.73e-07	163
GO:003112412	Esophagus	ESCC	mRNA 3'-end processing	47/8552	62/18723	1.29e-06	1.58e-05	47
GO:003144013	Esophagus	ESCC	regulation of mRNA 3'-end processing	25/8552	28/18723	1.77e-06	2.10e-05	25
GO:00311233	Esophagus	ESCC	RNA 3'-end processing	76/8552	116/18723	1.25e-05	1.15e-04	76
GO:00063783	Esophagus	ESCC	mRNA polyadenylation	33/8552	44/18723	7.30e-05	5.49e-04	33
GO:00436313	Esophagus	ESCC	RNA polyadenylation	33/8552	45/18723	1.54e-04	1.02e-03	33
GO:00512623	Esophagus	ESCC	protein tetramerization	54/8552	87/18723	1.50e-03	7.06e-03	54
GO:19003632	Esophagus	ESCC	regulation of mRNA polyadenylation	14/8552	17/18723	2.22e-03	9.78e-03	14
GO:00063793	Esophagus	ESCC	mRNA cleavage	17/8552	22/18723	2.60e-03	1.11e-02	17
GO:00512592	Esophagus	ESCC	protein complex oligomerization	130/8552	238/18723	3.29e-03	1.36e-02	130
GO:00987872	Esophagus	ESCC	mRNA cleavage involved in mRNA processing	11/8552	14/18723	1.30e-02	4.27e-02	11
GO:002261312	Liver	Cirrhotic	ribonucleoprotein complex biogenesis	231/4634	463/18723	3.28e-32	6.86e-29	231
GO:190331111	Liver	Cirrhotic	regulation of mRNA metabolic process	140/4634	288/18723	1.07e-18	1.91e-16	140
GO:005068411	Liver	Cirrhotic	regulation of mRNA processing	81/4634	137/18723	1.05e-17	1.60e-15	81

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa032509	Esophagus	ESCC	Viral life cycle - HIV-1	54/4205	63/8465	2.01e-09	2.17e-08	1.11e-08	54
hsa0301524	Esophagus	ESCC	mRNA surveillance pathway	72/4205	97/8465	6.12e-07	4.10e-06	2.10e-06	72
hsa0325014	Esophagus	ESCC	Viral life cycle - HIV-1	54/4205	63/8465	2.01e-09	2.17e-08	1.11e-08	54
hsa0301534	Esophagus	ESCC	mRNA surveillance pathway	72/4205	97/8465	6.12e-07	4.10e-06	2.10e-06	72
hsa030154	Liver	Cirrhotic	mRNA surveillance pathway	46/2530	97/8465	1.92e-04	1.30e-03	8.03e-04	46
hsa0301511	Liver	Cirrhotic	mRNA surveillance pathway	46/2530	97/8465	1.92e-04	1.30e-03	8.03e-04	46
hsa0301521	Liver	HCC	mRNA surveillance pathway	66/4020	97/8465	3.16e-05	1.88e-04	1.04e-04	66
hsa032502	Liver	HCC	Viral life cycle - HIV-1	46/4020	63/8465	3.25e-05	1.88e-04	1.04e-04	46
hsa0301531	Liver	HCC	mRNA surveillance pathway	66/4020	97/8465	3.16e-05	1.88e-04	1.04e-04	66
hsa0325011	Liver	HCC	Viral life cycle - HIV-1	46/4020	63/8465	3.25e-05	1.88e-04	1.04e-04	46
hsa030158	Oral cavity	OSCC	mRNA surveillance pathway	75/3704	97/8465	1.30e-11	2.01e-10	1.02e-10	75
hsa032508	Oral cavity	OSCC	Viral life cycle - HIV-1	45/3704	63/8465	7.62e-06	3.59e-05	1.83e-05	45
hsa0301513	Oral cavity	OSCC	mRNA surveillance pathway	75/3704	97/8465	1.30e-11	2.01e-10	1.02e-10	75
hsa0325013	Oral cavity	OSCC	Viral life cycle - HIV-1	45/3704	63/8465	7.62e-06	3.59e-05	1.83e-05	45
hsa0301523	Oral cavity	LP	mRNA surveillance pathway	50/2418	97/8465	1.39e-06	1.50e-05	9.66e-06	50
hsa0325022	Oral cavity	LP	Viral life cycle - HIV-1	32/2418	63/8465	1.55e-04	9.08e-04	5.86e-04	32
hsa0301533	Oral cavity	LP	mRNA surveillance pathway	50/2418	97/8465	1.39e-06	1.50e-05	9.66e-06	50
hsa0325031	Oral cavity	LP	Viral life cycle - HIV-1	32/2418	63/8465	1.55e-04	9.08e-04	5.86e-04	32
hsa0301541	Oral cavity	EOLP	mRNA surveillance pathway	30/1218	97/8465	2.26e-05	1.20e-04	7.07e-05	30
hsa0325041	Oral cavity	EOLP	Viral life cycle - HIV-1	16/1218	63/8465	1.46e-02	3.77e-02	2.22e-02	16

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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

CPSF7

SNV

Missense_Mutation

c.634N>A

p.Glu212Lys

p.E212K

Q8N684

protein_coding

deleterious(0)

benign(0.048)

TCGA-A2-A0YK-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

CPSF7

SNV

Missense_Mutation

c.1472N>G

p.His491Arg

p.H491R

Q8N684

protein_coding

deleterious(0.02)

probably_damaging(0.994)

TCGA-D8-A1XK-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicine+cyclophosphamide

CPSF7

insertion

Frame_Shift_Ins

novel

c.1260_1261insGAGAGTATGGTGTCTGCATTCAGGTACCAATTTGAATC

p.Ile421GlufsTer146

p.I421Efs*146

Q8N684

protein_coding

TCGA-A2-A04Y-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

CPSF7

SNV

Missense_Mutation

c.1528N>T

p.Arg510Trp

p.R510W

Q8N684

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.996)

TCGA-BI-A0VS-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

CPSF7

SNV

Missense_Mutation

c.1129N>A

p.Glu377Lys

p.E377K

Q8N684

protein_coding

deleterious(0.04)

probably_damaging(0.937)

TCGA-Q1-A73O-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

CPSF7

SNV

Missense_Mutation

novel

c.479N>C

p.Glu160Ala

p.E160A

Q8N684

protein_coding

deleterious(0.02)

benign(0.38)

TCGA-A6-2672-01

Colorectum

colon adenocarcinoma

Female

>=65

III/IV

Unknown

CPSF7

SNV

Missense_Mutation

c.1291C>T

p.Arg431Cys

p.R431C

Q8N684

protein_coding

deleterious(0)

benign(0.393)

TCGA-AA-3710-01

Colorectum

colon adenocarcinoma

Female

>=65

I/II

Unknown

CPSF7

SNV

Missense_Mutation

c.373G>A

p.Ala125Thr

p.A125T

Q8N684

protein_coding

tolerated(0.13)

possibly_damaging(0.475)

TCGA-CK-4951-01

Colorectum

colon adenocarcinoma

Female

>=65

I/II

Unknown

CPSF7

SNV

Missense_Mutation

c.1451T>C

p.Leu484Pro

p.L484P

Q8N684

protein_coding

deleterious_low_confidence(0.03)

probably_damaging(0.943)

TCGA-G4-6628-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

CPSF7

SNV

Missense_Mutation

c.343N>C

p.Tyr115His

p.Y115H

Q8N684

protein_coding

deleterious(0.04)

probably_damaging(0.961)

TCGA-NH-A5IV-01

Colorectum

colon adenocarcinoma

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

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