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: SCAF1

Gene summary for SCAF1

Gene summary.

Gene information	Species	Human
	Gene symbol	SCAF1
	Gene ID	58506
	Gene name	SR-related CTD associated factor 1
	Gene Alias	SRA1
	Cytomap	19q13.33
	Gene Type	protein-coding
	GO ID	GO:0006139
	UniProtAcc	Q9H7N4

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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
58506	SCAF1	LZE2T	Human	Esophagus	ESCC	2.21e-03	4.70e-01	0.082
58506	SCAF1	LZE4T	Human	Esophagus	ESCC	5.21e-07	1.87e-01	0.0811
58506	SCAF1	LZE5T	Human	Esophagus	ESCC	1.13e-03	2.63e-01	0.0514
58506	SCAF1	LZE7T	Human	Esophagus	ESCC	8.13e-05	2.90e-01	0.0667
58506	SCAF1	LZE8T	Human	Esophagus	ESCC	2.91e-03	1.22e-01	0.067
58506	SCAF1	LZE20T	Human	Esophagus	ESCC	6.52e-09	1.74e-01	0.0662
58506	SCAF1	LZE22D1	Human	Esophagus	HGIN	3.15e-04	1.75e-01	0.0595
58506	SCAF1	LZE22T	Human	Esophagus	ESCC	4.93e-03	3.18e-01	0.068
58506	SCAF1	LZE24T	Human	Esophagus	ESCC	1.78e-14	3.46e-01	0.0596
58506	SCAF1	LZE6T	Human	Esophagus	ESCC	2.31e-02	1.91e-01	0.0845
58506	SCAF1	P1T-E	Human	Esophagus	ESCC	1.20e-11	5.55e-01	0.0875
58506	SCAF1	P2T-E	Human	Esophagus	ESCC	2.06e-11	3.07e-01	0.1177
58506	SCAF1	P4T-E	Human	Esophagus	ESCC	1.70e-11	2.95e-01	0.1323
58506	SCAF1	P5T-E	Human	Esophagus	ESCC	5.14e-08	1.62e-01	0.1327
58506	SCAF1	P8T-E	Human	Esophagus	ESCC	9.06e-51	8.45e-01	0.0889
58506	SCAF1	P9T-E	Human	Esophagus	ESCC	1.26e-11	2.33e-01	0.1131
58506	SCAF1	P10T-E	Human	Esophagus	ESCC	7.48e-28	4.84e-01	0.116
58506	SCAF1	P11T-E	Human	Esophagus	ESCC	2.72e-11	4.08e-01	0.1426
58506	SCAF1	P12T-E	Human	Esophagus	ESCC	7.40e-18	3.82e-01	0.1122
58506	SCAF1	P15T-E	Human	Esophagus	ESCC	1.42e-22	4.59e-01	0.1149

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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
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:0008380	Colorectum	AD	RNA splicing	169/3918	434/18723	3.59e-18	2.04e-15	169
GO:0000377	Colorectum	AD	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	130/3918	320/18723	5.88e-16	2.16e-13	130
GO:0000398	Colorectum	AD	mRNA splicing, via spliceosome	130/3918	320/18723	5.88e-16	2.16e-13	130
GO:0000375	Colorectum	AD	RNA splicing, via transesterification reactions	131/3918	324/18723	7.11e-16	2.22e-13	131
GO:0022618	Colorectum	AD	ribonucleoprotein complex assembly	92/3918	220/18723	1.49e-12	2.60e-10	92
GO:0071826	Colorectum	AD	ribonucleoprotein complex subunit organization	94/3918	227/18723	1.70e-12	2.87e-10	94
GO:0022613	Colorectum	AD	ribonucleoprotein complex biogenesis	151/3918	463/18723	1.96e-09	1.39e-07	151
GO:0000245	Colorectum	AD	spliceosomal complex assembly	33/3918	79/18723	2.15e-05	4.33e-04	33
GO:00083802	Colorectum	MSS	RNA splicing	159/3467	434/18723	1.75e-19	1.22e-16	159
GO:00003772	Colorectum	MSS	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	121/3467	320/18723	2.52e-16	8.27e-14	121
GO:00003982	Colorectum	MSS	mRNA splicing, via spliceosome	121/3467	320/18723	2.52e-16	8.27e-14	121
GO:00003752	Colorectum	MSS	RNA splicing, via transesterification reactions	122/3467	324/18723	2.75e-16	8.58e-14	122
GO:00718262	Colorectum	MSS	ribonucleoprotein complex subunit organization	90/3467	227/18723	6.88e-14	1.78e-11	90
GO:00226182	Colorectum	MSS	ribonucleoprotein complex assembly	88/3467	220/18723	7.12e-14	1.78e-11	88
GO:00226132	Colorectum	MSS	ribonucleoprotein complex biogenesis	144/3467	463/18723	2.76e-11	3.67e-09	144
GO:00002451	Colorectum	MSS	spliceosomal complex assembly	31/3467	79/18723	1.33e-05	3.07e-04	31
GO:00226183	Colorectum	MSI-H	ribonucleoprotein complex assembly	62/1319	220/18723	7.13e-22	8.32e-19	62
GO:00718263	Colorectum	MSI-H	ribonucleoprotein complex subunit organization	63/1319	227/18723	8.08e-22	8.32e-19	63
GO:00226133	Colorectum	MSI-H	ribonucleoprotein complex biogenesis	95/1319	463/18723	1.04e-21	8.32e-19	95
GO:00083803	Colorectum	MSI-H	RNA splicing	82/1319	434/18723	1.22e-16	4.53e-14	82

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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

SCAF1

SNV

Missense_Mutation

c.2320N>T

p.Asp774Tyr

p.D774Y

Q9H7N4

protein_coding

deleterious_low_confidence(0)

possibly_damaging(0.663)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SCAF1

SNV

Missense_Mutation

rs751197713

c.2332N>T

p.Arg778Trp

p.R778W

Q9H7N4

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.965)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

SCAF1

SNV

Missense_Mutation

novel

c.1951N>A

p.Gly651Ser

p.G651S

Q9H7N4

protein_coding

tolerated_low_confidence(0.05)

benign(0.014)

TCGA-VS-A94Z-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

SCAF1

SNV

Missense_Mutation

novel

c.117C>G

p.Ile39Met

p.I39M

Q9H7N4

protein_coding

deleterious_low_confidence(0)

benign(0.235)

TCGA-VS-A958-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

SCAF1

SNV

Missense_Mutation

novel

c.895G>C

p.Glu299Gln

p.E299Q

Q9H7N4

protein_coding

deleterious_low_confidence(0)

benign(0.082)

TCGA-VS-A958-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

SCAF1

SNV

Missense_Mutation

rs772383494

c.2282C>G

p.Ser761Cys

p.S761C

Q9H7N4

protein_coding

deleterious_low_confidence(0.01)

probably_damaging(0.987)

TCGA-ZJ-AAXT-01

Cervix

cervical & endocervical cancer

Female

<65

III/IV

Unknown

SCAF1

SNV

Missense_Mutation

c.349C>A

p.Leu117Met

p.L117M

Q9H7N4

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.996)

TCGA-AA-A01P-01

Colorectum

colon adenocarcinoma

Female

>=65

III/IV

Unknown

SCAF1

SNV

Missense_Mutation

c.3802C>T

p.Arg1268Trp

p.R1268W

Q9H7N4

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.978)

TCGA-AD-6895-01

Colorectum

colon adenocarcinoma

Male

>=65

III/IV

Unknown

SCAF1

SNV

Missense_Mutation

c.3479N>T

p.Gly1160Val

p.G1160V

Q9H7N4

protein_coding

deleterious_low_confidence(0.03)

benign(0.187)

TCGA-AZ-6598-01

Colorectum

colon adenocarcinoma

Female

>=65

I/II

Unknown

SCAF1

SNV

Missense_Mutation

c.89N>A

p.Ser30Tyr

p.S30Y

Q9H7N4

protein_coding

deleterious_low_confidence(0)

possibly_damaging(0.663)

TCGA-CK-4951-01

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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