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: SCAF11

Gene summary for SCAF11

Gene summary.

Gene information	Species	Human
	Gene symbol	SCAF11
	Gene ID	9169
	Gene name	SR-related CTD associated factor 11
	Gene Alias	CASP11
	Cytomap	12q12
	Gene Type	protein-coding
	GO ID	GO:0000245
	UniProtAcc	Q99590

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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
9169	SCAF11	C30	Human	Oral cavity	OSCC	6.12e-29	1.34e+00	0.3055
9169	SCAF11	C38	Human	Oral cavity	OSCC	2.78e-15	1.71e+00	0.172
9169	SCAF11	C43	Human	Oral cavity	OSCC	2.69e-28	6.78e-01	0.1704
9169	SCAF11	C46	Human	Oral cavity	OSCC	3.44e-22	7.58e-01	0.1673
9169	SCAF11	C51	Human	Oral cavity	OSCC	2.06e-10	8.60e-01	0.2674
9169	SCAF11	C57	Human	Oral cavity	OSCC	4.94e-15	5.93e-01	0.1679
9169	SCAF11	C06	Human	Oral cavity	OSCC	2.33e-07	1.32e+00	0.2699
9169	SCAF11	C08	Human	Oral cavity	OSCC	2.18e-29	7.42e-01	0.1919
9169	SCAF11	C09	Human	Oral cavity	OSCC	1.32e-13	6.77e-01	0.1431
9169	SCAF11	LN22	Human	Oral cavity	OSCC	3.92e-14	1.46e+00	0.1733
9169	SCAF11	LN46	Human	Oral cavity	OSCC	1.52e-12	8.31e-01	0.1666
9169	SCAF11	LP15	Human	Oral cavity	LP	8.09e-07	1.20e+00	0.2174
9169	SCAF11	LP17	Human	Oral cavity	LP	3.23e-02	7.30e-01	0.2349
9169	SCAF11	EOLP-1	Human	Oral cavity	EOLP	6.31e-16	4.29e-01	-0.0202
9169	SCAF11	NEOLP-2	Human	Oral cavity	NEOLP	1.23e-06	3.08e-01	-0.0196
9169	SCAF11	NEOLP-3	Human	Oral cavity	NEOLP	2.39e-07	3.27e-01	-0.0191
9169	SCAF11	SYSMH1	Human	Oral cavity	OSCC	1.12e-24	7.98e-01	0.1127
9169	SCAF11	SYSMH2	Human	Oral cavity	OSCC	3.83e-32	1.12e+00	0.2326
9169	SCAF11	SYSMH3	Human	Oral cavity	OSCC	4.17e-51	1.28e+00	0.2442
9169	SCAF11	SYSMH5	Human	Oral cavity	OSCC	1.18e-16	5.15e-01	0.0647

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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
Endometrium		AEH: Atypical endometrial hyperplasia
		EEC: Endometrioid 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
Lung		AAH: Atypical adenomatous hyperplasia
		AIS: Adenocarcinoma in situ
		IAC: Invasive lung adenocarcinoma
		MIA: Minimally invasive adenocarcinoma
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: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

SCAF11

SNV

Missense_Mutation

c.3194N>T

p.Ser1065Phe

p.S1065F

Q99590

protein_coding

deleterious(0)

possibly_damaging(0.786)

TCGA-A8-A0A7-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

SCAF11

SNV

Missense_Mutation

novel

c.646N>C

p.Glu216Gln

p.E216Q

Q99590

protein_coding

deleterious(0)

possibly_damaging(0.805)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SCAF11

SNV

Missense_Mutation

c.2243C>T

p.Ser748Phe

p.S748F

Q99590

protein_coding

tolerated(0.08)

benign(0.007)

TCGA-BH-A18P-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

SCAF11

SNV

Missense_Mutation

rs372602350

c.4102N>A

p.Ala1368Thr

p.A1368T

Q99590

protein_coding

deleterious(0.01)

probably_damaging(0.999)

TCGA-BH-A42T-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SCAF11

SNV

Missense_Mutation

c.2708N>T

p.Pro903Leu

p.P903L

Q99590

protein_coding

deleterious(0)

possibly_damaging(0.726)

TCGA-C8-A1HM-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

doxorubicin

SCAF11

SNV

Missense_Mutation

c.2720N>T

p.Ser907Phe

p.S907F

Q99590

protein_coding

deleterious(0)

probably_damaging(0.972)

TCGA-E9-A243-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

5-fluorouracil

SCAF11

SNV

Missense_Mutation

rs533218274

c.3923N>G

p.Ser1308Cys

p.S1308C

Q99590

protein_coding

deleterious(0.03)

benign(0.014)

TCGA-EW-A6SA-01

Breast

breast invasive carcinoma

Male

<65

I/II

Unknown

SCAF11

SNV

Missense_Mutation

novel

c.493N>G

p.Lys165Glu

p.K165E

Q99590

protein_coding

tolerated(0.06)

possibly_damaging(0.473)

TCGA-EW-A6SB-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

SCAF11

insertion

Frame_Shift_Ins

novel

c.2_3insTAATCATGTCC

p.Met1?

p.M1?

Q99590

protein_coding

TCGA-A2-A0CP-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

SCAF11

insertion

Frame_Shift_Ins

novel

c.2967dupA

p.Glu990ArgfsTer5

p.E990Rfs*5

Q99590

protein_coding

TCGA-EW-A1IZ-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

taxotere

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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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