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: SCOC

Gene summary for SCOC

Gene summary.

Gene information	Species	Human
	Gene symbol	SCOC
	Gene ID	60592
	Gene name	short coiled-coil protein
	Gene Alias	HRIHFB2072
	Cytomap	4q31.1
	Gene Type	protein-coding
	GO ID	GO:0006914
	UniProtAcc	Q9UIL1

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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
60592	SCOC	GSM4909281	Human	Breast	IDC	8.87e-03	3.13e-01	0.21
60592	SCOC	GSM4909288	Human	Breast	IDC	1.56e-03	3.03e-01	0.0988
60592	SCOC	GSM4909294	Human	Breast	IDC	3.21e-08	4.32e-01	0.2022
60592	SCOC	GSM4909296	Human	Breast	IDC	2.91e-08	-2.67e-01	0.1524
60592	SCOC	GSM4909297	Human	Breast	IDC	1.54e-06	7.97e-02	0.1517
60592	SCOC	GSM4909301	Human	Breast	IDC	3.62e-07	-2.66e-01	0.1577
60592	SCOC	GSM4909307	Human	Breast	IDC	6.57e-03	-2.06e-01	0.1569
60592	SCOC	GSM4909309	Human	Breast	IDC	8.50e-04	-2.33e-01	0.0483
60592	SCOC	GSM4909311	Human	Breast	IDC	6.05e-19	-2.71e-01	0.1534
60592	SCOC	GSM4909312	Human	Breast	IDC	7.79e-05	2.47e-02	0.1552
60592	SCOC	GSM4909315	Human	Breast	IDC	2.91e-47	9.09e-01	0.21
60592	SCOC	GSM4909316	Human	Breast	IDC	6.83e-25	8.49e-01	0.21
60592	SCOC	GSM4909319	Human	Breast	IDC	6.93e-25	-2.42e-01	0.1563
60592	SCOC	GSM4909320	Human	Breast	IDC	8.03e-06	-3.67e-01	0.1575
60592	SCOC	GSM4909321	Human	Breast	IDC	1.12e-07	-1.17e-01	0.1559
60592	SCOC	brca2	Human	Breast	Precancer	5.70e-03	1.03e-01	-0.024
60592	SCOC	brca10	Human	Breast	Precancer	6.30e-04	-2.84e-01	-0.0029
60592	SCOC	NCCBC14	Human	Breast	DCIS	2.95e-08	1.59e-01	0.2021
60592	SCOC	NCCBC2	Human	Breast	DCIS	2.30e-04	1.84e-01	0.1554
60592	SCOC	NCCBC5	Human	Breast	DCIS	5.60e-10	-1.55e-01	0.2046

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Breast		IDC: Invasive ductal carcinoma
		DCIS: Ductal carcinoma in situ
		Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers
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:00098969	Breast	Precancer	positive regulation of catabolic process	48/1080	492/18723	2.62e-04	3.84e-03	48
GO:00313319	Breast	Precancer	positive regulation of cellular catabolic process	43/1080	427/18723	2.75e-04	4.00e-03	43
GO:000989614	Breast	IDC	positive regulation of catabolic process	62/1434	492/18723	7.06e-05	1.42e-03	62
GO:003133114	Breast	IDC	positive regulation of cellular catabolic process	54/1434	427/18723	1.85e-04	3.07e-03	54
GO:000989624	Breast	DCIS	positive regulation of catabolic process	61/1390	492/18723	5.32e-05	1.09e-03	61
GO:003133124	Breast	DCIS	positive regulation of cellular catabolic process	54/1390	427/18723	8.34e-05	1.58e-03	54
GO:000989626	Esophagus	HGIN	positive regulation of catabolic process	126/2587	492/18723	1.46e-12	2.09e-10	126
GO:003133126	Esophagus	HGIN	positive regulation of cellular catabolic process	112/2587	427/18723	5.15e-12	6.72e-10	112
GO:001050616	Esophagus	HGIN	regulation of autophagy	84/2587	317/18723	1.39e-09	1.08e-07	84
GO:001623616	Esophagus	HGIN	macroautophagy	77/2587	291/18723	7.15e-09	4.61e-07	77
GO:00162418	Esophagus	HGIN	regulation of macroautophagy	38/2587	141/18723	2.80e-05	7.21e-04	38
GO:00105088	Esophagus	HGIN	positive regulation of autophagy	28/2587	124/18723	5.34e-03	4.39e-02	28
GO:001623617	Esophagus	ESCC	macroautophagy	216/8552	291/18723	1.94e-23	4.57e-21	216
GO:0009896111	Esophagus	ESCC	positive regulation of catabolic process	332/8552	492/18723	4.36e-23	9.22e-21	332
GO:0031331111	Esophagus	ESCC	positive regulation of cellular catabolic process	292/8552	427/18723	8.67e-22	1.53e-19	292
GO:001050617	Esophagus	ESCC	regulation of autophagy	220/8552	317/18723	6.72e-18	6.36e-16	220
GO:001624114	Esophagus	ESCC	regulation of macroautophagy	102/8552	141/18723	1.09e-10	3.27e-09	102
GO:001050816	Esophagus	ESCC	positive regulation of autophagy	81/8552	124/18723	7.74e-06	7.65e-05	81
GO:00162394	Esophagus	ESCC	positive regulation of macroautophagy	41/8552	63/18723	1.48e-03	6.99e-03	41
GO:000989612	Liver	Cirrhotic	positive regulation of catabolic process	215/4634	492/18723	1.13e-20	3.56e-18	215

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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

SCOC

SNV

Missense_Mutation

c.389N>T

p.Ser130Leu

p.S130L

Q9UIL1

protein_coding

deleterious(0)

probably_damaging(0.998)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SCOC

SNV

Missense_Mutation

c.194N>T

p.Arg65Ile

p.R65I

Q9UIL1

protein_coding

deleterious(0.01)

benign(0.307)

TCGA-AZ-4315-01

Colorectum

colon adenocarcinoma

Male

<65

I/II

Unknown

SCOC

SNV

Missense_Mutation

c.145G>A

p.Ala49Thr

p.A49T

Q9UIL1

protein_coding

tolerated_low_confidence(0.42)

benign(0.011)

TCGA-F4-6570-01

Colorectum

colon adenocarcinoma

Female

>=65

I/II

Unknown

SCOC

SNV

Missense_Mutation

c.194N>T

p.Arg65Ile

p.R65I

Q9UIL1

protein_coding

deleterious(0.01)

benign(0.307)

TCGA-B5-A0JY-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

doxorubicin

SCOC

SNV

Missense_Mutation

novel

c.424C>A

p.Leu142Ile

p.L142I

Q9UIL1

protein_coding

deleterious(0.01)

probably_damaging(0.998)

TCGA-B5-A1MR-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

III/IV

Unknown

SCOC

SNV

Missense_Mutation

c.194G>T

p.Arg65Ile

p.R65I

Q9UIL1

protein_coding

deleterious(0.01)

benign(0.307)

TCGA-E6-A1LX-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

SCOC

SNV

Missense_Mutation

novel

c.467N>A

p.Ser156Asn

p.S156N

Q9UIL1

protein_coding

deleterious_low_confidence(0.03)

probably_damaging(0.966)

TCGA-FI-A2D5-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

carboplatinum

SCOC

SNV

Missense_Mutation

novel

c.101N>A

p.Ser34Asn

p.S34N

Q9UIL1

protein_coding

tolerated_low_confidence(0.15)

benign(0.027)

TCGA-SJ-A6ZI-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

SCOC

SNV

Missense_Mutation

novel

c.89N>A

p.Arg30Gln

p.R30Q

Q9UIL1

protein_coding

tolerated_low_confidence(0.11)

benign(0.003)

TCGA-DD-AACT-01

Liver

liver hepatocellular carcinoma

Female

>=65

I/II

Unknown

SCOC

deletion

Frame_Shift_Del

novel

c.45_54delCTGGGACGGG

p.Gly18SerfsTer58

p.G18Sfs*58

Q9UIL1

protein_coding

TCGA-WJ-A86L-01

Liver

liver hepatocellular carcinoma

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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