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: COX4I1

Gene summary for COX4I1

Gene summary.

Gene information	Species	Human
	Gene symbol	COX4I1
	Gene ID	1327
	Gene name	cytochrome c oxidase subunit 4I1
	Gene Alias	COX IV-1
	Cytomap	16q24.1
	Gene Type	protein-coding
	GO ID	GO:0006091
	UniProtAcc	P13073

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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
1327	COX4I1	GSM4909280	Human	Breast	Precancer	9.85e-05	-6.43e-01	0.0305
1327	COX4I1	GSM4909286	Human	Breast	IDC	1.92e-52	-3.89e-01	0.1081
1327	COX4I1	GSM4909287	Human	Breast	IDC	3.37e-22	-5.05e-01	0.2057
1327	COX4I1	GSM4909290	Human	Breast	IDC	4.37e-10	-2.99e-01	0.2096
1327	COX4I1	GSM4909291	Human	Breast	IDC	2.45e-03	1.80e-01	0.1753
1327	COX4I1	GSM4909293	Human	Breast	IDC	4.43e-37	-3.85e-01	0.1581
1327	COX4I1	GSM4909294	Human	Breast	IDC	1.95e-04	-1.29e-01	0.2022
1327	COX4I1	GSM4909296	Human	Breast	IDC	1.09e-04	-4.90e-02	0.1524
1327	COX4I1	GSM4909297	Human	Breast	IDC	4.69e-33	-7.51e-01	0.1517
1327	COX4I1	GSM4909298	Human	Breast	IDC	1.63e-34	-3.15e-01	0.1551
1327	COX4I1	GSM4909302	Human	Breast	IDC	2.27e-20	-5.23e-01	0.1545
1327	COX4I1	GSM4909303	Human	Breast	IDC	3.74e-04	-3.53e-01	0.0438
1327	COX4I1	GSM4909304	Human	Breast	IDC	1.43e-06	-1.22e-01	0.1636
1327	COX4I1	GSM4909306	Human	Breast	IDC	6.81e-12	-2.06e-01	0.1564
1327	COX4I1	GSM4909308	Human	Breast	IDC	1.57e-13	-1.28e-01	0.158
1327	COX4I1	GSM4909311	Human	Breast	IDC	1.63e-51	-6.85e-01	0.1534
1327	COX4I1	GSM4909312	Human	Breast	IDC	3.05e-37	-6.75e-01	0.1552
1327	COX4I1	GSM4909316	Human	Breast	IDC	3.60e-04	1.32e-01	0.21
1327	COX4I1	GSM4909317	Human	Breast	IDC	7.00e-03	-1.17e-01	0.1355
1327	COX4I1	GSM4909319	Human	Breast	IDC	6.74e-73	-8.45e-01	0.1563

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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
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
Endometrium		AEH: Atypical endometrial hyperplasia
		EEC: Endometrioid Cancer
Esophagus		ESCC: Esophageal squamous cell carcinoma
		HGIN: High-grade intraepithelial neoplasias
		LGIN: Low-grade intraepithelial neoplasias
GC		CAG: Chronic atrophic gastritis
		CAG with IM: Chronic atrophic gastritis with intestinal metaplasia
		CSG: Chronic superficial gastritis
		GC: Gastric cancer
		SIM: Severe intestinal metaplasia
		WIM: Wild intestinal metaplasia
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:004603422	Liver	HCC	ATP metabolic process	198/7958	277/18723	8.30e-23	1.55e-20	198
GO:001598022	Liver	HCC	energy derivation by oxidation of organic compounds	221/7958	318/18723	1.02e-22	1.86e-20	221
GO:002290022	Liver	HCC	electron transport chain	134/7958	175/18723	3.32e-20	4.68e-18	134
GO:000611912	Liver	HCC	oxidative phosphorylation	110/7958	141/18723	6.58e-18	7.45e-16	110
GO:002290412	Liver	HCC	respiratory electron transport chain	89/7958	114/18723	8.68e-15	5.73e-13	89
GO:004277312	Liver	HCC	ATP synthesis coupled electron transport	74/7958	95/18723	1.94e-12	9.18e-11	74
GO:004277512	Liver	HCC	mitochondrial ATP synthesis coupled electron transport	74/7958	95/18723	1.94e-12	9.18e-11	74
GO:003166722	Liver	HCC	response to nutrient levels	276/7958	474/18723	2.30e-12	1.08e-10	276
GO:001964612	Liver	HCC	aerobic electron transport chain	67/7958	87/18723	5.43e-11	2.00e-09	67
GO:000758421	Liver	HCC	response to nutrient	111/7958	174/18723	1.10e-08	2.73e-07	111
GO:19026007	Liver	HCC	proton transmembrane transport	87/7958	157/18723	7.27e-04	4.42e-03	87
GO:002290018	Oral cavity	OSCC	electron transport chain	126/7305	175/18723	6.65e-19	8.42e-17	126
GO:000609118	Oral cavity	OSCC	generation of precursor metabolites and energy	286/7305	490/18723	1.45e-18	1.71e-16	286
GO:000906018	Oral cavity	OSCC	aerobic respiration	133/7305	189/18723	1.79e-18	2.02e-16	133
GO:004533318	Oral cavity	OSCC	cellular respiration	153/7305	230/18723	2.07e-17	1.87e-15	153
GO:004277318	Oral cavity	OSCC	ATP synthesis coupled electron transport	75/7305	95/18723	1.95e-15	1.33e-13	75
GO:004277518	Oral cavity	OSCC	mitochondrial ATP synthesis coupled electron transport	75/7305	95/18723	1.95e-15	1.33e-13	75
GO:002290418	Oral cavity	OSCC	respiratory electron transport chain	86/7305	114/18723	2.43e-15	1.63e-13	86
GO:001598018	Oral cavity	OSCC	energy derivation by oxidation of organic compounds	190/7305	318/18723	4.10e-14	2.26e-12	190
GO:001964618	Oral cavity	OSCC	aerobic electron transport chain	68/7305	87/18723	9.88e-14	5.17e-12	68

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0501218	Breast	Precancer	Parkinson disease	99/684	266/8465	3.58e-42	5.65e-40	4.33e-40	99
hsa0502016	Breast	Precancer	Prion disease	95/684	273/8465	1.39e-37	1.46e-35	1.12e-35	95
hsa0501616	Breast	Precancer	Huntington disease	98/684	306/8465	2.85e-35	2.25e-33	1.72e-33	98
hsa0019016	Breast	Precancer	Oxidative phosphorylation	59/684	134/8465	6.15e-30	3.24e-28	2.48e-28	59
hsa0501016	Breast	Precancer	Alzheimer disease	103/684	384/8465	1.03e-29	4.66e-28	3.57e-28	103
hsa0501416	Breast	Precancer	Amyotrophic lateral sclerosis	98/684	364/8465	2.13e-28	8.41e-27	6.44e-27	98
hsa0502216	Breast	Precancer	Pathways of neurodegeneration - multiple diseases	112/684	476/8465	6.96e-27	2.44e-25	1.87e-25	112
hsa0520818	Breast	Precancer	Chemical carcinogenesis - reactive oxygen species	68/684	223/8465	3.61e-23	1.14e-21	8.73e-22	68
hsa0493216	Breast	Precancer	Non-alcoholic fatty liver disease	48/684	155/8465	6.16e-17	1.50e-15	1.15e-15	48
hsa0426016	Breast	Precancer	Cardiac muscle contraction	22/684	87/8465	9.72e-07	1.62e-05	1.24e-05	22
hsa0501219	Breast	Precancer	Parkinson disease	99/684	266/8465	3.58e-42	5.65e-40	4.33e-40	99
hsa0502017	Breast	Precancer	Prion disease	95/684	273/8465	1.39e-37	1.46e-35	1.12e-35	95
hsa0501617	Breast	Precancer	Huntington disease	98/684	306/8465	2.85e-35	2.25e-33	1.72e-33	98
hsa0019017	Breast	Precancer	Oxidative phosphorylation	59/684	134/8465	6.15e-30	3.24e-28	2.48e-28	59
hsa0501017	Breast	Precancer	Alzheimer disease	103/684	384/8465	1.03e-29	4.66e-28	3.57e-28	103
hsa0501417	Breast	Precancer	Amyotrophic lateral sclerosis	98/684	364/8465	2.13e-28	8.41e-27	6.44e-27	98
hsa0502217	Breast	Precancer	Pathways of neurodegeneration - multiple diseases	112/684	476/8465	6.96e-27	2.44e-25	1.87e-25	112
hsa0520819	Breast	Precancer	Chemical carcinogenesis - reactive oxygen species	68/684	223/8465	3.61e-23	1.14e-21	8.73e-22	68
hsa0493217	Breast	Precancer	Non-alcoholic fatty liver disease	48/684	155/8465	6.16e-17	1.50e-15	1.15e-15	48
hsa0426017	Breast	Precancer	Cardiac muscle contraction	22/684	87/8465	9.72e-07	1.62e-05	1.24e-05	22

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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

COX4I1

insertion

Frame_Shift_Ins

novel

c.252dupT

p.Lys85Ter

p.K85*

P13073

protein_coding

TCGA-A2-A04Q-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

COX4I1

insertion

Nonsense_Mutation

novel

c.421_422insTGGACTTCCTAGCCTGAGCTGGGTTTTCATCTCATTTCT

p.Gln141delinsLeuAspPheLeuAlaTerAlaGlyPheSerSerHisPheTer

p.Q141delinsLDFLA*AGFSSHF*

P13073

protein_coding

TCGA-A2-A04Y-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

COX4I1

SNV

Missense_Mutation

rs374125919

c.248G>A

p.Arg83His

p.R83H

P13073

protein_coding

tolerated(0.25)

benign(0.011)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

COX4I1

SNV

Missense_Mutation

c.53N>G

p.Ser18Cys

p.S18C

P13073

protein_coding

deleterious(0.03)

probably_damaging(0.997)

TCGA-JW-A5VL-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

COX4I1

SNV

Missense_Mutation

rs772180664

c.343N>A

p.Ala115Thr

p.A115T

P13073

protein_coding

tolerated(0.06)

benign(0.132)

TCGA-AA-3664-01

Colorectum

colon adenocarcinoma

Female

>=65

I/II

Unknown

COX4I1

SNV

Missense_Mutation

rs201058411

c.101C>T

p.Ser34Leu

p.S34L

P13073

protein_coding

deleterious(0.01)

benign(0.029)

TCGA-CK-6746-01

Colorectum

colon adenocarcinoma

Female

>=65

I/II

Unknown

COX4I1

SNV

Missense_Mutation

novel

c.371N>G

p.Tyr124Cys

p.Y124C

P13073

protein_coding

tolerated(0.06)

probably_damaging(0.929)

TCGA-A5-A0G2-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Unknown

COX4I1

SNV

Missense_Mutation

c.340N>G

p.Thr114Ala

p.T114A

P13073

protein_coding

tolerated(0.09)

benign(0.017)

TCGA-AP-A056-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

COX4I1

SNV

Missense_Mutation

c.258N>A

p.Phe86Leu

p.F86L

P13073

protein_coding

deleterious(0.01)

possibly_damaging(0.691)

TCGA-D1-A16F-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

COX4I1

SNV

Missense_Mutation

rs761492668

c.238G>A

p.Glu80Lys

p.E80K

P13073

protein_coding

tolerated(0.07)

benign(0.199)

TCGA-EY-A215-01

Endometrium

uterine corpus endometrioid 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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