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: TOMM40

Gene summary for TOMM40

Gene summary.

Gene information	Species	Human
	Gene symbol	TOMM40
	Gene ID	10452
	Gene name	translocase of outer mitochondrial membrane 40
	Gene Alias	C19orf1
	Cytomap	19q13.32
	Gene Type	protein-coding
	GO ID	GO:0006605
	UniProtAcc	O96008

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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
10452	TOMM40	HTA11_1938_2000001011	Human	Colorectum	AD	9.99e-09	4.46e-01	-0.0811
10452	TOMM40	HTA11_78_2000001011	Human	Colorectum	AD	1.30e-02	1.67e-01	-0.1088
10452	TOMM40	HTA11_347_2000001011	Human	Colorectum	AD	3.06e-07	2.90e-01	-0.1954
10452	TOMM40	HTA11_3361_2000001011	Human	Colorectum	AD	2.84e-02	3.29e-01	-0.1207
10452	TOMM40	HTA11_83_2000001011	Human	Colorectum	SER	8.45e-03	3.25e-01	-0.1526
10452	TOMM40	HTA11_696_2000001011	Human	Colorectum	AD	5.93e-04	2.47e-01	-0.1464
10452	TOMM40	HTA11_866_2000001011	Human	Colorectum	AD	3.47e-05	2.27e-01	-0.1001
10452	TOMM40	HTA11_1391_2000001011	Human	Colorectum	AD	4.90e-12	5.49e-01	-0.059
10452	TOMM40	HTA11_2992_2000001011	Human	Colorectum	SER	2.58e-04	4.09e-01	-0.1706
10452	TOMM40	HTA11_7862_2000001011	Human	Colorectum	AD	3.91e-02	2.38e-01	-0.0179
10452	TOMM40	HTA11_866_3004761011	Human	Colorectum	AD	3.20e-06	2.98e-01	0.096
10452	TOMM40	HTA11_8622_2000001021	Human	Colorectum	SER	2.60e-03	3.22e-01	0.0528
10452	TOMM40	HTA11_10623_2000001011	Human	Colorectum	AD	5.82e-05	3.36e-01	-0.0177
10452	TOMM40	HTA11_6801_2000001011	Human	Colorectum	SER	2.17e-02	4.80e-01	0.0171
10452	TOMM40	HTA11_7696_3000711011	Human	Colorectum	AD	1.08e-15	4.79e-01	0.0674
10452	TOMM40	HTA11_6818_2000001021	Human	Colorectum	AD	6.21e-04	3.32e-01	0.0588
10452	TOMM40	HTA11_99999970781_79442	Human	Colorectum	MSS	1.38e-20	4.89e-01	0.294
10452	TOMM40	HTA11_99999965104_69814	Human	Colorectum	MSS	3.38e-07	4.02e-01	0.281
10452	TOMM40	HTA11_99999971662_82457	Human	Colorectum	MSS	1.15e-19	6.19e-01	0.3859
10452	TOMM40	HTA11_99999974143_84620	Human	Colorectum	MSS	4.13e-09	3.55e-01	0.3005

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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
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
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:0006839	Colorectum	AD	mitochondrial transport	102/3918	254/18723	1.87e-12	3.08e-10	102
GO:0072594	Colorectum	AD	establishment of protein localization to organelle	148/3918	422/18723	7.95e-12	1.04e-09	148
GO:1990542	Colorectum	AD	mitochondrial transmembrane transport	47/3918	102/18723	1.09e-08	6.52e-07	47
GO:0006605	Colorectum	AD	protein targeting	105/3918	314/18723	1.39e-07	6.44e-06	105
GO:0070585	Colorectum	AD	protein localization to mitochondrion	51/3918	125/18723	3.40e-07	1.33e-05	51
GO:0072655	Colorectum	AD	establishment of protein localization to mitochondrion	47/3918	120/18723	3.76e-06	1.04e-04	47
GO:0017038	Colorectum	AD	protein import	67/3918	206/18723	6.34e-05	1.05e-03	67
GO:0006626	Colorectum	AD	protein targeting to mitochondrion	37/3918	100/18723	1.58e-04	2.20e-03	37
GO:0071806	Colorectum	AD	protein transmembrane transport	21/3918	59/18723	6.58e-03	4.08e-02	21
GO:00068391	Colorectum	SER	mitochondrial transport	87/2897	254/18723	7.91e-14	3.03e-11	87
GO:19905421	Colorectum	SER	mitochondrial transmembrane transport	42/2897	102/18723	3.65e-10	4.77e-08	42
GO:00725941	Colorectum	SER	establishment of protein localization to organelle	111/2897	422/18723	4.98e-09	4.49e-07	111
GO:00705851	Colorectum	SER	protein localization to mitochondrion	42/2897	125/18723	3.75e-07	1.98e-05	42
GO:00726551	Colorectum	SER	establishment of protein localization to mitochondrion	38/2897	120/18723	6.60e-06	2.33e-04	38
GO:00066051	Colorectum	SER	protein targeting	76/2897	314/18723	3.19e-05	8.47e-04	76
GO:00066261	Colorectum	SER	protein targeting to mitochondrion	31/2897	100/18723	7.09e-05	1.61e-03	31
GO:00170381	Colorectum	SER	protein import	49/2897	206/18723	1.12e-03	1.29e-02	49
GO:00718061	Colorectum	SER	protein transmembrane transport	17/2897	59/18723	6.64e-03	4.69e-02	17
GO:00725942	Colorectum	MSS	establishment of protein localization to organelle	139/3467	422/18723	5.75e-13	1.12e-10	139
GO:00068392	Colorectum	MSS	mitochondrial transport	93/3467	254/18723	6.14e-12	9.82e-10	93

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa05014	Colorectum	AD	Amyotrophic lateral sclerosis	164/2092	364/8465	4.28e-18	1.27e-16	8.09e-17	164
hsa05022	Colorectum	AD	Pathways of neurodegeneration - multiple diseases	201/2092	476/8465	4.54e-18	1.27e-16	8.09e-17	201
hsa050141	Colorectum	AD	Amyotrophic lateral sclerosis	164/2092	364/8465	4.28e-18	1.27e-16	8.09e-17	164
hsa050221	Colorectum	AD	Pathways of neurodegeneration - multiple diseases	201/2092	476/8465	4.54e-18	1.27e-16	8.09e-17	201
hsa050222	Colorectum	SER	Pathways of neurodegeneration - multiple diseases	168/1580	476/8465	6.23e-19	2.07e-17	1.50e-17	168
hsa050142	Colorectum	SER	Amyotrophic lateral sclerosis	138/1580	364/8465	9.89e-19	2.99e-17	2.17e-17	138
hsa050223	Colorectum	SER	Pathways of neurodegeneration - multiple diseases	168/1580	476/8465	6.23e-19	2.07e-17	1.50e-17	168
hsa050143	Colorectum	SER	Amyotrophic lateral sclerosis	138/1580	364/8465	9.89e-19	2.99e-17	2.17e-17	138
hsa050224	Colorectum	MSS	Pathways of neurodegeneration - multiple diseases	192/1875	476/8465	2.79e-20	1.04e-18	6.36e-19	192
hsa050144	Colorectum	MSS	Amyotrophic lateral sclerosis	156/1875	364/8465	1.43e-19	4.62e-18	2.83e-18	156
hsa050225	Colorectum	MSS	Pathways of neurodegeneration - multiple diseases	192/1875	476/8465	2.79e-20	1.04e-18	6.36e-19	192
hsa050145	Colorectum	MSS	Amyotrophic lateral sclerosis	156/1875	364/8465	1.43e-19	4.62e-18	2.83e-18	156
hsa05014210	Esophagus	ESCC	Amyotrophic lateral sclerosis	266/4205	364/8465	1.31e-20	2.20e-18	1.13e-18	266
hsa05022210	Esophagus	ESCC	Pathways of neurodegeneration - multiple diseases	318/4205	476/8465	6.10e-15	2.04e-13	1.05e-13	318
hsa0501438	Esophagus	ESCC	Amyotrophic lateral sclerosis	266/4205	364/8465	1.31e-20	2.20e-18	1.13e-18	266
hsa0502238	Esophagus	ESCC	Pathways of neurodegeneration - multiple diseases	318/4205	476/8465	6.10e-15	2.04e-13	1.05e-13	318
hsa0501414	Liver	Cirrhotic	Amyotrophic lateral sclerosis	187/2530	364/8465	1.56e-18	6.50e-17	4.01e-17	187
hsa0502214	Liver	Cirrhotic	Pathways of neurodegeneration - multiple diseases	217/2530	476/8465	7.30e-14	2.03e-12	1.25e-12	217
hsa0501415	Liver	Cirrhotic	Amyotrophic lateral sclerosis	187/2530	364/8465	1.56e-18	6.50e-17	4.01e-17	187
hsa0502215	Liver	Cirrhotic	Pathways of neurodegeneration - multiple diseases	217/2530	476/8465	7.30e-14	2.03e-12	1.25e-12	217

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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

TOMM40

SNV

Missense_Mutation

novel

c.919N>A

p.Leu307Met

p.L307M

O96008

protein_coding

deleterious(0)

possibly_damaging(0.842)

TCGA-AR-A24K-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unspecific

Paclitaxel

TOMM40

SNV

Missense_Mutation

c.788N>C

p.Val263Ala

p.V263A

O96008

protein_coding

tolerated(1)

benign(0.007)

TCGA-D8-A1XK-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicine+cyclophosphamide

TOMM40

SNV

Missense_Mutation

c.295N>C

p.Glu99Gln

p.E99Q

O96008

protein_coding

deleterious(0)

probably_damaging(0.94)

TCGA-EK-A2PM-01

Cervix

cervical & endocervical cancer

Female

>=65

I/II

Unknown

TOMM40

SNV

Missense_Mutation

novel

c.745T>G

p.Ser249Ala

p.S249A

O96008

protein_coding

deleterious(0)

benign(0.264)

TCGA-AG-A02X-01

Colorectum

rectum adenocarcinoma

Male

>=65

I/II

Unknown

TOMM40

SNV

Missense_Mutation

novel

c.1007N>T

p.Pro336Leu

p.P336L

O96008

protein_coding

deleterious(0.03)

possibly_damaging(0.905)

TCGA-A5-A1OF-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

TOMM40

SNV

Missense_Mutation

c.1047G>T

p.Lys349Asn

p.K349N

O96008

protein_coding

deleterious(0)

possibly_damaging(0.838)

TCGA-BS-A0UF-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

TOMM40

SNV

Missense_Mutation

novel

c.791N>T

p.Thr264Met

p.T264M

O96008

protein_coding

tolerated(0.06)

possibly_damaging(0.627)

TCGA-FI-A2D0-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

TOMM40

SNV

Missense_Mutation

novel

c.316N>G

p.Asn106Asp

p.N106D

O96008

protein_coding

deleterious(0)

probably_damaging(0.978)

TCGA-FI-A2D5-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

carboplatinum

TOMM40

SNV

Missense_Mutation

novel

c.298N>C

p.Gly100Arg

p.G100R

O96008

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-95-7043-01

Lung

lung adenocarcinoma

Female

<65

I/II

Unknown

TOMM40

SNV

Missense_Mutation

c.478N>G

p.Leu160Val

p.L160V

O96008

protein_coding

deleterious(0.04)

possibly_damaging(0.781)

TCGA-66-2789-01

Lung

lung squamous cell carcinoma

Male

>=65

III/IV

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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