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: MYO1E

Gene summary for MYO1E

Gene summary.

Gene information	Species	Human
	Gene symbol	MYO1E
	Gene ID	4643
	Gene name	myosin IE
	Gene Alias	FSGS6
	Cytomap	15q22.2
	Gene Type	protein-coding
	GO ID	GO:0001568
	UniProtAcc	Q12965

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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
4643	MYO1E	CCI_1	Human	Cervix	CC	1.62e-21	1.91e+00	0.528
4643	MYO1E	CCI_2	Human	Cervix	CC	7.39e-23	1.88e+00	0.5249
4643	MYO1E	CCI_3	Human	Cervix	CC	3.58e-19	1.26e+00	0.516
4643	MYO1E	CCII_1	Human	Cervix	CC	1.41e-08	5.29e-01	0.3249
4643	MYO1E	H2	Human	Cervix	HSIL_HPV	2.61e-02	2.01e-01	0.0632
4643	MYO1E	HTA11_3410_2000001011	Human	Colorectum	AD	8.76e-16	-5.77e-01	0.0155
4643	MYO1E	HTA11_2951_2000001011	Human	Colorectum	AD	3.70e-08	-7.12e-01	0.0216
4643	MYO1E	HTA11_347_2000001011	Human	Colorectum	AD	6.71e-07	5.50e-01	-0.1954
4643	MYO1E	HTA11_411_2000001011	Human	Colorectum	SER	3.42e-07	7.17e-01	-0.2602
4643	MYO1E	HTA11_7862_2000001011	Human	Colorectum	AD	6.53e-05	-4.46e-01	-0.0179
4643	MYO1E	HTA11_866_3004761011	Human	Colorectum	AD	3.15e-04	-4.01e-01	0.096
4643	MYO1E	HTA11_9408_2000001011	Human	Colorectum	AD	1.77e-02	-6.39e-01	0.0451
4643	MYO1E	HTA11_8622_2000001021	Human	Colorectum	SER	5.74e-07	-4.93e-01	0.0528
4643	MYO1E	HTA11_6801_2000001011	Human	Colorectum	SER	2.60e-02	-6.64e-01	0.0171
4643	MYO1E	HTA11_7696_3000711011	Human	Colorectum	AD	8.34e-05	-3.03e-01	0.0674
4643	MYO1E	HTA11_7469_2000001011	Human	Colorectum	AD	1.35e-03	-7.60e-01	-0.0124
4643	MYO1E	HTA11_6818_2000001021	Human	Colorectum	AD	1.03e-03	-4.61e-01	0.0588
4643	MYO1E	HTA11_99999970781_79442	Human	Colorectum	MSS	1.25e-56	-8.48e-01	0.294
4643	MYO1E	HTA11_99999971662_82457	Human	Colorectum	MSS	6.78e-24	-6.64e-01	0.3859
4643	MYO1E	HTA11_99999974143_84620	Human	Colorectum	MSS	4.25e-44	-7.42e-01	0.3005

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
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
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:000701510	Cervix	CC	actin filament organization	109/2311	442/18723	4.92e-13	2.45e-10	109
GO:00516567	Cervix	CC	establishment of organelle localization	76/2311	390/18723	3.17e-05	5.21e-04	76
GO:00017018	Cervix	CC	in utero embryonic development	71/2311	367/18723	7.21e-05	1.00e-03	71
GO:00015704	Cervix	CC	vasculogenesis	22/2311	80/18723	1.97e-04	2.26e-03	22
GO:000206410	Cervix	CC	epithelial cell development	45/2311	220/18723	4.14e-04	4.21e-03	45
GO:00300487	Cervix	CC	actin filament-based movement	29/2311	127/18723	6.91e-04	6.33e-03	29
GO:00307057	Cervix	CC	cytoskeleton-dependent intracellular transport	40/2311	195/18723	7.92e-04	6.99e-03	40
GO:00097915	Cervix	CC	post-embryonic development	20/2311	80/18723	1.40e-03	1.10e-02	20
GO:00995157	Cervix	CC	actin filament-based transport	8/2311	21/18723	2.44e-03	1.71e-02	8
GO:00300507	Cervix	CC	vesicle transport along actin filament	7/2311	19/18723	5.65e-03	3.25e-02	7
GO:00480084	Cervix	CC	platelet-derived growth factor receptor signaling pathway	14/2311	56/18723	6.93e-03	3.74e-02	14
GO:0030198	Cervix	CC	extracellular matrix organization	52/2311	301/18723	7.43e-03	3.98e-02	52
GO:0043062	Cervix	CC	extracellular structure organization	52/2311	302/18723	7.92e-03	4.17e-02	52
GO:0045229	Cervix	CC	external encapsulating structure organization	52/2311	304/18723	9.00e-03	4.57e-02	52
GO:000701515	Cervix	HSIL_HPV	actin filament organization	43/737	442/18723	4.77e-08	3.59e-06	43
GO:00030943	Cervix	HSIL_HPV	glomerular filtration	6/737	25/18723	3.40e-04	5.39e-03	6
GO:00972054	Cervix	HSIL_HPV	renal filtration	6/737	26/18723	4.27e-04	6.41e-03	6
GO:003004813	Cervix	HSIL_HPV	actin filament-based movement	12/737	127/18723	4.37e-03	3.68e-02	12
GO:0007015	Colorectum	AD	actin filament organization	167/3918	442/18723	1.65e-16	7.94e-14	167
GO:0002064	Colorectum	AD	epithelial cell development	89/3918	220/18723	2.98e-11	3.52e-09	89

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0513020	Cervix	CC	Pathogenic Escherichia coli infection	63/1267	197/8465	9.28e-10	2.00e-08	1.19e-08	63
hsa05130110	Cervix	CC	Pathogenic Escherichia coli infection	63/1267	197/8465	9.28e-10	2.00e-08	1.19e-08	63
hsa0513025	Cervix	HSIL_HPV	Pathogenic Escherichia coli infection	28/459	197/8465	2.36e-06	4.61e-05	3.73e-05	28
hsa0513035	Cervix	HSIL_HPV	Pathogenic Escherichia coli infection	28/459	197/8465	2.36e-06	4.61e-05	3.73e-05	28
hsa05130	Colorectum	AD	Pathogenic Escherichia coli infection	79/2092	197/8465	1.05e-06	1.36e-05	8.65e-06	79
hsa051301	Colorectum	AD	Pathogenic Escherichia coli infection	79/2092	197/8465	1.05e-06	1.36e-05	8.65e-06	79
hsa051302	Colorectum	SER	Pathogenic Escherichia coli infection	60/1580	197/8465	3.63e-05	4.31e-04	3.13e-04	60
hsa051303	Colorectum	SER	Pathogenic Escherichia coli infection	60/1580	197/8465	3.63e-05	4.31e-04	3.13e-04	60
hsa051304	Colorectum	MSS	Pathogenic Escherichia coli infection	73/1875	197/8465	1.10e-06	1.48e-05	9.06e-06	73
hsa051305	Colorectum	MSS	Pathogenic Escherichia coli infection	73/1875	197/8465	1.10e-06	1.48e-05	9.06e-06	73
hsa051308	Colorectum	FAP	Pathogenic Escherichia coli infection	62/1404	197/8465	1.37e-07	3.08e-06	1.87e-06	62
hsa051309	Colorectum	FAP	Pathogenic Escherichia coli infection	62/1404	197/8465	1.37e-07	3.08e-06	1.87e-06	62
hsa0513010	Colorectum	CRC	Pathogenic Escherichia coli infection	47/1091	197/8465	1.49e-05	3.84e-04	2.60e-04	47
hsa0513011	Colorectum	CRC	Pathogenic Escherichia coli infection	47/1091	197/8465	1.49e-05	3.84e-04	2.60e-04	47
hsa0513026	Endometrium	AEH	Pathogenic Escherichia coli infection	50/1197	197/8465	1.72e-05	1.86e-04	1.36e-04	50
hsa048144	Endometrium	AEH	Motor proteins	42/1197	193/8465	2.41e-03	1.42e-02	1.04e-02	42
hsa05130112	Endometrium	AEH	Pathogenic Escherichia coli infection	50/1197	197/8465	1.72e-05	1.86e-04	1.36e-04	50
hsa0481411	Endometrium	AEH	Motor proteins	42/1197	193/8465	2.41e-03	1.42e-02	1.04e-02	42
hsa0513027	Endometrium	EEC	Pathogenic Escherichia coli infection	51/1237	197/8465	1.98e-05	2.28e-04	1.70e-04	51
hsa048142	Endometrium	EEC	Motor proteins	42/1237	193/8465	4.43e-03	2.39e-02	1.78e-02	42

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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

MYO1E

SNV

Missense_Mutation

rs773856184

c.3088N>G

p.Arg1030Gly

p.R1030G

Q12965

protein_coding

deleterious(0.03)

benign(0.367)

TCGA-A8-A06X-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

MYO1E

SNV

Missense_Mutation

c.1961G>T

p.Gly654Val

p.G654V

Q12965

protein_coding

deleterious(0)

probably_damaging(0.989)

TCGA-A8-A085-01

Breast

breast invasive carcinoma

Male

<65

I/II

Hormone Therapy

tamoxiphen

MYO1E

SNV

Missense_Mutation

novel

c.247N>C

p.Glu83Gln

p.E83Q

Q12965

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-AO-A0J3-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

cyclophosphamide

MYO1E

SNV

Missense_Mutation

c.1343N>G

p.Asp448Gly

p.D448G

Q12965

protein_coding

deleterious(0)

probably_damaging(0.986)

TCGA-AO-A128-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

MYO1E

SNV

Missense_Mutation

c.907G>C

p.Glu303Gln

p.E303Q

Q12965

protein_coding

tolerated(0.21)

benign(0.01)

TCGA-C8-A1HM-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

doxorubicin

MYO1E

SNV

Missense_Mutation

rs546799247

c.971C>A

p.Thr324Lys

p.T324K

Q12965

protein_coding

deleterious(0.01)

probably_damaging(0.994)

TCGA-D8-A1Y1-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Hormone Therapy

tamoxiphen

MYO1E

SNV

Missense_Mutation

c.470N>T

p.Gly157Val

p.G157V

Q12965

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-E2-A1LB-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

MYO1E

SNV

Missense_Mutation

novel

c.1669C>T

p.Arg557Cys

p.R557C

Q12965

protein_coding

deleterious(0)

probably_damaging(0.998)

TCGA-E2-A9RU-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Hormone Therapy

arimidex

MYO1E

insertion

Frame_Shift_Ins

novel

c.3085_3086insACCTTGAATATCCATTATTAAAGCAGTCCAT

p.Arg1029AsnfsTer45

p.R1029Nfs*45

Q12965

protein_coding

TCGA-A8-A06X-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

MYO1E

insertion

Nonsense_Mutation

novel

c.245_246insACCCCATC

p.Tyr82Ter

p.Y82*

Q12965

protein_coding

TCGA-AO-A0J3-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

cyclophosphamide

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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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