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: MYO5B

Gene summary for MYO5B

Gene summary.

Gene information	Species	Human
	Gene symbol	MYO5B
	Gene ID	4645
	Gene name	myosin VB
	Gene Alias	DIAR2
	Cytomap	18q21.1
	Gene Type	protein-coding
	GO ID	GO:0003008
	UniProtAcc	Q7Z7A5

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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
4645	MYO5B	HTA11_3410_2000001011	Human	Colorectum	AD	3.40e-18	-6.06e-01	0.0155
4645	MYO5B	HTA11_3361_2000001011	Human	Colorectum	AD	4.31e-04	-4.73e-01	-0.1207
4645	MYO5B	HTA11_8622_2000001021	Human	Colorectum	SER	1.17e-02	-6.35e-01	0.0528
4645	MYO5B	HTA11_7696_3000711011	Human	Colorectum	AD	5.21e-03	-3.40e-01	0.0674
4645	MYO5B	HTA11_99999970781_79442	Human	Colorectum	MSS	4.48e-17	-5.89e-01	0.294
4645	MYO5B	HTA11_99999971662_82457	Human	Colorectum	MSS	1.46e-13	-5.58e-01	0.3859
4645	MYO5B	HTA11_99999974143_84620	Human	Colorectum	MSS	1.22e-35	-7.09e-01	0.3005
4645	MYO5B	F007	Human	Colorectum	FAP	1.85e-03	-2.57e-01	0.1176
4645	MYO5B	A001-C-207	Human	Colorectum	FAP	9.71e-03	-2.62e-01	0.1278
4645	MYO5B	A015-C-203	Human	Colorectum	FAP	2.40e-46	-6.91e-01	-0.1294
4645	MYO5B	A015-C-204	Human	Colorectum	FAP	1.93e-07	-3.77e-01	-0.0228
4645	MYO5B	A014-C-040	Human	Colorectum	FAP	7.43e-09	-6.17e-01	-0.1184
4645	MYO5B	A002-C-201	Human	Colorectum	FAP	5.68e-18	-3.65e-01	0.0324
4645	MYO5B	A002-C-203	Human	Colorectum	FAP	6.43e-07	-2.90e-01	0.2786
4645	MYO5B	A001-C-119	Human	Colorectum	FAP	8.37e-11	-5.21e-01	-0.1557
4645	MYO5B	A001-C-108	Human	Colorectum	FAP	2.16e-27	-4.78e-01	-0.0272
4645	MYO5B	A002-C-205	Human	Colorectum	FAP	4.56e-30	-6.27e-01	-0.1236
4645	MYO5B	A001-C-104	Human	Colorectum	FAP	4.34e-05	-3.17e-01	0.0184
4645	MYO5B	A015-C-005	Human	Colorectum	FAP	1.15e-03	-3.18e-01	-0.0336
4645	MYO5B	A015-C-006	Human	Colorectum	FAP	1.57e-23	-6.32e-01	-0.0994

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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
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
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:0007015	Colorectum	AD	actin filament organization	167/3918	442/18723	1.65e-16	7.94e-14	167
GO:0016197	Colorectum	AD	endosomal transport	90/3918	230/18723	1.88e-10	1.73e-08	90
GO:0051656	Colorectum	AD	establishment of organelle localization	131/3918	390/18723	3.00e-09	2.06e-07	131
GO:0051650	Colorectum	AD	establishment of vesicle localization	57/3918	161/18723	1.47e-05	3.15e-04	57
GO:0051648	Colorectum	AD	vesicle localization	59/3918	177/18723	7.83e-05	1.25e-03	59
GO:0030048	Colorectum	AD	actin filament-based movement	44/3918	127/18723	2.31e-04	2.99e-03	44
GO:0050878	Colorectum	AD	regulation of body fluid levels	108/3918	379/18723	2.54e-04	3.20e-03	108
GO:0099515	Colorectum	AD	actin filament-based transport	12/3918	21/18723	3.02e-04	3.62e-03	12
GO:0030050	Colorectum	AD	vesicle transport along actin filament	11/3918	19/18723	4.66e-04	5.15e-03	11
GO:0030705	Colorectum	AD	cytoskeleton-dependent intracellular transport	60/3918	195/18723	7.56e-04	7.59e-03	60
GO:0003014	Colorectum	AD	renal system process	35/3918	110/18723	4.85e-03	3.27e-02	35
GO:00070151	Colorectum	SER	actin filament organization	134/2897	442/18723	1.39e-15	5.70e-13	134
GO:00516561	Colorectum	SER	establishment of organelle localization	100/2897	390/18723	1.11e-07	6.79e-06	100
GO:00161971	Colorectum	SER	endosomal transport	61/2897	230/18723	1.03e-05	3.35e-04	61
GO:00300481	Colorectum	SER	actin filament-based movement	38/2897	127/18723	2.80e-05	7.56e-04	38
GO:00995151	Colorectum	SER	actin filament-based transport	11/2897	21/18723	9.28e-05	1.98e-03	11
GO:00300501	Colorectum	SER	vesicle transport along actin filament	10/2897	19/18723	1.86e-04	3.43e-03	10
GO:00516501	Colorectum	SER	establishment of vesicle localization	42/2897	161/18723	3.38e-04	5.35e-03	42
GO:00030141	Colorectum	SER	renal system process	30/2897	110/18723	1.05e-03	1.22e-02	30
GO:00508781	Colorectum	SER	regulation of body fluid levels	81/2897	379/18723	1.28e-03	1.43e-02	81

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
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
hsa0513036	Endometrium	EEC	Pathogenic Escherichia coli infection	51/1237	197/8465	1.98e-05	2.28e-04	1.70e-04	51
hsa048143	Endometrium	EEC	Motor proteins	42/1237	193/8465	4.43e-03	2.39e-02	1.78e-02	42
hsa05130211	Esophagus	ESCC	Pathogenic Escherichia coli infection	142/4205	197/8465	8.21e-11	1.06e-09	5.42e-10	142
hsa05130310	Esophagus	ESCC	Pathogenic Escherichia coli infection	142/4205	197/8465	8.21e-11	1.06e-09	5.42e-10	142

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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

MYO5B

SNV

Missense_Mutation

c.3526N>C

p.Lys1176Gln

p.K1176Q

Q9ULV0

protein_coding

tolerated(0.16)

benign(0.003)

TCGA-A2-A04N-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

cytoxan

MYO5B

SNV

Missense_Mutation

novel

c.2095G>C

p.Ala699Pro

p.A699P

Q9ULV0

protein_coding

deleterious(0)

benign(0.001)

TCGA-A2-A04P-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

taxol

MYO5B

SNV

Missense_Mutation

c.1436N>C

p.Met479Thr

p.M479T

Q9ULV0

protein_coding

deleterious(0.03)

benign(0.015)

TCGA-A2-A0YJ-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

cytoxan

MYO5B

SNV

Missense_Mutation

c.2566N>T

p.Arg856Cys

p.R856C

Q9ULV0

protein_coding

deleterious(0.04)

benign(0.026)

TCGA-A7-A0CG-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

MYO5B

SNV

Missense_Mutation

rs745968678

c.1214N>T

p.Ala405Val

p.A405V

Q9ULV0

protein_coding

deleterious(0)

possibly_damaging(0.707)

TCGA-A8-A07W-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Hormone Therapy

exemestane

MYO5B

SNV

Missense_Mutation

rs575729461

c.2395C>T

p.Arg799Trp

p.R799W

Q9ULV0

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-A8-A096-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

MYO5B

SNV

Missense_Mutation

rs748776509

c.5146A>G

p.Ile1716Val

p.I1716V

Q9ULV0

protein_coding

tolerated(0.69)

benign(0.015)

TCGA-A8-A09C-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

MYO5B

SNV

Missense_Mutation

c.5332N>T

p.Leu1778Phe

p.L1778F

Q9ULV0

protein_coding

deleterious(0.01)

probably_damaging(1)

TCGA-A8-A09Z-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

MYO5B

SNV

Missense_Mutation

novel

c.559G>A

p.Ala187Thr

p.A187T

Q9ULV0

protein_coding

tolerated(0.08)

benign(0.007)

TCGA-AC-A5EH-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

MYO5B

SNV

Missense_Mutation

c.5497N>G

p.Ser1833Ala

p.S1833A

Q9ULV0

protein_coding

tolerated(0.15)

benign(0.044)

TCGA-B6-A0IE-01

Breast

breast invasive carcinoma

Female

<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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