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: MYH11

Gene summary for MYH11

Gene summary.

Gene information	Species	Human
	Gene symbol	MYH11
	Gene ID	4629
	Gene name	myosin heavy chain 11
	Gene Alias	AAT4
	Cytomap	16p13.11
	Gene Type	protein-coding
	GO ID	GO:0003008
	UniProtAcc	P35749

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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
4629	MYH11	P4T-E	Human	Esophagus	ESCC	2.90e-03	2.11e-01	0.1323
4629	MYH11	P9T-E	Human	Esophagus	ESCC	1.09e-51	2.46e+00	0.1131
4629	MYH11	P15T-E	Human	Esophagus	ESCC	2.72e-24	1.44e+00	0.1149
4629	MYH11	P28T-E	Human	Esophagus	ESCC	2.08e-03	7.45e-02	0.1149
4629	MYH11	P52T-E	Human	Esophagus	ESCC	1.01e-16	1.54e+00	0.1555
4629	MYH11	P76T-E	Human	Esophagus	ESCC	8.40e-04	1.50e-01	0.1207
4629	MYH11	HCC1	Human	Liver	HCC	2.28e-12	5.51e-01	0.5336
4629	MYH11	Pt14.d	Human	Liver	HCC	7.90e-14	5.46e-01	0.0143
4629	MYH11	C04	Human	Oral cavity	OSCC	1.29e-06	-5.71e-01	0.2633
4629	MYH11	C21	Human	Oral cavity	OSCC	5.15e-08	-6.93e-01	0.2678
4629	MYH11	C30	Human	Oral cavity	OSCC	4.31e-03	-6.93e-01	0.3055
4629	MYH11	C43	Human	Oral cavity	OSCC	7.23e-14	-6.57e-01	0.1704
4629	MYH11	C46	Human	Oral cavity	OSCC	3.75e-14	-6.64e-01	0.1673
4629	MYH11	C51	Human	Oral cavity	OSCC	4.31e-03	-6.93e-01	0.2674
4629	MYH11	C57	Human	Oral cavity	OSCC	7.73e-09	-6.76e-01	0.1679
4629	MYH11	C08	Human	Oral cavity	OSCC	1.57e-02	-2.93e-01	0.1919
4629	MYH11	C09	Human	Oral cavity	OSCC	1.92e-10	-6.93e-01	0.1431
4629	MYH11	LN46	Human	Oral cavity	OSCC	5.25e-05	-5.91e-01	0.1666
4629	MYH11	SYSMH1	Human	Oral cavity	OSCC	3.82e-16	-6.64e-01	0.1127
4629	MYH11	SYSMH2	Human	Oral cavity	OSCC	4.03e-13	-6.34e-01	0.2326

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Endometrium		AEH: Atypical endometrial hyperplasia
		EEC: Endometrioid 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

∗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:00301984	Esophagus	ESCC	extracellular matrix organization	171/8552	301/18723	6.08e-05	4.67e-04	171
GO:00430624	Esophagus	ESCC	extracellular structure organization	171/8552	302/18723	7.73e-05	5.76e-04	171
GO:00452294	Esophagus	ESCC	external encapsulating structure organization	172/8552	304/18723	7.80e-05	5.80e-04	172
GO:006053716	Esophagus	ESCC	muscle tissue development	211/8552	403/18723	3.84e-03	1.56e-02	211
GO:003103219	Esophagus	ESCC	actomyosin structure organization	108/8552	196/18723	4.86e-03	1.88e-02	108
GO:00850292	Esophagus	ESCC	extracellular matrix assembly	29/8552	45/18723	8.63e-03	3.04e-02	29
GO:00350512	Esophagus	ESCC	cardiocyte differentiation	86/8552	156/18723	1.09e-02	3.68e-02	86
GO:001470615	Esophagus	ESCC	striated muscle tissue development	197/8552	384/18723	1.46e-02	4.74e-02	197
GO:003103222	Liver	HCC	actomyosin structure organization	109/7958	196/18723	1.39e-04	1.13e-03	109
GO:00301983	Oral cavity	OSCC	extracellular matrix organization	146/7305	301/18723	4.67e-04	2.77e-03	146
GO:0085029	Oral cavity	OSCC	extracellular matrix assembly	29/7305	45/18723	4.85e-04	2.86e-03	29
GO:00452293	Oral cavity	OSCC	external encapsulating structure organization	147/7305	304/18723	5.30e-04	3.08e-03	147
GO:00430623	Oral cavity	OSCC	extracellular structure organization	146/7305	302/18723	5.59e-04	3.23e-03	146
GO:00605378	Oral cavity	OSCC	muscle tissue development	185/7305	403/18723	2.60e-03	1.14e-02	185
GO:00426927	Oral cavity	OSCC	muscle cell differentiation	175/7305	384/18723	4.79e-03	1.92e-02	175
GO:00147067	Oral cavity	OSCC	striated muscle tissue development	174/7305	384/18723	6.45e-03	2.40e-02	174
GO:003103217	Oral cavity	OSCC	actomyosin structure organization	93/7305	196/18723	9.63e-03	3.41e-02	93
GO:0048251	Oral cavity	OSCC	elastic fiber assembly	8/7305	10/18723	1.03e-02	3.53e-02	8

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa05130211	Esophagus	ESCC	Pathogenic Escherichia coli infection	142/4205	197/8465	8.21e-11	1.06e-09	5.42e-10	142
hsa04530211	Esophagus	ESCC	Tight junction	105/4205	169/8465	6.73e-04	2.23e-03	1.14e-03	105
hsa0481028	Esophagus	ESCC	Regulation of actin cytoskeleton	133/4205	229/8465	5.94e-03	1.48e-02	7.56e-03	133
hsa05130310	Esophagus	ESCC	Pathogenic Escherichia coli infection	142/4205	197/8465	8.21e-11	1.06e-09	5.42e-10	142
hsa04530310	Esophagus	ESCC	Tight junction	105/4205	169/8465	6.73e-04	2.23e-03	1.14e-03	105
hsa04810112	Esophagus	ESCC	Regulation of actin cytoskeleton	133/4205	229/8465	5.94e-03	1.48e-02	7.56e-03	133
hsa0513042	Liver	HCC	Pathogenic Escherichia coli infection	129/4020	197/8465	2.02e-07	2.50e-06	1.39e-06	129
hsa0453042	Liver	HCC	Tight junction	110/4020	169/8465	2.45e-06	2.28e-05	1.27e-05	110
hsa0481041	Liver	HCC	Regulation of actin cytoskeleton	134/4020	229/8465	4.48e-04	1.94e-03	1.08e-03	134
hsa0513052	Liver	HCC	Pathogenic Escherichia coli infection	129/4020	197/8465	2.02e-07	2.50e-06	1.39e-06	129
hsa0453052	Liver	HCC	Tight junction	110/4020	169/8465	2.45e-06	2.28e-05	1.27e-05	110
hsa0481051	Liver	HCC	Regulation of actin cytoskeleton	134/4020	229/8465	4.48e-04	1.94e-03	1.08e-03	134
hsa0513030	Oral cavity	OSCC	Pathogenic Escherichia coli infection	129/3704	197/8465	4.32e-10	5.17e-09	2.63e-09	129
hsa0453030	Oral cavity	OSCC	Tight junction	102/3704	169/8465	8.68e-06	3.93e-05	2.00e-05	102
hsa0481026	Oral cavity	OSCC	Regulation of actin cytoskeleton	129/3704	229/8465	7.14e-05	2.74e-04	1.40e-04	129
hsa05130114	Oral cavity	OSCC	Pathogenic Escherichia coli infection	129/3704	197/8465	4.32e-10	5.17e-09	2.63e-09	129
hsa04530114	Oral cavity	OSCC	Tight junction	102/3704	169/8465	8.68e-06	3.93e-05	2.00e-05	102
hsa04810111	Oral cavity	OSCC	Regulation of actin cytoskeleton	129/3704	229/8465	7.14e-05	2.74e-04	1.40e-04	129

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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

MYH11

SNV

Missense_Mutation

rs778694636

c.4119N>G

p.Ile1373Met

p.I1373M

P35749

protein_coding

tolerated(0.15)

benign(0.02)

TCGA-A2-A0CT-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

cytoxan

MYH11

SNV

Missense_Mutation

c.2971N>C

p.Glu991Gln

p.E991Q

P35749

protein_coding

deleterious(0)

possibly_damaging(0.725)

TCGA-A2-A0T0-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

taxotere

MYH11

SNV

Missense_Mutation

c.1652N>A

p.Ala551Asp

p.A551D

P35749

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-A2-A0T0-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

taxotere

MYH11

SNV

Missense_Mutation

c.1199N>A

p.Thr400Asn

p.T400N

P35749

protein_coding

deleterious(0.02)

possibly_damaging(0.849)

TCGA-A8-A08L-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Unknown

MYH11

SNV

Missense_Mutation

c.3367N>A

p.Leu1123Met

p.L1123M

P35749

protein_coding

tolerated(0.06)

possibly_damaging(0.513)

TCGA-A8-A09M-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Chemotherapy

paclitaxel

MYH11

SNV

Missense_Mutation

c.1403N>A

p.Ala468Asp

p.A468D

P35749

protein_coding

deleterious(0)

probably_damaging(0.986)

TCGA-BH-A0HY-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

taxotere

MYH11

SNV

Missense_Mutation

rs771297865

c.3146G>A

p.Arg1049Gln

p.R1049Q

P35749

protein_coding

deleterious(0.05)

possibly_damaging(0.83)

TCGA-BH-A18G-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

MYH11

SNV

Missense_Mutation

c.5024N>A

p.Arg1675Lys

p.R1675K

P35749

protein_coding

tolerated(0.27)

possibly_damaging(0.803)

TCGA-D8-A1J8-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

nolvadex

MYH11

SNV

Missense_Mutation

c.1411G>A

p.Glu471Lys

p.E471K

P35749

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-D8-A1JA-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

adriamycin

MYH11

SNV

Missense_Mutation

c.2417N>A

p.Gly806Asp

p.G806D

P35749

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-D8-A1JJ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicine

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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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