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: MYDGF

Gene summary for MYDGF

Gene summary.

Gene information	Species	Human
	Gene symbol	MYDGF
	Gene ID	56005
	Gene name	myeloid derived growth factor
	Gene Alias	C19orf10
	Cytomap	19p13.3
	Gene Type	protein-coding
	GO ID	GO:0000165
	UniProtAcc	Q969H8

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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
56005	MYDGF	CA_HPV_1	Human	Cervix	CC	3.18e-04	-1.95e-01	0.0264
56005	MYDGF	N_HPV_1	Human	Cervix	N_HPV	9.17e-04	-1.27e-01	0.0079
56005	MYDGF	CCI_1	Human	Cervix	CC	1.09e-03	-5.09e-01	0.528
56005	MYDGF	CCI_3	Human	Cervix	CC	3.09e-08	-5.70e-01	0.516
56005	MYDGF	CCII_1	Human	Cervix	CC	8.47e-12	-5.69e-01	0.3249
56005	MYDGF	L1	Human	Cervix	CC	1.49e-06	-3.73e-01	0.0802
56005	MYDGF	HTA11_2487_2000001011	Human	Colorectum	SER	2.43e-08	5.02e-01	-0.1808
56005	MYDGF	HTA11_1938_2000001011	Human	Colorectum	AD	5.83e-03	3.44e-01	-0.0811
56005	MYDGF	HTA11_347_2000001011	Human	Colorectum	AD	2.54e-15	5.12e-01	-0.1954
56005	MYDGF	HTA11_3361_2000001011	Human	Colorectum	AD	5.73e-05	3.86e-01	-0.1207
56005	MYDGF	HTA11_696_2000001011	Human	Colorectum	AD	2.20e-12	5.34e-01	-0.1464
56005	MYDGF	HTA11_866_2000001011	Human	Colorectum	AD	2.10e-03	2.87e-01	-0.1001
56005	MYDGF	HTA11_1391_2000001011	Human	Colorectum	AD	1.95e-13	6.00e-01	-0.059
56005	MYDGF	HTA11_5216_2000001011	Human	Colorectum	SER	2.73e-02	3.84e-01	-0.1462
56005	MYDGF	HTA11_866_3004761011	Human	Colorectum	AD	3.15e-03	2.69e-01	0.096
56005	MYDGF	HTA11_6801_2000001011	Human	Colorectum	SER	3.12e-02	5.62e-01	0.0171
56005	MYDGF	HTA11_7696_3000711011	Human	Colorectum	AD	8.27e-07	3.73e-01	0.0674
56005	MYDGF	HTA11_99999965062_69753	Human	Colorectum	MSI-H	2.43e-08	1.27e+00	0.3487
56005	MYDGF	HTA11_99999971662_82457	Human	Colorectum	MSS	9.21e-15	5.49e-01	0.3859
56005	MYDGF	HTA11_99999973899_84307	Human	Colorectum	MSS	2.21e-02	3.76e-01	0.2585

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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
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:00506737	Cervix	CC	epithelial cell proliferation	98/2311	437/18723	2.01e-09	2.15e-07	98
GO:00506787	Cervix	CC	regulation of epithelial cell proliferation	83/2311	381/18723	1.31e-07	6.42e-06	83
GO:00506794	Cervix	CC	positive regulation of epithelial cell proliferation	47/2311	207/18723	2.18e-05	3.90e-04	47
GO:00434104	Cervix	CC	positive regulation of MAPK cascade	90/2311	480/18723	2.92e-05	4.83e-04	90
GO:00518964	Cervix	CC	regulation of protein kinase B signaling	39/2311	185/18723	5.25e-04	5.10e-03	39
GO:00518973	Cervix	CC	positive regulation of protein kinase B signaling	28/2311	120/18723	5.90e-04	5.59e-03	28
GO:00434913	Cervix	CC	protein kinase B signaling	43/2311	211/18723	5.95e-04	5.60e-03	43
GO:19013423	Cervix	CC	regulation of vasculature development	60/2311	348/18723	4.48e-03	2.72e-02	60
GO:00457653	Cervix	CC	regulation of angiogenesis	59/2311	342/18723	4.73e-03	2.83e-02	59
GO:0014065	Cervix	CC	phosphatidylinositol 3-kinase signaling	28/2311	144/18723	9.50e-03	4.72e-02	28
GO:004576611	Cervix	N_HPV	positive regulation of angiogenesis	18/534	181/18723	4.51e-06	1.71e-04	18
GO:190401811	Cervix	N_HPV	positive regulation of vasculature development	18/534	181/18723	4.51e-06	1.71e-04	18
GO:004576521	Cervix	N_HPV	regulation of angiogenesis	25/534	342/18723	1.80e-05	5.30e-04	25
GO:190134221	Cervix	N_HPV	regulation of vasculature development	25/534	348/18723	2.41e-05	6.66e-04	25
GO:005189711	Cervix	N_HPV	positive regulation of protein kinase B signaling	10/534	120/18723	2.30e-03	2.13e-02	10
GO:005189611	Cervix	N_HPV	regulation of protein kinase B signaling	12/534	185/18723	6.94e-03	4.59e-02	12
GO:004349112	Cervix	N_HPV	protein kinase B signaling	13/534	211/18723	7.72e-03	4.97e-02	13
GO:0050673	Colorectum	AD	epithelial cell proliferation	119/3918	437/18723	8.75e-04	8.51e-03	119
GO:0048017	Colorectum	AD	inositol lipid-mediated signaling	53/3918	182/18723	5.35e-03	3.52e-02	53
GO:0048015	Colorectum	AD	phosphatidylinositol-mediated signaling	52/3918	178/18723	5.37e-03	3.54e-02	52

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Enriched KEGG pathways.

Pathway ID

Tissue

Disease Stage

Description

Gene Ratio

Bg Ratio

pvalue

p.adjust

qvalue

Count

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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

MYDGF

SNV

Missense_Mutation

c.218N>A

p.Thr73Asn

p.T73N

Q969H8

protein_coding

deleterious(0)

probably_damaging(0.998)

TCGA-AO-A0JD-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

cyclophosphamide

MYDGF

SNV

Missense_Mutation

c.394N>C

p.Ser132Arg

p.S132R

Q969H8

protein_coding

tolerated(0.09)

possibly_damaging(0.744)

TCGA-EW-A1OZ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Targeted Molecular therapy

trastuzumab

MYDGF

deletion

Frame_Shift_Del

c.394delN

p.Ser132ValfsTer5

p.S132Vfs*5

Q969H8

protein_coding

TCGA-D8-A27V-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

tamoxiphen

MYDGF

SNV

Missense_Mutation

c.353A>T

p.Glu118Val

p.E118V

Q969H8

protein_coding

deleterious(0)

probably_damaging(0.998)

TCGA-AA-3864-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

MYDGF

SNV

Missense_Mutation

novel

c.397G>T

p.Asp133Tyr

p.D133Y

Q969H8

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-A5-A2K5-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

MYDGF

SNV

Missense_Mutation

c.264N>T

p.Gln88His

p.Q88H

Q969H8

protein_coding

tolerated(0.11)

possibly_damaging(0.855)

TCGA-AP-A059-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

MYDGF

SNV

Missense_Mutation

rs200622596

c.253N>A

p.Glu85Lys

p.E85K

Q969H8

protein_coding

tolerated(0.05)

benign(0.015)

TCGA-AP-A1DV-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

MYDGF

SNV

Missense_Mutation

rs769735674

c.358N>A

p.Ala120Thr

p.A120T

Q969H8

protein_coding

deleterious(0.01)

benign(0.314)

TCGA-D1-A103-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

MYDGF

SNV

Missense_Mutation

novel

c.268N>C

p.Phe90Leu

p.F90L

Q969H8

protein_coding

tolerated(0.07)

benign(0.048)

TCGA-D1-A175-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Chemotherapy

paclitaxel

MYDGF

SNV

Missense_Mutation

novel

c.182N>G

p.Tyr61Cys

p.Y61C

Q969H8

protein_coding

deleterious(0)

possibly_damaging(0.807)

TCGA-EO-A22X-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Unspecific

Carboplatin

Complete Response

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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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