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: DIAPH1

Gene summary for DIAPH1

Gene summary.

Gene information	Species	Human
	Gene symbol	DIAPH1
	Gene ID	1729
	Gene name	diaphanous related formin 1
	Gene Alias	DFNA1
	Cytomap	5q31.3
	Gene Type	protein-coding
	GO ID	GO:0000902
	UniProtAcc	O60610

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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
1729	DIAPH1	AEH-subject1	Human	Endometrium	AEH	2.41e-14	4.29e-01	-0.3059
1729	DIAPH1	AEH-subject2	Human	Endometrium	AEH	1.04e-02	2.05e-01	-0.2525
1729	DIAPH1	AEH-subject3	Human	Endometrium	AEH	2.40e-05	2.51e-01	-0.2576
1729	DIAPH1	AEH-subject4	Human	Endometrium	AEH	2.40e-02	1.84e-01	-0.2657
1729	DIAPH1	AEH-subject5	Human	Endometrium	AEH	4.77e-12	4.46e-01	-0.2953
1729	DIAPH1	EEC-subject1	Human	Endometrium	EEC	1.14e-10	4.19e-01	-0.2682
1729	DIAPH1	EEC-subject2	Human	Endometrium	EEC	1.93e-06	2.95e-01	-0.2607
1729	DIAPH1	EEC-subject3	Human	Endometrium	EEC	7.34e-08	3.48e-01	-0.2525
1729	DIAPH1	EEC-subject4	Human	Endometrium	EEC	1.95e-07	3.32e-01	-0.2571
1729	DIAPH1	EEC-subject5	Human	Endometrium	EEC	5.59e-08	3.60e-01	-0.249
1729	DIAPH1	GSM6177620_NYU_UCEC1_lib1_lib1	Human	Endometrium	EEC	5.49e-08	1.62e-01	-0.1869
1729	DIAPH1	GSM6177620_NYU_UCEC1_lib2_lib2	Human	Endometrium	EEC	2.41e-09	2.17e-01	-0.1875
1729	DIAPH1	GSM6177620_NYU_UCEC1_lib3_lib3	Human	Endometrium	EEC	4.90e-13	1.77e-01	-0.1883
1729	DIAPH1	GSM6177621_NYU_UCEC2_lib1_lib1	Human	Endometrium	EEC	1.32e-07	1.20e-01	-0.1934
1729	DIAPH1	GSM6177622_NYU_UCEC3_lib1_lib1	Human	Endometrium	EEC	2.04e-13	1.15e-01	-0.1917
1729	DIAPH1	GSM6177622_NYU_UCEC3_lib2_lib2	Human	Endometrium	EEC	7.72e-14	9.01e-02	-0.1916
1729	DIAPH1	LZE4T	Human	Esophagus	ESCC	5.01e-13	3.14e-02	0.0811
1729	DIAPH1	LZE7T	Human	Esophagus	ESCC	2.54e-02	5.60e-02	0.0667
1729	DIAPH1	LZE20T	Human	Esophagus	ESCC	3.79e-03	1.51e-01	0.0662
1729	DIAPH1	LZE22D1	Human	Esophagus	HGIN	6.87e-03	4.53e-02	0.0595

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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
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:002260415	Endometrium	AEH	regulation of cell morphogenesis	79/2100	309/18723	1.04e-12	2.24e-10	79
GO:000701516	Endometrium	AEH	actin filament organization	98/2100	442/18723	1.99e-11	2.98e-09	98
GO:005125816	Endometrium	AEH	protein polymerization	62/2100	297/18723	9.04e-07	3.19e-05	62
GO:005165116	Endometrium	AEH	maintenance of location in cell	44/2100	214/18723	4.84e-05	7.94e-04	44
GO:000815410	Endometrium	AEH	actin polymerization or depolymerization	44/2100	218/18723	7.64e-05	1.15e-03	44
GO:00083609	Endometrium	AEH	regulation of cell shape	34/2100	154/18723	7.85e-05	1.18e-03	34
GO:005123510	Endometrium	AEH	maintenance of location	60/2100	327/18723	8.19e-05	1.22e-03	60
GO:003004110	Endometrium	AEH	actin filament polymerization	39/2100	191/18723	1.47e-04	1.96e-03	39
GO:00109597	Endometrium	AEH	regulation of metal ion transport	66/2100	406/18723	1.24e-03	1.07e-02	66
GO:19040623	Endometrium	AEH	regulation of cation transmembrane transport	55/2100	357/18723	9.18e-03	4.96e-02	55
GO:002260416	Endometrium	EEC	regulation of cell morphogenesis	78/2168	309/18723	1.45e-11	2.28e-09	78
GO:000701517	Endometrium	EEC	actin filament organization	95/2168	442/18723	1.31e-09	1.09e-07	95
GO:005125817	Endometrium	EEC	protein polymerization	63/2168	297/18723	1.24e-06	4.07e-05	63
GO:005123515	Endometrium	EEC	maintenance of location	62/2168	327/18723	5.92e-05	9.13e-04	62
GO:005165117	Endometrium	EEC	maintenance of location in cell	44/2168	214/18723	1.02e-04	1.41e-03	44
GO:000836014	Endometrium	EEC	regulation of cell shape	34/2168	154/18723	1.47e-04	1.87e-03	34
GO:000815415	Endometrium	EEC	actin polymerization or depolymerization	44/2168	218/18723	1.59e-04	2.00e-03	44
GO:003004115	Endometrium	EEC	actin filament polymerization	39/2168	191/18723	2.85e-04	3.22e-03	39
GO:001095914	Endometrium	EEC	regulation of metal ion transport	70/2168	406/18723	4.12e-04	4.35e-03	70
GO:005165126	Esophagus	HGIN	maintenance of location in cell	53/2587	214/18723	1.22e-05	3.45e-04	53

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0513126	Endometrium	AEH	Shigellosis	78/1197	247/8465	9.23e-13	2.00e-11	1.46e-11	78
hsa0451015	Endometrium	AEH	Focal adhesion	58/1197	203/8465	4.99e-08	7.37e-07	5.39e-07	58
hsa049337	Endometrium	AEH	AGE-RAGE signaling pathway in diabetic complications	28/1197	100/8465	2.11e-04	1.80e-03	1.32e-03	28
hsa0481018	Endometrium	AEH	Regulation of actin cytoskeleton	50/1197	229/8465	9.08e-04	5.78e-03	4.23e-03	50
hsa05131111	Endometrium	AEH	Shigellosis	78/1197	247/8465	9.23e-13	2.00e-11	1.46e-11	78
hsa0451016	Endometrium	AEH	Focal adhesion	58/1197	203/8465	4.99e-08	7.37e-07	5.39e-07	58
hsa0493314	Endometrium	AEH	AGE-RAGE signaling pathway in diabetic complications	28/1197	100/8465	2.11e-04	1.80e-03	1.32e-03	28
hsa0481019	Endometrium	AEH	Regulation of actin cytoskeleton	50/1197	229/8465	9.08e-04	5.78e-03	4.23e-03	50
hsa0513127	Endometrium	EEC	Shigellosis	79/1237	247/8465	1.80e-12	3.95e-11	2.95e-11	79
hsa0451024	Endometrium	EEC	Focal adhesion	58/1237	203/8465	1.61e-07	2.30e-06	1.71e-06	58
hsa0493321	Endometrium	EEC	AGE-RAGE signaling pathway in diabetic complications	28/1237	100/8465	3.68e-04	3.03e-03	2.26e-03	28
hsa0481024	Endometrium	EEC	Regulation of actin cytoskeleton	49/1237	229/8465	3.20e-03	1.78e-02	1.33e-02	49
hsa0513136	Endometrium	EEC	Shigellosis	79/1237	247/8465	1.80e-12	3.95e-11	2.95e-11	79
hsa0451034	Endometrium	EEC	Focal adhesion	58/1237	203/8465	1.61e-07	2.30e-06	1.71e-06	58
hsa0493331	Endometrium	EEC	AGE-RAGE signaling pathway in diabetic complications	28/1237	100/8465	3.68e-04	3.03e-03	2.26e-03	28
hsa0481034	Endometrium	EEC	Regulation of actin cytoskeleton	49/1237	229/8465	3.20e-03	1.78e-02	1.33e-02	49
hsa0513139	Esophagus	HGIN	Shigellosis	71/1383	247/8465	4.89e-07	7.98e-06	6.34e-06	71
hsa05131114	Esophagus	HGIN	Shigellosis	71/1383	247/8465	4.89e-07	7.98e-06	6.34e-06	71
hsa05131211	Esophagus	ESCC	Shigellosis	176/4205	247/8465	2.27e-12	4.01e-11	2.05e-11	176
hsa0493310	Esophagus	ESCC	AGE-RAGE signaling pathway in diabetic complications	72/4205	100/8465	4.15e-06	2.28e-05	1.17e-05	72

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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

DIAPH1

SNV

Missense_Mutation

c.791N>T

p.Ser264Phe

p.S264F

O60610

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-A7-A56D-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

DIAPH1

SNV

Missense_Mutation

rs201927388

c.890N>T

p.Pro297Leu

p.P297L

O60610

protein_coding

deleterious(0.01)

probably_damaging(1)

TCGA-A8-A06P-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unspecific

DIAPH1

SNV

Missense_Mutation

c.758N>T

p.Pro253Leu

p.P253L

O60610

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-BH-A0HF-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

DIAPH1

SNV

Missense_Mutation

c.512N>T

p.Ser171Phe

p.S171F

O60610

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-BH-A0HF-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

DIAPH1

SNV

Missense_Mutation

c.2218C>G

p.Pro740Ala

p.P740A

O60610

protein_coding

tolerated(0.11)

probably_damaging(0.953)

TCGA-D8-A1XW-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin+cyclophosphamide

DIAPH1

SNV

Missense_Mutation

c.675N>A

p.Met225Ile

p.M225I

O60610

protein_coding

deleterious(0)

probably_damaging(0.985)

TCGA-E2-A150-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

DIAPH1

SNV

Missense_Mutation

c.770N>G

p.Ile257Ser

p.I257S

O60610

protein_coding

deleterious(0)

probably_damaging(0.989)

TCGA-E2-A1IG-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cyclophosphamide

DIAPH1

SNV

Missense_Mutation

novel

c.3676N>T

p.Gly1226Trp

p.G1226W

O60610

protein_coding

deleterious(0)

probably_damaging(0.977)

TCGA-OL-A6VO-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

taxotere

DIAPH1

deletion

In_Frame_Del

c.3584_3592delAGACAGGTG

p.Glu1195_Gly1197del

p.E1195_G1197del

O60610

protein_coding

TCGA-A2-A0YC-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

arimidex

DIAPH1

SNV

Missense_Mutation

c.392C>T

p.Thr131Ile

p.T131I

O60610

protein_coding

deleterious(0)

probably_damaging(0.997)

TCGA-C5-A2LX-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

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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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