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: DIAPH2

Gene summary for DIAPH2

Gene summary.

Gene information	Species	Human
	Gene symbol	DIAPH2
	Gene ID	1730
	Gene name	diaphanous related formin 2
	Gene Alias	DIA
	Cytomap	Xq21.33
	Gene Type	protein-coding
	GO ID	GO:0000003
	UniProtAcc	O60879

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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
1730	DIAPH2	CA_HPV_3	Human	Cervix	CC	2.56e-05	1.22e-01	0.0414
1730	DIAPH2	HSIL_HPV_2	Human	Cervix	HSIL_HPV	1.28e-02	1.65e-01	0.0208
1730	DIAPH2	N_HPV_2	Human	Cervix	N_HPV	2.07e-04	1.81e-01	-0.0131
1730	DIAPH2	CCI_3	Human	Cervix	CC	2.42e-04	5.87e-01	0.516
1730	DIAPH2	Tumor	Human	Cervix	CC	8.11e-04	-1.34e-01	0.1241
1730	DIAPH2	sample3	Human	Cervix	CC	3.83e-04	-1.34e-01	0.1387
1730	DIAPH2	T3	Human	Cervix	CC	1.72e-03	-1.34e-01	0.1389
1730	DIAPH2	HTA11_3410_2000001011	Human	Colorectum	AD	5.71e-34	-7.44e-01	0.0155
1730	DIAPH2	HTA11_2951_2000001011	Human	Colorectum	AD	5.57e-05	-6.83e-01	0.0216
1730	DIAPH2	HTA11_347_2000001011	Human	Colorectum	AD	5.89e-10	5.94e-01	-0.1954
1730	DIAPH2	HTA11_3361_2000001011	Human	Colorectum	AD	2.76e-17	-6.45e-01	-0.1207
1730	DIAPH2	HTA11_5212_2000001011	Human	Colorectum	AD	2.82e-17	-8.96e-01	-0.2061
1730	DIAPH2	HTA11_5216_2000001011	Human	Colorectum	SER	3.20e-17	-7.20e-01	-0.1462
1730	DIAPH2	HTA11_9341_2000001011	Human	Colorectum	SER	2.85e-03	-6.13e-01	-0.00410000000000005
1730	DIAPH2	HTA11_866_3004761011	Human	Colorectum	AD	9.10e-38	-7.60e-01	0.096
1730	DIAPH2	HTA11_9408_2000001011	Human	Colorectum	AD	1.90e-03	-7.93e-01	0.0451
1730	DIAPH2	HTA11_8622_2000001021	Human	Colorectum	SER	2.24e-14	-9.72e-01	0.0528
1730	DIAPH2	HTA11_10711_2000001011	Human	Colorectum	AD	3.74e-03	-3.87e-01	0.0338
1730	DIAPH2	HTA11_7696_3000711011	Human	Colorectum	AD	4.18e-09	-4.26e-01	0.0674
1730	DIAPH2	HTA11_11156_2000001011	Human	Colorectum	AD	8.80e-06	-7.70e-01	0.0397

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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
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:000701515	Cervix	HSIL_HPV	actin filament organization	43/737	442/18723	4.77e-08	3.59e-06	43
GO:000701525	Cervix	N_HPV	actin filament organization	29/534	442/18723	3.00e-05	8.02e-04	29
GO:0007015	Colorectum	AD	actin filament organization	167/3918	442/18723	1.65e-16	7.94e-14	167
GO:00070151	Colorectum	SER	actin filament organization	134/2897	442/18723	1.39e-15	5.70e-13	134
GO:00070152	Colorectum	MSS	actin filament organization	146/3467	442/18723	1.16e-13	2.67e-11	146
GO:00070153	Colorectum	MSI-H	actin filament organization	50/1319	442/18723	6.19e-04	1.21e-02	50
GO:00070154	Colorectum	FAP	actin filament organization	125/2622	442/18723	1.97e-15	3.03e-12	125
GO:00070155	Colorectum	CRC	actin filament organization	104/2078	442/18723	4.75e-14	7.12e-11	104
GO:000701516	Endometrium	AEH	actin filament organization	98/2100	442/18723	1.99e-11	2.98e-09	98
GO:000701517	Endometrium	EEC	actin filament organization	95/2168	442/18723	1.31e-09	1.09e-07	95
GO:000701527	Esophagus	ESCC	actin filament organization	259/8552	442/18723	2.37e-08	4.50e-07	259
GO:00070157	Liver	NAFLD	actin filament organization	78/1882	442/18723	5.44e-07	3.21e-05	78
GO:000701512	Liver	Cirrhotic	actin filament organization	171/4634	442/18723	3.93e-11	2.30e-09	171
GO:000701522	Liver	HCC	actin filament organization	252/7958	442/18723	3.83e-10	1.25e-08	252
GO:00070158	Lung	IAC	actin filament organization	92/2061	442/18723	1.01e-09	1.93e-07	92
GO:000701513	Lung	AIS	actin filament organization	88/1849	442/18723	1.02e-10	3.13e-08	88
GO:000701523	Lung	AAH	actin filament organization	37/613	442/18723	1.88e-07	9.56e-05	37
GO:000701533	Lung	MIAC	actin filament organization	50/967	442/18723	1.64e-07	3.81e-05	50
GO:000701520	Oral cavity	OSCC	actin filament organization	230/7305	442/18723	1.37e-08	2.77e-07	230

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0481016	Cervix	CC	Regulation of actin cytoskeleton	64/1267	229/8465	2.24e-07	2.59e-06	1.53e-06	64
hsa0481017	Cervix	CC	Regulation of actin cytoskeleton	64/1267	229/8465	2.24e-07	2.59e-06	1.53e-06	64
hsa04810	Colorectum	AD	Regulation of actin cytoskeleton	75/2092	229/8465	3.36e-03	1.76e-02	1.12e-02	75
hsa048101	Colorectum	AD	Regulation of actin cytoskeleton	75/2092	229/8465	3.36e-03	1.76e-02	1.12e-02	75
hsa048102	Colorectum	SER	Regulation of actin cytoskeleton	60/1580	229/8465	2.74e-03	2.02e-02	1.47e-02	60
hsa048103	Colorectum	SER	Regulation of actin cytoskeleton	60/1580	229/8465	2.74e-03	2.02e-02	1.47e-02	60
hsa048104	Colorectum	MSS	Regulation of actin cytoskeleton	68/1875	229/8465	4.27e-03	1.86e-02	1.14e-02	68
hsa048105	Colorectum	MSS	Regulation of actin cytoskeleton	68/1875	229/8465	4.27e-03	1.86e-02	1.14e-02	68
hsa048106	Colorectum	FAP	Regulation of actin cytoskeleton	65/1404	229/8465	4.07e-06	5.91e-05	3.59e-05	65
hsa048107	Colorectum	FAP	Regulation of actin cytoskeleton	65/1404	229/8465	4.07e-06	5.91e-05	3.59e-05	65
hsa048108	Colorectum	CRC	Regulation of actin cytoskeleton	52/1091	229/8465	2.34e-05	5.57e-04	3.78e-04	52
hsa048109	Colorectum	CRC	Regulation of actin cytoskeleton	52/1091	229/8465	2.34e-05	5.57e-04	3.78e-04	52
hsa0481018	Endometrium	AEH	Regulation of actin cytoskeleton	50/1197	229/8465	9.08e-04	5.78e-03	4.23e-03	50
hsa0481019	Endometrium	AEH	Regulation of actin cytoskeleton	50/1197	229/8465	9.08e-04	5.78e-03	4.23e-03	50
hsa0481024	Endometrium	EEC	Regulation of actin cytoskeleton	49/1237	229/8465	3.20e-03	1.78e-02	1.33e-02	49
hsa0481034	Endometrium	EEC	Regulation of actin cytoskeleton	49/1237	229/8465	3.20e-03	1.78e-02	1.33e-02	49
hsa0481028	Esophagus	ESCC	Regulation of actin cytoskeleton	133/4205	229/8465	5.94e-03	1.48e-02	7.56e-03	133
hsa04810112	Esophagus	ESCC	Regulation of actin cytoskeleton	133/4205	229/8465	5.94e-03	1.48e-02	7.56e-03	133
hsa0481010	Liver	NAFLD	Regulation of actin cytoskeleton	50/1043	229/8465	3.01e-05	7.59e-04	6.11e-04	50
hsa0481011	Liver	NAFLD	Regulation of actin cytoskeleton	50/1043	229/8465	3.01e-05	7.59e-04	6.11e-04	50

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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

DIAPH2

SNV

Missense_Mutation

novel

c.1496N>G

p.Glu499Gly

p.E499G

O60879

protein_coding

deleterious(0)

probably_damaging(0.968)

TCGA-A2-A3XT-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cyclophosphamide

DIAPH2

SNV

Missense_Mutation

novel

c.877A>G

p.Lys293Glu

p.K293E

O60879

protein_coding

tolerated(0.35)

benign(0.429)

TCGA-A8-A094-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

DIAPH2

SNV

Missense_Mutation

novel

c.157G>T

p.Asp53Tyr

p.D53Y

O60879

protein_coding

deleterious(0.01)

probably_damaging(0.997)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

DIAPH2

SNV

Missense_Mutation

c.2875N>C

p.Glu959Gln

p.E959Q

O60879

protein_coding

tolerated(0.13)

benign(0.336)

TCGA-AR-A24H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

tamoxiphen

DIAPH2

SNV

Missense_Mutation

c.1837N>T

p.Pro613Ser

p.P613S

O60879

protein_coding

tolerated(0.33)

benign(0.001)

TCGA-AR-A2LE-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

tamoxiphen

DIAPH2

SNV

Missense_Mutation

c.218N>G

p.Leu73Arg

p.L73R

O60879

protein_coding

tolerated(0.35)

possibly_damaging(0.658)

TCGA-BH-A0AY-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

DIAPH2

SNV

Missense_Mutation

novel

c.2221G>C

p.Asp741His

p.D741H

O60879

protein_coding

deleterious(0.05)

benign(0.309)

TCGA-BH-A0DZ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

docetaxel

DIAPH2

SNV

Missense_Mutation

c.3248G>A

p.Arg1083Lys

p.R1083K

O60879

protein_coding

tolerated(0.16)

benign(0.039)

TCGA-BH-A0HF-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

DIAPH2

SNV

Missense_Mutation

rs775206145

c.2800N>T

p.Pro934Ser

p.P934S

O60879

protein_coding

tolerated(0.07)

possibly_damaging(0.565)

TCGA-D8-A1J8-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

nolvadex

DIAPH2

SNV

Missense_Mutation

c.1040N>A

p.Ile347Lys

p.I347K

O60879

protein_coding

deleterious(0)

probably_damaging(0.986)

TCGA-D8-A1XM-01

Breast

breast invasive carcinoma

Female

<65

I/II

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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