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: SSH2

Gene summary for SSH2

Gene summary.

Gene information	Species	Human
	Gene symbol	SSH2
	Gene ID	85464
	Gene name	slingshot protein phosphatase 2
	Gene Alias	SSH-2
	Cytomap	17q11.2
	Gene Type	protein-coding
	GO ID	GO:0006464
	UniProtAcc	B4DK64

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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
85464	SSH2	CCI_1	Human	Cervix	CC	8.18e-19	1.35e+00	0.528
85464	SSH2	CCI_2	Human	Cervix	CC	2.65e-03	5.11e-01	0.5249
85464	SSH2	CCI_3	Human	Cervix	CC	1.26e-22	1.11e+00	0.516
85464	SSH2	CCII_1	Human	Cervix	CC	1.79e-08	4.03e-01	0.3249
85464	SSH2	HTA11_3410_2000001011	Human	Colorectum	AD	5.09e-07	-4.88e-01	0.0155
85464	SSH2	HTA11_1938_2000001011	Human	Colorectum	AD	1.84e-02	3.57e-01	-0.0811
85464	SSH2	HTA11_347_2000001011	Human	Colorectum	AD	1.83e-14	6.70e-01	-0.1954
85464	SSH2	HTA11_411_2000001011	Human	Colorectum	SER	5.04e-12	8.38e-01	-0.2602
85464	SSH2	HTA11_7862_2000001011	Human	Colorectum	AD	2.33e-02	-4.91e-01	-0.0179
85464	SSH2	HTA11_866_3004761011	Human	Colorectum	AD	4.89e-03	-4.11e-01	0.096
85464	SSH2	HTA11_99999970781_79442	Human	Colorectum	MSS	2.32e-22	-6.65e-01	0.294
85464	SSH2	HTA11_99999974143_84620	Human	Colorectum	MSS	2.08e-03	-3.41e-01	0.3005
85464	SSH2	A001-C-207	Human	Colorectum	FAP	1.17e-02	-3.17e-01	0.1278
85464	SSH2	A015-C-203	Human	Colorectum	FAP	3.55e-33	-5.84e-01	-0.1294
85464	SSH2	A015-C-204	Human	Colorectum	FAP	1.76e-09	-5.28e-01	-0.0228
85464	SSH2	A014-C-040	Human	Colorectum	FAP	2.98e-05	-5.21e-01	-0.1184
85464	SSH2	A002-C-201	Human	Colorectum	FAP	1.12e-10	-4.03e-01	0.0324
85464	SSH2	A001-C-119	Human	Colorectum	FAP	2.77e-08	-5.72e-01	-0.1557
85464	SSH2	A001-C-108	Human	Colorectum	FAP	3.73e-16	-4.68e-01	-0.0272
85464	SSH2	A002-C-205	Human	Colorectum	FAP	2.24e-32	-6.98e-01	-0.1236

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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
Prostate		BPH: Benign Prostatic Hyperplasia
Skin		AK: Actinic keratosis
		cSCC: Cutaneous squamous cell carcinoma
		SCCIS:squamous cell carcinoma in situ

∗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:003083320	Esophagus	ESCC	regulation of actin filament polymerization	103/8552	172/18723	1.19e-04	8.15e-04	103
GO:0031333110	Esophagus	ESCC	negative regulation of protein-containing complex assembly	86/8552	141/18723	1.74e-04	1.14e-03	86
GO:00070157	Liver	NAFLD	actin filament organization	78/1882	442/18723	5.44e-07	3.21e-05	78
GO:19029037	Liver	NAFLD	regulation of supramolecular fiber organization	66/1882	383/18723	8.97e-06	2.96e-04	66
GO:00163115	Liver	NAFLD	dephosphorylation	69/1882	417/18723	2.27e-05	6.23e-04	69
GO:00329707	Liver	NAFLD	regulation of actin filament-based process	66/1882	397/18723	2.92e-05	7.72e-04	66
GO:00064706	Liver	NAFLD	protein dephosphorylation	50/1882	281/18723	4.53e-05	1.09e-03	50
GO:00329567	Liver	NAFLD	regulation of actin cytoskeleton organization	60/1882	358/18723	5.20e-05	1.20e-03	60
GO:01100537	Liver	NAFLD	regulation of actin filament organization	49/1882	278/18723	6.88e-05	1.46e-03	49
GO:00432547	Liver	NAFLD	regulation of protein-containing complex assembly	66/1882	428/18723	2.83e-04	4.53e-03	66
GO:00512587	Liver	NAFLD	protein polymerization	49/1882	297/18723	3.54e-04	5.36e-03	49
GO:00322717	Liver	NAFLD	regulation of protein polymerization	38/1882	233/18723	1.90e-03	1.93e-02	38
GO:00081547	Liver	NAFLD	actin polymerization or depolymerization	36/1882	218/18723	1.98e-03	1.98e-02	36
GO:00325356	Liver	NAFLD	regulation of cellular component size	55/1882	383/18723	4.31e-03	3.55e-02	55
GO:00300417	Liver	NAFLD	actin filament polymerization	31/1882	191/18723	5.06e-03	3.96e-02	31
GO:00308337	Liver	NAFLD	regulation of actin filament polymerization	28/1882	172/18723	7.15e-03	4.96e-02	28
GO:004325412	Liver	Cirrhotic	regulation of protein-containing complex assembly	169/4634	428/18723	7.40e-12	4.99e-10	169
GO:000701512	Liver	Cirrhotic	actin filament organization	171/4634	442/18723	3.93e-11	2.30e-09	171
GO:190290312	Liver	Cirrhotic	regulation of supramolecular fiber organization	148/4634	383/18723	8.85e-10	4.08e-08	148
GO:003297012	Liver	Cirrhotic	regulation of actin filament-based process	152/4634	397/18723	1.12e-09	5.00e-08	152

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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
hsa043609	Cervix	CC	Axon guidance	47/1267	182/8465	8.13e-05	5.38e-04	3.18e-04	47
hsa0481017	Cervix	CC	Regulation of actin cytoskeleton	64/1267	229/8465	2.24e-07	2.59e-06	1.53e-06	64
hsa0436012	Cervix	CC	Axon guidance	47/1267	182/8465	8.13e-05	5.38e-04	3.18e-04	47
hsa04810	Colorectum	AD	Regulation of actin cytoskeleton	75/2092	229/8465	3.36e-03	1.76e-02	1.12e-02	75
hsa04360	Colorectum	AD	Axon guidance	61/2092	182/8465	4.36e-03	2.17e-02	1.38e-02	61
hsa048101	Colorectum	AD	Regulation of actin cytoskeleton	75/2092	229/8465	3.36e-03	1.76e-02	1.12e-02	75
hsa043601	Colorectum	AD	Axon guidance	61/2092	182/8465	4.36e-03	2.17e-02	1.38e-02	61
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
hsa043602	Colorectum	MSS	Axon guidance	54/1875	182/8465	1.03e-02	3.69e-02	2.26e-02	54
hsa048105	Colorectum	MSS	Regulation of actin cytoskeleton	68/1875	229/8465	4.27e-03	1.86e-02	1.14e-02	68
hsa043603	Colorectum	MSS	Axon guidance	54/1875	182/8465	1.03e-02	3.69e-02	2.26e-02	54
hsa048106	Colorectum	FAP	Regulation of actin cytoskeleton	65/1404	229/8465	4.07e-06	5.91e-05	3.59e-05	65
hsa043604	Colorectum	FAP	Axon guidance	47/1404	182/8465	9.09e-04	5.20e-03	3.16e-03	47
hsa048107	Colorectum	FAP	Regulation of actin cytoskeleton	65/1404	229/8465	4.07e-06	5.91e-05	3.59e-05	65
hsa043605	Colorectum	FAP	Axon guidance	47/1404	182/8465	9.09e-04	5.20e-03	3.16e-03	47
hsa048108	Colorectum	CRC	Regulation of actin cytoskeleton	52/1091	229/8465	2.34e-05	5.57e-04	3.78e-04	52
hsa043606	Colorectum	CRC	Axon guidance	43/1091	182/8465	4.38e-05	8.70e-04	5.90e-04	43

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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

SSH2

SNV

Missense_Mutation

novel

c.4126N>A

p.Glu1376Lys

p.E1376K

protein_coding

deleterious_low_confidence(0)

possibly_damaging(0.737)

TCGA-5L-AAT1-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Hormone Therapy

letrozol

SSH2

SNV

Missense_Mutation

novel

c.343N>T

p.Asp115Tyr

p.D115Y

protein_coding

deleterious(0)

probably_damaging(0.997)

TCGA-A2-A4S1-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SSH2

SNV

Missense_Mutation

c.3790N>C

p.Glu1264Gln

p.E1264Q

protein_coding

deleterious(0.01)

possibly_damaging(0.801)

TCGA-AN-A0XW-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

SSH2

SNV

Missense_Mutation

c.2452N>C

p.Glu818Gln

p.E818Q

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.997)

TCGA-AO-A03V-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

fluorouracil

SSH2

SNV

Missense_Mutation

c.3183G>C

p.Glu1061Asp

p.E1061D

protein_coding

tolerated_low_confidence(0.54)

benign(0.074)

TCGA-C8-A275-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

SSH2

SNV

Missense_Mutation

novel

c.989N>A

p.Gly330Asp

p.G330D

protein_coding

deleterious(0)

probably_damaging(0.997)

TCGA-E9-A3Q9-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Chemotherapy

cyclophosphane

SSH2

insertion

Frame_Shift_Ins

novel

c.3966_3967insTTTTACTGTTTCT

p.Asp1323PhefsTer5

p.D1323Ffs*5

protein_coding

TCGA-A8-A0A4-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

tamoxiphen

SSH2

insertion

In_Frame_Ins

novel

c.3964_3965insTATTTTGGT

p.Thr1322delinsIlePheTrpSer

p.T1322delinsIFWS

protein_coding

TCGA-A8-A0A4-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

tamoxiphen

SSH2

insertion

Frame_Shift_Ins

novel

c.2813_2814insGGAGGCCTTCCCGTGCTACAGACCCAGGGACTGCAGTGTGCATG

p.Gly939GlufsTer34

p.G939Efs*34

protein_coding

TCGA-B6-A0I5-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

SSH2

deletion

Frame_Shift_Del

novel

c.1929delG

p.Thr644HisfsTer4

p.T644Hfs*4

protein_coding

TCGA-EW-A2FV-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

docetaxel

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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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