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: CD9

Gene summary for CD9

Gene summary.

Gene information	Species	Human
	Gene symbol	CD9
	Gene ID	928
	Gene name	CD9 molecule
	Gene Alias	BTCC-1
	Cytomap	12p13.31
	Gene Type	protein-coding
	GO ID	GO:0000003
	UniProtAcc	A6NNI4

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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
928	CD9	GSM4909282	Human	Breast	IDC	1.16e-38	5.88e-01	-0.0288
928	CD9	GSM4909285	Human	Breast	IDC	1.71e-36	5.48e-01	0.21
928	CD9	GSM4909286	Human	Breast	IDC	1.31e-05	-6.95e-02	0.1081
928	CD9	GSM4909290	Human	Breast	IDC	2.83e-20	5.13e-01	0.2096
928	CD9	GSM4909292	Human	Breast	IDC	4.06e-03	-7.59e-01	0.1236
928	CD9	GSM4909293	Human	Breast	IDC	4.17e-48	6.22e-01	0.1581
928	CD9	GSM4909294	Human	Breast	IDC	1.48e-21	-7.65e-02	0.2022
928	CD9	GSM4909296	Human	Breast	IDC	8.98e-23	3.25e-01	0.1524
928	CD9	GSM4909297	Human	Breast	IDC	2.63e-21	-1.49e-02	0.1517
928	CD9	GSM4909298	Human	Breast	IDC	4.67e-02	1.04e-01	0.1551
928	CD9	GSM4909299	Human	Breast	IDC	2.30e-02	2.52e-01	0.035
928	CD9	GSM4909300	Human	Breast	IDC	1.20e-02	3.23e-01	0.0334
928	CD9	GSM4909301	Human	Breast	IDC	8.33e-05	-3.94e-01	0.1577
928	CD9	GSM4909304	Human	Breast	IDC	1.97e-21	4.41e-01	0.1636
928	CD9	GSM4909305	Human	Breast	IDC	4.38e-15	4.55e-01	0.0436
928	CD9	GSM4909306	Human	Breast	IDC	7.13e-50	6.97e-01	0.1564
928	CD9	GSM4909309	Human	Breast	IDC	2.04e-14	3.33e-01	0.0483
928	CD9	GSM4909311	Human	Breast	IDC	2.76e-41	-1.76e-01	0.1534
928	CD9	GSM4909312	Human	Breast	IDC	1.47e-13	2.46e-01	0.1552
928	CD9	GSM4909313	Human	Breast	IDC	2.98e-08	2.16e-01	0.0391

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Breast		IDC: Invasive ductal carcinoma
		DCIS: Ductal carcinoma in situ
		Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers
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
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:00975297	Breast	Precancer	myeloid leukocyte migration	34/1080	220/18723	1.42e-07	7.82e-06	34
GO:00509006	Breast	Precancer	leukocyte migration	47/1080	369/18723	2.82e-07	1.39e-05	47
GO:00341099	Breast	Precancer	homotypic cell-cell adhesion	18/1080	90/18723	3.15e-06	1.03e-04	18
GO:00975307	Breast	Precancer	granulocyte migration	24/1080	148/18723	4.04e-06	1.26e-04	24
GO:00420609	Breast	Precancer	wound healing	48/1080	422/18723	5.48e-06	1.63e-04	48
GO:19902665	Breast	Precancer	neutrophil migration	20/1080	122/18723	2.13e-05	4.99e-04	20
GO:00026856	Breast	Precancer	regulation of leukocyte migration	27/1080	210/18723	7.93e-05	1.54e-03	27
GO:00508789	Breast	Precancer	regulation of body fluid levels	40/1080	379/18723	1.68e-04	2.77e-03	40
GO:00310995	Breast	Precancer	regeneration	25/1080	198/18723	1.91e-04	3.06e-03	25
GO:00224079	Breast	Precancer	regulation of cell-cell adhesion	45/1080	448/18723	2.12e-04	3.30e-03	45
GO:19055173	Breast	Precancer	macrophage migration	11/1080	55/18723	2.57e-04	3.83e-03	11
GO:00420633	Breast	Precancer	gliogenesis	33/1080	301/18723	3.06e-04	4.40e-03	33
GO:0035036	Breast	Precancer	sperm-egg recognition	10/1080	48/18723	3.43e-04	4.81e-03	10
GO:00705278	Breast	Precancer	platelet aggregation	12/1080	67/18723	4.02e-04	5.43e-03	12
GO:00716744	Breast	Precancer	mononuclear cell migration	24/1080	196/18723	4.03e-04	5.44e-03	24
GO:0009988	Breast	Precancer	cell-cell recognition	12/1080	68/18723	4.63e-04	6.12e-03	12
GO:00026877	Breast	Precancer	positive regulation of leukocyte migration	18/1080	135/18723	7.60e-04	9.04e-03	18
GO:00068986	Breast	Precancer	receptor-mediated endocytosis	27/1080	244/18723	9.01e-04	1.03e-02	27
GO:00100013	Breast	Precancer	glial cell differentiation	25/1080	225/18723	1.29e-03	1.37e-02	25
GO:00316235	Breast	Precancer	receptor internalization	15/1080	113/18723	2.11e-03	2.00e-02	15

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa04640	Cervix	HSIL_HPV	Hematopoietic cell lineage	18/459	99/8465	4.97e-06	8.10e-05	6.54e-05	18
hsa046401	Cervix	HSIL_HPV	Hematopoietic cell lineage	18/459	99/8465	4.97e-06	8.10e-05	6.54e-05	18
hsa046402	Cervix	N_HPV	Hematopoietic cell lineage	13/349	99/8465	1.98e-04	1.74e-03	1.36e-03	13
hsa046403	Cervix	N_HPV	Hematopoietic cell lineage	13/349	99/8465	1.98e-04	1.74e-03	1.36e-03	13

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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
HLA-E	CD94:NKG2A	HLA-E_CD94:NKG2A	MHC-I	Breast	ADJ
HLA-E	CD94:NKG2C	HLA-E_CD94:NKG2C	MHC-I	Breast	ADJ
CD99	CD99	CD99_CD99	CD99	Breast	ADJ
HLA-E	CD94:NKG2A	HLA-E_CD94:NKG2A	MHC-I	Breast	DCIS
CD99	CD99	CD99_CD99	CD99	Breast	DCIS
HLA-E	CD94:NKG2A	HLA-E_CD94:NKG2A	MHC-I	Breast	Healthy
HLA-E	CD94:NKG2A	HLA-E_CD94:NKG2A	MHC-I	Breast	IDC
HLA-E	CD94:NKG2C	HLA-E_CD94:NKG2C	MHC-I	Breast	IDC
CD99	CD99	CD99_CD99	CD99	Breast	IDC
HLA-E	CD94:NKG2A	HLA-E_CD94:NKG2A	MHC-I	Breast	Precancer
CD99	CD99	CD99_CD99	CD99	Breast	Precancer
HLA-E	CD94:NKG2A	HLA-E_CD94:NKG2A	MHC-I	Cervix	ADJ
HLA-E	CD94:NKG2C	HLA-E_CD94:NKG2C	MHC-I	Cervix	ADJ
HLA-E	CD94:NKG2E	HLA-E_CD94:NKG2E	MHC-I	Cervix	ADJ
CD99	CD99	CD99_CD99	CD99	Cervix	ADJ
HLA-E	CD94:NKG2A	HLA-E_CD94:NKG2A	MHC-I	Cervix	CC
HLA-E	CD94:NKG2C	HLA-E_CD94:NKG2C	MHC-I	Cervix	CC
HLA-E	CD94:NKG2E	HLA-E_CD94:NKG2E	MHC-I	Cervix	CC
CD99	CD99	CD99_CD99	CD99	Cervix	CC
CD99	CD99L2	CD99_CD99L2	CD99	Cervix	CC

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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

CD9

SNV

Missense_Mutation

novel

c.361G>T

p.Val121Phe

p.V121F

P21926

protein_coding

deleterious(0.01)

possibly_damaging(0.649)

TCGA-A8-A07U-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Chemotherapy

5-fluorouracil

CD9

SNV

Missense_Mutation

c.8N>A

p.Val3Asp

p.V3D

P21926

protein_coding

deleterious(0.04)

possibly_damaging(0.723)

TCGA-AO-A124-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

CD9

SNV

Missense_Mutation

c.286C>A

p.Leu96Ile

p.L96I

P21926

protein_coding

deleterious(0.03)

probably_damaging(0.936)

TCGA-EW-A1P8-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

fluorouracil

CD9

insertion

Nonsense_Mutation

novel

c.481_482insCTCACTAACCAGGCTGGTCTTGAACTCCTGGTCTCAAG

p.Gln161ProfsTer3

p.Q161Pfs*3

P21926

protein_coding

TCGA-A2-A0CP-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

CD9

insertion

Nonsense_Mutation

novel

c.363_364insTCGAGGACCACGTTTGCTTTTTTTCCCTGAATCCA

p.Gln122SerfsTer10

p.Q122Sfs*10

P21926

protein_coding

TCGA-A8-A07U-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Chemotherapy

5-fluorouracil

CD9

SNV

Missense_Mutation

rs146304211

c.664N>T

p.Arg222Cys

p.R222C

P21926

protein_coding

deleterious(0)

probably_damaging(0.993)

TCGA-AA-A01R-01

Colorectum

colon adenocarcinoma

Male

<65

III/IV

Chemotherapy

5-fluorouracil

CD9

SNV

Missense_Mutation

rs777932393

c.679N>G

p.Met227Val

p.M227V

P21926

protein_coding

tolerated(0.94)

benign(0.001)

TCGA-AY-6197-01

Colorectum

colon adenocarcinoma

Male

<65

I/II

Unknown

CD9

SNV

Missense_Mutation

c.142N>C

p.Glu48Gln

p.E48Q

P21926

protein_coding

tolerated(0.1)

possibly_damaging(0.557)

TCGA-G4-6294-01

Colorectum

colon adenocarcinoma

Male

>=65

III/IV

Chemotherapy

fluorouracil

CD9

SNV

Missense_Mutation

novel

c.446N>T

p.Ala149Val

p.A149V

P21926

protein_coding

tolerated(0.18)

possibly_damaging(0.87)

TCGA-AJ-A3BH-01

Endometrium

uterine corpus endometrioid carcinoma

Female

Unknown

I/II

Unknown

CD9

SNV

Missense_Mutation

c.199N>A

p.Gly67Ser

p.G67S

P21926

protein_coding

deleterious(0.01)

probably_damaging(0.999)

TCGA-AP-A0LG-01

Endometrium

uterine corpus endometrioid 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
928	CD9	DRUGGABLE GENOME, EXTERNAL SIDE OF PLASMA MEMBRANE		PROPIONIBACTERIUM ACNES		15902693
928	CD9	DRUGGABLE GENOME, EXTERNAL SIDE OF PLASMA MEMBRANE		EOTAXIN		10704064
928	CD9	DRUGGABLE GENOME, EXTERNAL SIDE OF PLASMA MEMBRANE		TYROSINE KINASE INHIBITOR		7592610
928	CD9	DRUGGABLE GENOME, EXTERNAL SIDE OF PLASMA MEMBRANE		ANDROGENS		16128989
928	CD9	DRUGGABLE GENOME, EXTERNAL SIDE OF PLASMA MEMBRANE		INTERLEUKIN-16		16144798
928	CD9	DRUGGABLE GENOME, EXTERNAL SIDE OF PLASMA MEMBRANE		IL-5		10704064
928	CD9	DRUGGABLE GENOME, EXTERNAL SIDE OF PLASMA MEMBRANE		STEROID HORMONE		17126340
928	CD9	DRUGGABLE GENOME, EXTERNAL SIDE OF PLASMA MEMBRANE		LIF		11950938
928	CD9	DRUGGABLE GENOME, EXTERNAL SIDE OF PLASMA MEMBRANE		HERBIMYCIN A		7592610

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