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: CXCL12

Gene summary for CXCL12

Gene summary.

Gene information	Species	Human
	Gene symbol	CXCL12
	Gene ID	6387
	Gene name	C-X-C motif chemokine ligand 12
	Gene Alias	IRH
	Cytomap	10q11.21
	Gene Type	protein-coding
	GO ID	GO:0000902
	UniProtAcc	P48061

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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
6387	CXCL12	AEH-subject1	Human	Endometrium	AEH	1.98e-28	-4.98e-01	-0.3059
6387	CXCL12	AEH-subject2	Human	Endometrium	AEH	7.24e-25	-4.90e-01	-0.2525
6387	CXCL12	AEH-subject3	Human	Endometrium	AEH	2.34e-22	-4.71e-01	-0.2576
6387	CXCL12	AEH-subject4	Human	Endometrium	AEH	8.28e-16	-4.43e-01	-0.2657
6387	CXCL12	AEH-subject5	Human	Endometrium	AEH	6.25e-29	-5.04e-01	-0.2953
6387	CXCL12	EEC-subject1	Human	Endometrium	EEC	8.01e-32	-5.03e-01	-0.2682
6387	CXCL12	EEC-subject2	Human	Endometrium	EEC	8.75e-29	-5.07e-01	-0.2607
6387	CXCL12	EEC-subject3	Human	Endometrium	EEC	1.92e-32	-4.22e-01	-0.2525
6387	CXCL12	EEC-subject4	Human	Endometrium	EEC	2.64e-28	-4.98e-01	-0.2571
6387	CXCL12	EEC-subject5	Human	Endometrium	EEC	8.89e-30	-4.99e-01	-0.249
6387	CXCL12	GSM5276934	Human	Endometrium	EEC	2.99e-15	-4.04e-01	-0.0913
6387	CXCL12	GSM5276935	Human	Endometrium	EEC	4.05e-29	-5.04e-01	-0.123
6387	CXCL12	GSM5276937	Human	Endometrium	EEC	6.09e-10	-3.98e-01	-0.0897
6387	CXCL12	GSM6177620_NYU_UCEC1_lib1_lib1	Human	Endometrium	EEC	9.64e-24	-5.09e-01	-0.1869
6387	CXCL12	GSM6177620_NYU_UCEC1_lib2_lib2	Human	Endometrium	EEC	3.92e-21	-5.09e-01	-0.1875
6387	CXCL12	GSM6177620_NYU_UCEC1_lib3_lib3	Human	Endometrium	EEC	1.07e-21	-4.98e-01	-0.1883
6387	CXCL12	GSM6177621_NYU_UCEC2_lib1_lib1	Human	Endometrium	EEC	3.18e-32	-5.02e-01	-0.1934
6387	CXCL12	GSM6177622_NYU_UCEC3_lib1_lib1	Human	Endometrium	EEC	2.64e-31	-4.95e-01	-0.1917
6387	CXCL12	GSM6177622_NYU_UCEC3_lib2_lib2	Human	Endometrium	EEC	3.51e-30	-4.97e-01	-0.1916
6387	CXCL12	GSM6177623_NYU_UCEC3_Vis	Human	Endometrium	EEC	6.99e-04	-2.98e-01	-0.1269

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Endometrium		AEH: Atypical endometrial hyperplasia
		EEC: Endometrioid Cancer
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:009719316	Endometrium	AEH	intrinsic apoptotic signaling pathway	75/2100	288/18723	1.46e-12	2.83e-10	75
GO:200123316	Endometrium	AEH	regulation of apoptotic signaling pathway	86/2100	356/18723	2.97e-12	4.95e-10	86
GO:000701516	Endometrium	AEH	actin filament organization	98/2100	442/18723	1.99e-11	2.98e-09	98
GO:004578516	Endometrium	AEH	positive regulation of cell adhesion	96/2100	437/18723	5.50e-11	7.18e-09	96
GO:200124216	Endometrium	AEH	regulation of intrinsic apoptotic signaling pathway	49/2100	164/18723	6.39e-11	8.16e-09	49
GO:003297016	Endometrium	AEH	regulation of actin filament-based process	89/2100	397/18723	9.14e-11	1.10e-08	89
GO:190290316	Endometrium	AEH	regulation of supramolecular fiber organization	83/2100	383/18723	2.20e-09	1.78e-07	83
GO:003295616	Endometrium	AEH	regulation of actin cytoskeleton organization	77/2100	358/18723	1.18e-08	7.76e-07	77
GO:00160499	Endometrium	AEH	cell growth	93/2100	482/18723	1.00e-07	4.99e-06	93
GO:003253510	Endometrium	AEH	regulation of cellular component size	78/2100	383/18723	1.10e-07	5.29e-06	78
GO:011005316	Endometrium	AEH	regulation of actin filament organization	61/2100	278/18723	1.83e-07	8.11e-06	61
GO:00605607	Endometrium	AEH	developmental growth involved in morphogenesis	53/2100	234/18723	4.02e-07	1.67e-05	53
GO:00506738	Endometrium	AEH	epithelial cell proliferation	84/2100	437/18723	4.88e-07	1.94e-05	84
GO:00074098	Endometrium	AEH	axonogenesis	81/2100	418/18723	5.54e-07	2.12e-05	81
GO:00615648	Endometrium	AEH	axon development	88/2100	467/18723	6.39e-07	2.38e-05	88
GO:00506788	Endometrium	AEH	regulation of epithelial cell proliferation	73/2100	381/18723	3.04e-06	8.44e-05	73
GO:200123416	Endometrium	AEH	negative regulation of apoptotic signaling pathway	49/2100	224/18723	3.12e-06	8.58e-05	49
GO:00486757	Endometrium	AEH	axon extension	31/2100	120/18723	6.13e-06	1.50e-04	31
GO:00303364	Endometrium	AEH	negative regulation of cell migration	65/2100	344/18723	1.65e-05	3.42e-04	65
GO:00015589	Endometrium	AEH	regulation of cell growth	75/2100	414/18723	1.79e-05	3.65e-04	75

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0467026	Endometrium	AEH	Leukocyte transendothelial migration	37/1197	114/8465	4.51e-07	6.11e-06	4.47e-06	37
hsa0481018	Endometrium	AEH	Regulation of actin cytoskeleton	50/1197	229/8465	9.08e-04	5.78e-03	4.23e-03	50
hsa0532316	Endometrium	AEH	Rheumatoid arthritis	23/1197	93/8465	4.43e-03	2.46e-02	1.80e-02	23
hsa0436010	Endometrium	AEH	Axon guidance	39/1197	182/8465	4.47e-03	2.46e-02	1.80e-02	39
hsa0516320	Endometrium	AEH	Human cytomegalovirus infection	45/1197	225/8465	8.98e-03	4.56e-02	3.34e-02	45
hsa04670111	Endometrium	AEH	Leukocyte transendothelial migration	37/1197	114/8465	4.51e-07	6.11e-06	4.47e-06	37
hsa0481019	Endometrium	AEH	Regulation of actin cytoskeleton	50/1197	229/8465	9.08e-04	5.78e-03	4.23e-03	50
hsa0532317	Endometrium	AEH	Rheumatoid arthritis	23/1197	93/8465	4.43e-03	2.46e-02	1.80e-02	23
hsa0436013	Endometrium	AEH	Axon guidance	39/1197	182/8465	4.47e-03	2.46e-02	1.80e-02	39
hsa05163110	Endometrium	AEH	Human cytomegalovirus infection	45/1197	225/8465	8.98e-03	4.56e-02	3.34e-02	45
hsa0467027	Endometrium	EEC	Leukocyte transendothelial migration	36/1237	114/8465	2.97e-06	3.91e-05	2.91e-05	36
hsa0532323	Endometrium	EEC	Rheumatoid arthritis	24/1237	93/8465	3.14e-03	1.78e-02	1.33e-02	24
hsa0481024	Endometrium	EEC	Regulation of actin cytoskeleton	49/1237	229/8465	3.20e-03	1.78e-02	1.33e-02	49
hsa0516325	Endometrium	EEC	Human cytomegalovirus infection	47/1237	225/8465	6.17e-03	3.12e-02	2.33e-02	47
hsa0436022	Endometrium	EEC	Axon guidance	39/1237	182/8465	7.78e-03	3.66e-02	2.73e-02	39
hsa0467036	Endometrium	EEC	Leukocyte transendothelial migration	36/1237	114/8465	2.97e-06	3.91e-05	2.91e-05	36
hsa0532333	Endometrium	EEC	Rheumatoid arthritis	24/1237	93/8465	3.14e-03	1.78e-02	1.33e-02	24
hsa0481034	Endometrium	EEC	Regulation of actin cytoskeleton	49/1237	229/8465	3.20e-03	1.78e-02	1.33e-02	49
hsa0516335	Endometrium	EEC	Human cytomegalovirus infection	47/1237	225/8465	6.17e-03	3.12e-02	2.33e-02	47
hsa0436032	Endometrium	EEC	Axon guidance	39/1237	182/8465	7.78e-03	3.66e-02	2.73e-02	39

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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
CXCL12	CXCR4	CXCL12_CXCR4	CXCL	Breast	ADJ
CXCL12	ACKR3	CXCL12_ACKR3	CXCL	Breast	ADJ
CXCL12	CXCR4	CXCL12_CXCR4	CXCL	Breast	DCIS
CXCL12	ACKR3	CXCL12_ACKR3	CXCL	Breast	DCIS
CXCL12	CXCR4	CXCL12_CXCR4	CXCL	Breast	Healthy
CXCL12	ACKR3	CXCL12_ACKR3	CXCL	Breast	Healthy
CXCL12	CXCR4	CXCL12_CXCR4	CXCL	Breast	IDC
CXCL12	CXCR4	CXCL12_CXCR4	CXCL	Breast	Precancer
CXCL12	CXCR4	CXCL12_CXCR4	CXCL	Cervix	ADJ
CXCL12	ACKR3	CXCL12_ACKR3	CXCL	Cervix	ADJ
CXCL12	CXCR4	CXCL12_CXCR4	CXCL	Cervix	CC
CXCL12	ACKR3	CXCL12_ACKR3	CXCL	Cervix	CC
CXCL12	CXCR4	CXCL12_CXCR4	CXCL	Cervix	Healthy
CXCL12	CXCR4	CXCL12_CXCR4	CXCL	Cervix	Precancer
CXCL12	CXCR4	CXCL12_CXCR4	CXCL	CRC	AD
CXCL12	ACKR3	CXCL12_ACKR3	CXCL	CRC	AD
CXCL12	CXCR4	CXCL12_CXCR4	CXCL	CRC	ADJ
CXCL12	ACKR3	CXCL12_ACKR3	CXCL	CRC	ADJ
CXCL12	CXCR4	CXCL12_CXCR4	CXCL	CRC	MSI-H
CXCL12	ACKR3	CXCL12_ACKR3	CXCL	CRC	MSI-H

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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

CXCL12

insertion

Frame_Shift_Ins

novel

c.126_127insTGGAGAGGATTTGATTGCTCAGAAGTTCTAGT

p.Asn43TrpfsTer29

p.N43Wfs*29

P48061

protein_coding

TCGA-B6-A0IB-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

CXCL12

insertion

Frame_Shift_Ins

novel

c.124_125insGCTCAGGGAGTCT

p.Ala42GlyfsTer36

p.A42Gfs*36

P48061

protein_coding

TCGA-B6-A0IB-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

CXCL12

SNV

Missense_Mutation

c.223N>G

p.Lys75Glu

p.K75E

P48061

protein_coding

tolerated(0.56)

benign(0.084)

TCGA-AP-A059-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

CXCL12

SNV

Missense_Mutation

novel

c.224A>C

p.Lys75Thr

p.K75T

P48061

protein_coding

deleterious(0)

benign(0.198)

TCGA-AX-A06F-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

carboplatin

CXCL12

SNV

Missense_Mutation

rs371332557

c.98G>A

p.Arg33Gln

p.R33Q

P48061

protein_coding

deleterious(0.02)

probably_damaging(0.947)

TCGA-AX-A2HC-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

paclitaxel

CXCL12

SNV

Missense_Mutation

novel

c.299N>C

p.Val100Ala

p.V100A

P48061

protein_coding

tolerated_low_confidence(1)

possibly_damaging(0.737)

TCGA-AX-A2HD-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

III/IV

Unknown

CXCL12

SNV

Missense_Mutation

c.158N>T

p.Pro53Leu

p.P53L

P48061

protein_coding

deleterious(0)

possibly_damaging(0.541)

TCGA-B5-A11E-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

CXCL12

SNV

Missense_Mutation

c.212G>A

p.Cys71Tyr

p.C71Y

P48061

protein_coding

deleterious(0)

probably_damaging(0.991)

TCGA-D1-A103-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

CXCL12

SNV

Missense_Mutation

novel

c.174N>T

p.Gln58His

p.Q58H

P48061

protein_coding

tolerated(0.05)

benign(0.005)

TCGA-D1-A16X-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

CXCL12

SNV

Missense_Mutation

novel

c.106N>A

p.Glu36Lys

p.E36K

P48061

protein_coding

tolerated(0.19)

benign(0.32)

TCGA-EO-A3AV-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

carboplatin

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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
6387	CXCL12	DRUGGABLE GENOME, EXTERNAL SIDE OF PLASMA MEMBRANE, GROWTH FACTOR, KINASE		fludarabine	FLUDARABINE	27173875
6387	CXCL12	DRUGGABLE GENOME, EXTERNAL SIDE OF PLASMA MEMBRANE, GROWTH FACTOR, KINASE		REC-02
6387	CXCL12	DRUGGABLE GENOME, EXTERNAL SIDE OF PLASMA MEMBRANE, GROWTH FACTOR, KINASE		SDF-1
6387	CXCL12	DRUGGABLE GENOME, EXTERNAL SIDE OF PLASMA MEMBRANE, GROWTH FACTOR, KINASE		chlorambucil	CHLORAMBUCIL	27173875
6387	CXCL12	DRUGGABLE GENOME, EXTERNAL SIDE OF PLASMA MEMBRANE, GROWTH FACTOR, KINASE		vincristine	VINCRISTINE	27173875
6387	CXCL12	DRUGGABLE GENOME, EXTERNAL SIDE OF PLASMA MEMBRANE, GROWTH FACTOR, KINASE		rituximab	RITUXIMAB	27173875
6387	CXCL12	DRUGGABLE GENOME, EXTERNAL SIDE OF PLASMA MEMBRANE, GROWTH FACTOR, KINASE		NOX-A12
6387	CXCL12	DRUGGABLE GENOME, EXTERNAL SIDE OF PLASMA MEMBRANE, GROWTH FACTOR, KINASE		prednisone	PREDNISONE	27173875
6387	CXCL12	DRUGGABLE GENOME, EXTERNAL SIDE OF PLASMA MEMBRANE, GROWTH FACTOR, KINASE		MYOCELL SDF-1
6387	CXCL12	DRUGGABLE GENOME, EXTERNAL SIDE OF PLASMA MEMBRANE, GROWTH FACTOR, KINASE		cyclophosphamide	CYCLOPHOSPHAMIDE	27173875

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