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: SLC25A1

Gene summary for SLC25A1

Gene summary.

Gene information	Species	Human
	Gene symbol	SLC25A1
	Gene ID	6576
	Gene name	solute carrier family 25 member 1
	Gene Alias	CMS23
	Cytomap	22q11.21
	Gene Type	protein-coding
	GO ID	GO:0005975
	UniProtAcc	D9HTE9

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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
6576	SLC25A1	GSM4909281	Human	Breast	IDC	1.23e-04	2.69e-01	0.21
6576	SLC25A1	GSM4909291	Human	Breast	IDC	1.74e-26	7.71e-01	0.1753
6576	SLC25A1	GSM4909304	Human	Breast	IDC	9.75e-27	6.31e-01	0.1636
6576	SLC25A1	GSM4909311	Human	Breast	IDC	3.56e-05	-2.54e-02	0.1534
6576	SLC25A1	GSM4909315	Human	Breast	IDC	4.47e-02	2.69e-01	0.21
6576	SLC25A1	GSM4909317	Human	Breast	IDC	1.78e-16	5.27e-01	0.1355
6576	SLC25A1	GSM4909319	Human	Breast	IDC	3.63e-10	-4.10e-02	0.1563
6576	SLC25A1	GSM4909320	Human	Breast	IDC	9.92e-03	2.70e-01	0.1575
6576	SLC25A1	GSM4909321	Human	Breast	IDC	6.39e-08	2.37e-01	0.1559
6576	SLC25A1	DCIS2	Human	Breast	DCIS	3.71e-40	1.24e-01	0.0085
6576	SLC25A1	HTA11_3410_2000001011	Human	Colorectum	AD	1.67e-08	1.58e-01	0.0155
6576	SLC25A1	HTA11_2487_2000001011	Human	Colorectum	SER	5.17e-22	9.58e-01	-0.1808
6576	SLC25A1	HTA11_1938_2000001011	Human	Colorectum	AD	1.45e-13	4.96e-01	-0.0811
6576	SLC25A1	HTA11_78_2000001011	Human	Colorectum	AD	3.30e-09	4.39e-01	-0.1088
6576	SLC25A1	HTA11_347_2000001011	Human	Colorectum	AD	5.19e-23	5.27e-01	-0.1954
6576	SLC25A1	HTA11_411_2000001011	Human	Colorectum	SER	1.96e-10	1.12e+00	-0.2602
6576	SLC25A1	HTA11_2112_2000001011	Human	Colorectum	SER	1.23e-06	9.45e-01	-0.2196
6576	SLC25A1	HTA11_3361_2000001011	Human	Colorectum	AD	4.70e-09	5.36e-01	-0.1207
6576	SLC25A1	HTA11_83_2000001011	Human	Colorectum	SER	5.90e-10	5.75e-01	-0.1526
6576	SLC25A1	HTA11_696_2000001011	Human	Colorectum	AD	6.77e-27	7.00e-01	-0.1464

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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
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
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
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:19016051	Liver	Cirrhotic	alpha-amino acid metabolic process	82/4634	195/18723	7.72e-08	2.30e-06	82
GO:000600611	Liver	Cirrhotic	glucose metabolic process	82/4634	196/18723	1.01e-07	2.93e-06	82
GO:000652011	Liver	Cirrhotic	cellular amino acid metabolic process	103/4634	284/18723	8.88e-06	1.30e-04	103
GO:005159211	Liver	Cirrhotic	response to calcium ion	61/4634	149/18723	9.47e-06	1.38e-04	61
GO:00463641	Liver	Cirrhotic	monosaccharide biosynthetic process	37/4634	82/18723	4.52e-05	5.30e-04	37
GO:00442721	Liver	Cirrhotic	sulfur compound biosynthetic process	58/4634	148/18723	6.93e-05	7.83e-04	58
GO:00463905	Liver	Cirrhotic	ribose phosphate biosynthetic process	71/4634	190/18723	7.09e-05	7.98e-04	71
GO:00092605	Liver	Cirrhotic	ribonucleotide biosynthetic process	68/4634	182/18723	1.00e-04	1.05e-03	68
GO:00091654	Liver	Cirrhotic	nucleotide biosynthetic process	89/4634	254/18723	1.45e-04	1.40e-03	89
GO:00160511	Liver	Cirrhotic	carbohydrate biosynthetic process	73/4634	202/18723	1.91e-04	1.77e-03	73
GO:19012934	Liver	Cirrhotic	nucleoside phosphate biosynthetic process	89/4634	256/18723	1.97e-04	1.82e-03	89
GO:00338651	Liver	Cirrhotic	nucleoside bisphosphate metabolic process	50/4634	128/18723	2.32e-04	2.11e-03	50
GO:00338751	Liver	Cirrhotic	ribonucleoside bisphosphate metabolic process	50/4634	128/18723	2.32e-04	2.11e-03	50
GO:00340321	Liver	Cirrhotic	purine nucleoside bisphosphate metabolic process	50/4634	128/18723	2.32e-04	2.11e-03	50
GO:00091526	Liver	Cirrhotic	purine ribonucleotide biosynthetic process	62/4634	169/18723	3.52e-04	3.00e-03	62
GO:19905425	Liver	Cirrhotic	mitochondrial transmembrane transport	41/4634	102/18723	4.08e-04	3.37e-03	41
GO:00193191	Liver	Cirrhotic	hexose biosynthetic process	33/4634	78/18723	4.94e-04	3.96e-03	33
GO:00060941	Liver	Cirrhotic	gluconeogenesis	32/4634	75/18723	5.00e-04	3.98e-03	32
GO:00066371	Liver	Cirrhotic	acyl-CoA metabolic process	38/4634	96/18723	9.23e-04	6.57e-03	38
GO:00353831	Liver	Cirrhotic	thioester metabolic process	38/4634	96/18723	9.23e-04	6.57e-03	38

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Enriched KEGG pathways.

Pathway ID

Tissue

Disease Stage

Description

Gene Ratio

Bg Ratio

pvalue

p.adjust

qvalue

Count

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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

SLC25A1

SNV

Missense_Mutation

c.709N>A

p.Gly237Arg

p.G237R

P53007

protein_coding

deleterious(0)

probably_damaging(0.996)

TCGA-C8-A27B-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

5-fluorouracil

SLC25A1

SNV

Missense_Mutation

rs782258354

c.694N>A

p.Ala232Thr

p.A232T

P53007

protein_coding

deleterious(0.03)

possibly_damaging(0.846)

TCGA-LL-A7SZ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

SLC25A1

insertion

Frame_Shift_Ins

novel

c.226_227insTTACCTTCTCACCTATCAGCTGCTTTTACTTTCAGAATTG

p.Arg76LeufsTer26

p.R76Lfs*26

P53007

protein_coding

TCGA-A2-A0D1-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

taxotere

SLC25A1

SNV

Missense_Mutation

c.358G>A

p.Asp120Asn

p.D120N

P53007

protein_coding

tolerated(0.27)

benign(0.007)

TCGA-EX-A1H5-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

SLC25A1

SNV

Missense_Mutation

rs431905510

c.845N>A

p.Arg282His

p.R282H

P53007

protein_coding

deleterious(0)

probably_damaging(0.975)

TCGA-QG-A5Z2-01

Colorectum

colon adenocarcinoma

Male

<65

I/II

Unknown

SLC25A1

SNV

Missense_Mutation

novel

c.593N>A

p.Arg198His

p.R198H

P53007

protein_coding

deleterious(0)

probably_damaging(0.998)

TCGA-AP-A051-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

SLC25A1

SNV

Missense_Mutation

novel

c.631N>A

p.Gly211Arg

p.G211R

P53007

protein_coding

deleterious(0.02)

benign(0.445)

TCGA-AP-A1DK-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

SLC25A1

SNV

Missense_Mutation

novel

c.631N>T

p.Gly211Trp

p.G211W

P53007

protein_coding

deleterious(0)

probably_damaging(0.994)

TCGA-AP-A1DM-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

SLC25A1

SNV

Missense_Mutation

c.457N>A

p.Asp153Asn

p.D153N

P53007

protein_coding

deleterious(0.03)

possibly_damaging(0.709)

TCGA-AP-A1E0-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

paclitaxel

SLC25A1

SNV

Missense_Mutation

novel

c.725N>G

p.Asp242Gly

p.D242G

P53007

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-B5-A3FA-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
6576	SLC25A1	TRANSPORTER, DRUGGABLE GENOME	inhibitor	178101413

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