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: CHCHD2

Gene summary for CHCHD2

Gene summary.

Gene information	Species	Human
	Gene symbol	CHCHD2
	Gene ID	51142
	Gene name	coiled-coil-helix-coiled-coil-helix domain containing 2
	Gene Alias	C7orf17
	Cytomap	7p11.2
	Gene Type	protein-coding
	GO ID	GO:0001666
	UniProtAcc	Q9Y6H1

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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
51142	CHCHD2	GSM4909280	Human	Breast	Precancer	5.09e-04	-5.66e-01	0.0305
51142	CHCHD2	GSM4909281	Human	Breast	IDC	1.28e-02	1.59e-01	0.21
51142	CHCHD2	GSM4909282	Human	Breast	IDC	1.94e-22	3.03e-01	-0.0288
51142	CHCHD2	GSM4909285	Human	Breast	IDC	2.57e-34	3.84e-01	0.21
51142	CHCHD2	GSM4909286	Human	Breast	IDC	6.16e-08	-1.17e-01	0.1081
51142	CHCHD2	GSM4909287	Human	Breast	IDC	9.92e-38	3.38e-01	0.2057
51142	CHCHD2	GSM4909288	Human	Breast	IDC	2.18e-06	6.89e-02	0.0988
51142	CHCHD2	GSM4909290	Human	Breast	IDC	1.19e-18	3.24e-01	0.2096
51142	CHCHD2	GSM4909291	Human	Breast	IDC	7.47e-11	2.83e-01	0.1753
51142	CHCHD2	GSM4909293	Human	Breast	IDC	1.04e-28	-3.85e-01	0.1581
51142	CHCHD2	GSM4909294	Human	Breast	IDC	3.76e-10	-1.45e-01	0.2022
51142	CHCHD2	GSM4909295	Human	Breast	IDC	7.07e-03	-2.82e-01	0.0898
51142	CHCHD2	GSM4909296	Human	Breast	IDC	2.56e-47	3.80e-01	0.1524
51142	CHCHD2	GSM4909297	Human	Breast	IDC	9.43e-29	-7.81e-03	0.1517
51142	CHCHD2	GSM4909298	Human	Breast	IDC	2.06e-06	2.22e-01	0.1551
51142	CHCHD2	GSM4909301	Human	Breast	IDC	8.69e-09	1.57e-01	0.1577
51142	CHCHD2	GSM4909302	Human	Breast	IDC	1.43e-10	6.21e-02	0.1545
51142	CHCHD2	GSM4909304	Human	Breast	IDC	2.77e-12	2.59e-01	0.1636
51142	CHCHD2	GSM4909306	Human	Breast	IDC	4.84e-05	2.07e-01	0.1564
51142	CHCHD2	GSM4909307	Human	Breast	IDC	1.87e-07	1.99e-01	0.1569

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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
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:000611917	Prostate	BPH	oxidative phosphorylation	77/3107	141/18723	5.53e-25	1.14e-21	77
GO:000906016	Prostate	BPH	aerobic respiration	86/3107	189/18723	9.81e-21	1.01e-17	86
GO:004277316	Prostate	BPH	ATP synthesis coupled electron transport	55/3107	95/18723	7.64e-20	5.25e-17	55
GO:004277516	Prostate	BPH	mitochondrial ATP synthesis coupled electron transport	55/3107	95/18723	7.64e-20	5.25e-17	55
GO:000609116	Prostate	BPH	generation of precursor metabolites and energy	161/3107	490/18723	3.05e-19	1.45e-16	161
GO:002290416	Prostate	BPH	respiratory electron transport chain	59/3107	114/18723	5.71e-18	1.68e-15	59
GO:001598016	Prostate	BPH	energy derivation by oxidation of organic compounds	115/3107	318/18723	1.55e-17	4.36e-15	115
GO:004533316	Prostate	BPH	cellular respiration	92/3107	230/18723	1.67e-17	4.49e-15	92
GO:002290016	Prostate	BPH	electron transport chain	75/3107	175/18723	1.80e-16	3.85e-14	75
GO:000697918	Prostate	BPH	response to oxidative stress	142/3107	446/18723	8.11e-16	1.36e-13	142
GO:006219718	Prostate	BPH	cellular response to chemical stress	110/3107	337/18723	2.44e-13	2.40e-11	110
GO:007048217	Prostate	BPH	response to oxygen levels	104/3107	347/18723	3.13e-10	1.67e-08	104
GO:003459918	Prostate	BPH	cellular response to oxidative stress	90/3107	288/18723	4.70e-10	2.43e-08	90
GO:003629317	Prostate	BPH	response to decreased oxygen levels	96/3107	322/18723	2.03e-09	8.26e-08	96
GO:000166617	Prostate	BPH	response to hypoxia	92/3107	307/18723	3.29e-09	1.27e-07	92
GO:007145315	Prostate	BPH	cellular response to oxygen levels	56/3107	177/18723	5.50e-07	1.09e-05	56
GO:004346710	Prostate	BPH	regulation of generation of precursor metabolites and energy	44/3107	130/18723	1.16e-06	2.07e-05	44
GO:003629415	Prostate	BPH	cellular response to decreased oxygen levels	51/3107	161/18723	1.66e-06	2.79e-05	51
GO:00714568	Prostate	BPH	cellular response to hypoxia	47/3107	151/18723	7.09e-06	1.02e-04	47
GO:004603419	Prostate	Tumor	ATP metabolic process	122/3246	277/18723	1.71e-25	5.33e-22	122

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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

CHCHD2

SNV

Missense_Mutation

rs769442639

c.271N>A

p.Glu91Lys

p.E91K

Q9Y6H1

protein_coding

deleterious(0.01)

probably_damaging(0.987)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

CHCHD2

SNV

Missense_Mutation

c.293C>T

p.Thr98Ile

p.T98I

Q9Y6H1

protein_coding

deleterious(0.01)

possibly_damaging(0.806)

TCGA-C8-A12Q-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Unknown

CHCHD2

insertion

Frame_Shift_Ins

novel

c.90_91insATAATTCCACTTTATT

p.Val31IlefsTer64

p.V31Ifs*64

Q9Y6H1

protein_coding

TCGA-A8-A097-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

tamoxiphen

CHCHD2

SNV

Missense_Mutation

rs776234231

c.41C>T

p.Pro14Leu

p.P14L

Q9Y6H1

protein_coding

tolerated(0.07)

benign(0.036)

TCGA-C5-A3HL-01

Cervix

cervical & endocervical cancer

Female

>=65

I/II

Unknown

CHCHD2

SNV

Missense_Mutation

c.43N>G

p.Pro15Ala

p.P15A

Q9Y6H1

protein_coding

tolerated(0.06)

probably_damaging(0.994)

TCGA-EK-A3GK-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

CHCHD2

SNV

Missense_Mutation

c.448N>G

p.Leu150Val

p.L150V

Q9Y6H1

protein_coding

tolerated(0.15)

benign(0.178)

TCGA-A6-3808-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

CHCHD2

SNV

Missense_Mutation

rs200784526

c.235G>A

p.Ala79Thr

p.A79T

Q9Y6H1

protein_coding

deleterious(0.02)

possibly_damaging(0.84)

TCGA-AA-3947-01

Colorectum

colon adenocarcinoma

Female

<65

I/II

Unknown

CHCHD2

SNV

Missense_Mutation

rs780172272

c.52N>T

p.Arg18Trp

p.R18W

Q9Y6H1

protein_coding

deleterious(0.04)

possibly_damaging(0.649)

TCGA-AP-A059-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

CHCHD2

SNV

Missense_Mutation

c.110N>T

p.Ala37Val

p.A37V

Q9Y6H1

protein_coding

tolerated(0.44)

benign(0)

TCGA-AX-A0J1-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

CHCHD2

SNV

Missense_Mutation

rs780172272

c.52N>T

p.Arg18Trp

p.R18W

Q9Y6H1

protein_coding

deleterious(0.04)

possibly_damaging(0.649)

TCGA-BS-A0TE-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

adriamycin

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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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