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: FAM172A

Gene summary for FAM172A

Gene summary.

Gene information	Species	Human
	Gene symbol	FAM172A
	Gene ID	83989
	Gene name	family with sequence similarity 172 member A
	Gene Alias	C5orf21
	Cytomap	5q15
	Gene Type	protein-coding
	GO ID	GO:0000375
	UniProtAcc	Q8WUF8

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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
83989	FAM172A	CCI_1	Human	Cervix	CC	1.35e-02	5.34e-01	0.528
83989	FAM172A	CCI_2	Human	Cervix	CC	1.76e-10	1.19e+00	0.5249
83989	FAM172A	CCI_3	Human	Cervix	CC	1.41e-10	8.32e-01	0.516
83989	FAM172A	HTA11_3410_2000001011	Human	Colorectum	AD	1.71e-21	-7.44e-01	0.0155
83989	FAM172A	HTA11_2487_2000001011	Human	Colorectum	SER	1.85e-02	-4.40e-01	-0.1808
83989	FAM172A	HTA11_3361_2000001011	Human	Colorectum	AD	1.12e-04	-6.31e-01	-0.1207
83989	FAM172A	HTA11_696_2000001011	Human	Colorectum	AD	3.04e-08	-4.38e-01	-0.1464
83989	FAM172A	HTA11_866_2000001011	Human	Colorectum	AD	4.44e-03	-3.45e-01	-0.1001
83989	FAM172A	HTA11_9408_2000001011	Human	Colorectum	AD	1.12e-02	-8.34e-01	0.0451
83989	FAM172A	HTA11_6818_2000001021	Human	Colorectum	AD	1.05e-05	5.93e-01	0.0588
83989	FAM172A	HTA11_99999965104_69814	Human	Colorectum	MSS	3.08e-05	5.71e-01	0.281
83989	FAM172A	HTA11_99999971662_82457	Human	Colorectum	MSS	1.09e-02	5.94e-01	0.3859
83989	FAM172A	A001-C-207	Human	Colorectum	FAP	2.22e-03	-2.87e-01	0.1278
83989	FAM172A	A015-C-203	Human	Colorectum	FAP	4.78e-32	-4.54e-01	-0.1294
83989	FAM172A	A015-C-204	Human	Colorectum	FAP	2.82e-06	-3.77e-01	-0.0228
83989	FAM172A	A014-C-040	Human	Colorectum	FAP	8.36e-05	-3.94e-01	-0.1184
83989	FAM172A	A002-C-201	Human	Colorectum	FAP	5.82e-16	-4.62e-01	0.0324
83989	FAM172A	A001-C-119	Human	Colorectum	FAP	5.72e-13	-7.25e-01	-0.1557
83989	FAM172A	A001-C-108	Human	Colorectum	FAP	3.77e-16	-3.73e-01	-0.0272
83989	FAM172A	A002-C-205	Human	Colorectum	FAP	1.76e-23	-4.54e-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
Lung		AAH: Atypical adenomatous hyperplasia
		AIS: Adenocarcinoma in situ
		IAC: Invasive lung adenocarcinoma
		MIA: Minimally invasive adenocarcinoma
Prostate		BPH: Benign Prostatic Hyperplasia
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:0000381	Colorectum	AD	regulation of alternative mRNA splicing, via spliceosome	27/3918	60/18723	2.41e-05	4.66e-04	27
GO:0006325	Colorectum	AD	chromatin organization	119/3918	409/18723	4.85e-05	8.33e-04	119
GO:00083801	Colorectum	SER	RNA splicing	123/2897	434/18723	3.84e-12	8.41e-10	123
GO:00003751	Colorectum	SER	RNA splicing, via transesterification reactions	90/2897	324/18723	8.68e-09	7.50e-07	90
GO:00003771	Colorectum	SER	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	89/2897	320/18723	9.82e-09	8.14e-07	89
GO:00003981	Colorectum	SER	mRNA splicing, via spliceosome	89/2897	320/18723	9.82e-09	8.14e-07	89
GO:00434841	Colorectum	SER	regulation of RNA splicing	49/2897	148/18723	7.02e-08	4.49e-06	49
GO:19033111	Colorectum	SER	regulation of mRNA metabolic process	78/2897	288/18723	2.61e-07	1.43e-05	78
GO:00480241	Colorectum	SER	regulation of mRNA splicing, via spliceosome	35/2897	101/18723	1.52e-06	6.85e-05	35
GO:00506841	Colorectum	SER	regulation of mRNA processing	42/2897	137/18723	5.57e-06	2.01e-04	42
GO:00003801	Colorectum	SER	alternative mRNA splicing, via spliceosome	24/2897	77/18723	4.08e-04	6.09e-03	24
GO:00063251	Colorectum	SER	chromatin organization	89/2897	409/18723	4.15e-04	6.17e-03	89
GO:00003811	Colorectum	SER	regulation of alternative mRNA splicing, via spliceosome	20/2897	60/18723	4.60e-04	6.65e-03	20
GO:00083802	Colorectum	MSS	RNA splicing	159/3467	434/18723	1.75e-19	1.22e-16	159
GO:19033112	Colorectum	MSS	regulation of mRNA metabolic process	115/3467	288/18723	1.23e-17	6.41e-15	115
GO:00003772	Colorectum	MSS	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	121/3467	320/18723	2.52e-16	8.27e-14	121
GO:00003982	Colorectum	MSS	mRNA splicing, via spliceosome	121/3467	320/18723	2.52e-16	8.27e-14	121
GO:00003752	Colorectum	MSS	RNA splicing, via transesterification reactions	122/3467	324/18723	2.75e-16	8.58e-14	122
GO:00434842	Colorectum	MSS	regulation of RNA splicing	66/3467	148/18723	2.44e-13	5.25e-11	66
GO:00506842	Colorectum	MSS	regulation of mRNA processing	57/3467	137/18723	2.88e-10	2.68e-08	57

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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

FAM172A

SNV

Missense_Mutation

rs758166608

c.1007N>A

p.Arg336Gln

p.R336Q

Q8WUF8

protein_coding

tolerated(1)

benign(0.003)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

FAM172A

SNV

Missense_Mutation

c.497N>T

p.Ala166Val

p.A166V

Q8WUF8

protein_coding

deleterious(0.01)

probably_damaging(0.946)

TCGA-AR-A251-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

doxorubicin

FAM172A

SNV

Missense_Mutation

c.1133N>A

p.Ser378Tyr

p.S378Y

Q8WUF8

protein_coding

deleterious(0)

possibly_damaging(0.895)

TCGA-BH-A1FN-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

FAM172A

SNV

Missense_Mutation

rs200535189

c.779N>G

p.Tyr260Cys

p.Y260C

Q8WUF8

protein_coding

tolerated(0.17)

benign(0)

TCGA-GM-A2DM-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

taxol

FAM172A

insertion

Nonsense_Mutation

novel

c.31_32insATAAACCTCTCATAAAATATCAGTAA

p.Leu11TyrfsTer9

p.L11Yfs*9

Q8WUF8

protein_coding

TCGA-AR-A0U0-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

FAM172A

SNV

Missense_Mutation

c.652G>C

p.Asp218His

p.D218H

Q8WUF8

protein_coding

deleterious(0.03)

possibly_damaging(0.866)

TCGA-C5-A7UH-01

Cervix

cervical & endocervical cancer

Female

<65

III/IV

Chemotherapy

cisplatin

FAM172A

SNV

Missense_Mutation

novel

c.388N>A

p.Glu130Lys

p.E130K

Q8WUF8

protein_coding

tolerated(0.05)

benign(0.025)

TCGA-VS-A9V5-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

carboplatin

FAM172A

SNV

Missense_Mutation

rs761232649

c.925N>A

p.Asp309Asn

p.D309N

Q8WUF8

protein_coding

deleterious(0.01)

benign(0.088)

TCGA-AA-A00N-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

FAM172A

SNV

Missense_Mutation

novel

c.503N>T

p.Arg168Ile

p.R168I

Q8WUF8

protein_coding

deleterious(0)

probably_damaging(0.961)

TCGA-AG-3892-01

Colorectum

rectum adenocarcinoma

Female

<65

I/II

Unknown

FAM172A

insertion

Frame_Shift_Ins

novel

c.928_929insCTCACACCCATTCATCTCAGCAC

p.Val310AlafsTer9

p.V310Afs*9

Q8WUF8

protein_coding

TCGA-AM-5820-01

Colorectum

colon adenocarcinoma

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

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