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: PCM1

Gene summary for PCM1

Gene summary.

Gene information	Species	Human
	Gene symbol	PCM1
	Gene ID	5108
	Gene name	pericentriolar material 1
	Gene Alias	PTC4
	Cytomap	8p22
	Gene Type	protein-coding
	GO ID	GO:0000226
	UniProtAcc	B9EIS5

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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
5108	PCM1	HTA11_3410_2000001011	Human	Colorectum	AD	8.29e-21	-5.64e-01	0.0155
5108	PCM1	HTA11_2487_2000001011	Human	Colorectum	SER	1.31e-06	-4.64e-01	-0.1808
5108	PCM1	HTA11_2112_2000001011	Human	Colorectum	SER	1.10e-02	-6.85e-01	-0.2196
5108	PCM1	HTA11_3361_2000001011	Human	Colorectum	AD	6.61e-09	-4.79e-01	-0.1207
5108	PCM1	HTA11_83_2000001011	Human	Colorectum	SER	2.46e-03	-3.87e-01	-0.1526
5108	PCM1	HTA11_696_2000001011	Human	Colorectum	AD	2.36e-03	-3.16e-01	-0.1464
5108	PCM1	HTA11_866_2000001011	Human	Colorectum	AD	3.89e-02	-2.80e-01	-0.1001
5108	PCM1	HTA11_1391_2000001011	Human	Colorectum	AD	1.01e-03	-3.63e-01	-0.059
5108	PCM1	HTA11_5212_2000001011	Human	Colorectum	AD	3.15e-04	-6.17e-01	-0.2061
5108	PCM1	HTA11_5216_2000001011	Human	Colorectum	SER	1.23e-03	-7.35e-01	-0.1462
5108	PCM1	HTA11_7862_2000001011	Human	Colorectum	AD	3.27e-03	-4.93e-01	-0.0179
5108	PCM1	HTA11_866_3004761011	Human	Colorectum	AD	4.84e-06	-3.92e-01	0.096
5108	PCM1	HTA11_10711_2000001011	Human	Colorectum	AD	2.55e-02	-3.90e-01	0.0338
5108	PCM1	HTA11_7696_3000711011	Human	Colorectum	AD	8.90e-08	-3.42e-01	0.0674
5108	PCM1	HTA11_99999971662_82457	Human	Colorectum	MSS	4.92e-19	-5.83e-01	0.3859
5108	PCM1	HTA11_99999974143_84620	Human	Colorectum	MSS	3.66e-12	-4.21e-01	0.3005
5108	PCM1	A015-C-203	Human	Colorectum	FAP	1.90e-23	-6.10e-02	-0.1294
5108	PCM1	A014-C-040	Human	Colorectum	FAP	3.97e-03	-7.61e-02	-0.1184
5108	PCM1	A002-C-201	Human	Colorectum	FAP	4.03e-11	-1.13e-01	0.0324
5108	PCM1	A001-C-119	Human	Colorectum	FAP	5.81e-05	9.19e-02	-0.1557

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
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
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:00987276	Prostate	BPH	maintenance of cell number	43/3107	134/18723	7.29e-06	1.04e-04	43
GO:00198275	Prostate	BPH	stem cell population maintenance	42/3107	131/18723	9.49e-06	1.33e-04	42
GO:00507678	Prostate	BPH	regulation of neurogenesis	92/3107	364/18723	1.36e-05	1.78e-04	92
GO:00109705	Prostate	BPH	transport along microtubule	47/3107	155/18723	1.53e-05	1.95e-04	47
GO:00311225	Prostate	BPH	cytoplasmic microtubule organization	22/3107	56/18723	4.21e-05	4.48e-04	22
GO:00315033	Prostate	BPH	protein-containing complex localization	59/3107	220/18723	8.01e-05	7.66e-04	59
GO:00519604	Prostate	BPH	regulation of nervous system development	100/3107	443/18723	6.02e-04	4.16e-03	100
GO:00991112	Prostate	BPH	microtubule-based transport	49/3107	190/18723	8.05e-04	5.27e-03	49
GO:00107214	Prostate	BPH	negative regulation of cell development	45/3107	180/18723	2.49e-03	1.34e-02	45
GO:00310231	Prostate	BPH	microtubule organizing center organization	35/3107	143/18723	9.88e-03	4.16e-02	35
GO:00070977	Prostate	BPH	nuclear migration	8/3107	20/18723	1.09e-02	4.50e-02	8
GO:00516476	Prostate	BPH	nucleus localization	9/3107	24/18723	1.14e-02	4.64e-02	9
GO:00309004	Prostate	BPH	forebrain development	80/3107	379/18723	1.19e-02	4.82e-02	80
GO:003238614	Prostate	Tumor	regulation of intracellular transport	111/3246	337/18723	1.83e-12	1.65e-10	111
GO:190495118	Prostate	Tumor	positive regulation of establishment of protein localization	106/3246	319/18723	3.13e-12	2.70e-10	106
GO:003315717	Prostate	Tumor	regulation of intracellular protein transport	81/3246	229/18723	3.47e-11	2.37e-09	81
GO:005122218	Prostate	Tumor	positive regulation of protein transport	97/3246	303/18723	2.67e-10	1.48e-08	97
GO:003238817	Prostate	Tumor	positive regulation of intracellular transport	70/3246	202/18723	2.01e-09	8.86e-08	70
GO:003070515	Prostate	Tumor	cytoskeleton-dependent intracellular transport	67/3246	195/18723	6.56e-09	2.53e-07	67
GO:009031614	Prostate	Tumor	positive regulation of intracellular protein transport	57/3246	160/18723	2.01e-08	7.03e-07	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

PCM1

SNV

Missense_Mutation

rs374857257

c.5357N>G

p.Ser1786Cys

p.S1786C

Q15154

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-A7-A0DA-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

PCM1

SNV

Missense_Mutation

novel

c.1067N>A

p.Ser356Tyr

p.S356Y

Q15154

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

PCM1

SNV

Missense_Mutation

c.3985N>C

p.Lys1329Gln

p.K1329Q

Q15154

protein_coding

tolerated(0.46)

benign(0.077)

TCGA-E2-A1BD-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

arimidex

PCM1

insertion

Frame_Shift_Ins

novel

c.142_143insG

p.Asn48ArgfsTer2

p.N48Rfs*2

Q15154

protein_coding

TCGA-A7-A26I-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

cytoxan

PCM1

insertion

Nonsense_Mutation

novel

c.1270_1271insTCTAGGCTACTTATA

p.His424delinsLeuTerAlaThrTyrAsn

p.H424delinsL*ATYN

Q15154

protein_coding

TCGA-A8-A07L-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

PCM1

insertion

Frame_Shift_Ins

novel

c.2643_2644insGGGCAGATCATGAGGTCAGGTATTCA

p.Arg882GlyfsTer26

p.R882Gfs*26

Q15154

protein_coding

TCGA-BH-A0AY-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

PCM1

SNV

Missense_Mutation

rs768119487

c.6034N>G

p.Thr2012Ala

p.T2012A

Q15154

protein_coding

tolerated(0.59)

benign(0.014)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

PCM1

SNV

Missense_Mutation

c.1435N>A

p.Glu479Lys

p.E479K

Q15154

protein_coding

deleterious(0.01)

probably_damaging(0.998)

TCGA-EK-A3GK-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

PCM1

SNV

Missense_Mutation

c.4408G>C

p.Asp1470His

p.D1470H

Q15154

protein_coding

deleterious(0.01)

probably_damaging(1)

TCGA-Q1-A73O-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

PCM1

SNV

Missense_Mutation

novel

c.3398C>T

p.Ser1133Leu

p.S1133L

Q15154

protein_coding

deleterious(0)

benign(0.225)

TCGA-VS-A954-01

Cervix

cervical & endocervical cancer

Female

>=65

III/IV

Chemotherapy

cisplatin

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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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