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: CEP350

Gene summary for CEP350

Gene summary.

Gene information	Species	Human
	Gene symbol	CEP350
	Gene ID	9857
	Gene name	centrosomal protein 350
	Gene Alias	CAP350
	Cytomap	1q25.2
	Gene Type	protein-coding
	GO ID	GO:0000226
	UniProtAcc	Q5VT06

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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
9857	CEP350	HSIL_HPV_2	Human	Cervix	HSIL_HPV	2.73e-02	2.25e-01	0.0208
9857	CEP350	CCI_2	Human	Cervix	CC	1.64e-10	1.11e+00	0.5249
9857	CEP350	CCI_3	Human	Cervix	CC	1.52e-07	9.06e-01	0.516
9857	CEP350	HTA11_3410_2000001011	Human	Colorectum	AD	3.06e-13	-5.64e-01	0.0155
9857	CEP350	HTA11_3361_2000001011	Human	Colorectum	AD	1.47e-03	-5.10e-01	-0.1207
9857	CEP350	HTA11_696_2000001011	Human	Colorectum	AD	1.67e-02	-2.42e-01	-0.1464
9857	CEP350	HTA11_866_3004761011	Human	Colorectum	AD	2.17e-09	-4.95e-01	0.096
9857	CEP350	HTA11_10711_2000001011	Human	Colorectum	AD	1.27e-02	-4.32e-01	0.0338
9857	CEP350	HTA11_7696_3000711011	Human	Colorectum	AD	8.24e-13	-4.13e-01	0.0674
9857	CEP350	HTA11_99999970781_79442	Human	Colorectum	MSS	2.21e-12	-4.37e-01	0.294
9857	CEP350	HTA11_99999971662_82457	Human	Colorectum	MSS	1.68e-09	-3.70e-01	0.3859
9857	CEP350	HTA11_99999973899_84307	Human	Colorectum	MSS	7.15e-03	-5.22e-01	0.2585
9857	CEP350	HTA11_99999974143_84620	Human	Colorectum	MSS	1.14e-20	-5.56e-01	0.3005
9857	CEP350	A001-C-207	Human	Colorectum	FAP	1.33e-02	-2.58e-02	0.1278
9857	CEP350	A015-C-203	Human	Colorectum	FAP	1.17e-32	-1.62e-01	-0.1294
9857	CEP350	A015-C-204	Human	Colorectum	FAP	2.51e-06	-9.62e-02	-0.0228
9857	CEP350	A014-C-040	Human	Colorectum	FAP	1.70e-03	-1.65e-01	-0.1184
9857	CEP350	A002-C-201	Human	Colorectum	FAP	1.18e-11	-1.34e-01	0.0324
9857	CEP350	A002-C-203	Human	Colorectum	FAP	2.69e-07	-1.51e-01	0.2786
9857	CEP350	A001-C-119	Human	Colorectum	FAP	8.07e-04	2.54e-02	-0.1557

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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
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:0071539	Colorectum	AD	protein localization to centrosome	16/3918	33/18723	3.86e-04	4.41e-03	16
GO:1905508	Colorectum	AD	protein localization to microtubule organizing center	16/3918	35/18723	8.76e-04	8.51e-03	16
GO:00715391	Colorectum	MSS	protein localization to centrosome	16/3467	33/18723	8.66e-05	1.40e-03	16
GO:19055081	Colorectum	MSS	protein localization to microtubule organizing center	16/3467	35/18723	2.07e-04	2.89e-03	16
GO:0044380	Colorectum	MSS	protein localization to cytoskeleton	19/3467	58/18723	6.69e-03	4.38e-02	19
GO:0072698	Colorectum	MSS	protein localization to microtubule cytoskeleton	18/3467	54/18723	6.70e-03	4.38e-02	18
GO:00715392	Colorectum	FAP	protein localization to centrosome	14/2622	33/18723	6.39e-05	1.23e-03	14
GO:19055082	Colorectum	FAP	protein localization to microtubule organizing center	14/2622	35/18723	1.38e-04	2.18e-03	14
GO:00726981	Colorectum	FAP	protein localization to microtubule cytoskeleton	16/2622	54/18723	2.26e-03	1.84e-02	16
GO:00443801	Colorectum	FAP	protein localization to cytoskeleton	16/2622	58/18723	4.97e-03	3.32e-02	16
GO:00715393	Colorectum	CRC	protein localization to centrosome	11/2078	33/18723	5.80e-04	7.89e-03	11
GO:19055083	Colorectum	CRC	protein localization to microtubule organizing center	11/2078	35/18723	1.02e-03	1.20e-02	11
GO:00726982	Colorectum	CRC	protein localization to microtubule cytoskeleton	13/2078	54/18723	5.25e-03	3.98e-02	13
GO:00726985	Esophagus	ESCC	protein localization to microtubule cytoskeleton	43/8552	54/18723	3.28e-07	4.61e-06	43
GO:00443804	Esophagus	ESCC	protein localization to cytoskeleton	45/8552	58/18723	6.89e-07	8.99e-06	45
GO:19055086	Esophagus	ESCC	protein localization to microtubule organizing center	28/8552	35/18723	3.40e-05	2.78e-04	28
GO:00715396	Esophagus	ESCC	protein localization to centrosome	26/8552	33/18723	1.06e-04	7.43e-04	26
GO:19055153	Esophagus	ESCC	non-motile cilium assembly	39/8552	61/18723	3.08e-03	1.28e-02	39
GO:00443802	Liver	HCC	protein localization to cytoskeleton	38/7958	58/18723	3.37e-04	2.36e-03	38
GO:007269811	Liver	HCC	protein localization to microtubule cytoskeleton	35/7958	54/18723	7.73e-04	4.65e-03	35

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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

CEP350

SNV

Missense_Mutation

c.3789N>C

p.Gln1263His

p.Q1263H

Q5VT06

protein_coding

deleterious(0.01)

possibly_damaging(0.541)

TCGA-A1-A0SI-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

CEP350

SNV

Missense_Mutation

c.5794N>T

p.Val1932Leu

p.V1932L

Q5VT06

protein_coding

tolerated(0.25)

benign(0)

TCGA-A2-A0D3-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

carboplatin

CEP350

SNV

Missense_Mutation

novel

c.6331N>C

p.Asp2111His

p.D2111H

Q5VT06

protein_coding

deleterious(0)

probably_damaging(0.997)

TCGA-A2-A0EQ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

CEP350

SNV

Missense_Mutation

rs755417181

c.8458G>A

p.Glu2820Lys

p.E2820K

Q5VT06

protein_coding

tolerated(0.12)

possibly_damaging(0.476)

TCGA-A7-A56D-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

CEP350

SNV

Missense_Mutation

c.7213N>T

p.Leu2405Phe

p.L2405F

Q5VT06

protein_coding

tolerated(0.41)

possibly_damaging(0.768)

TCGA-A8-A09E-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Hormone Therapy

anastrozole

CEP350

SNV

Missense_Mutation

c.9160N>G

p.Lys3054Glu

p.K3054E

Q5VT06

protein_coding

deleterious(0)

probably_damaging(0.989)

TCGA-A8-A09Z-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

CEP350

SNV

Missense_Mutation

novel

c.6892C>A

p.Leu2298Ile

p.L2298I

Q5VT06

protein_coding

tolerated(0.12)

benign(0.003)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

CEP350

SNV

Missense_Mutation

c.2484N>C

p.Leu828Phe

p.L828F

Q5VT06

protein_coding

deleterious(0)

probably_damaging(0.993)

TCGA-BH-A0AW-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

carboplatin

CEP350

SNV

Missense_Mutation

novel

c.4185N>C

p.Gln1395His

p.Q1395H

Q5VT06

protein_coding

deleterious(0)

possibly_damaging(0.818)

TCGA-BH-A0B6-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

CEP350

SNV

Missense_Mutation

c.3688G>C

p.Asp1230His

p.D1230H

Q5VT06

protein_coding

deleterious(0)

possibly_damaging(0.65)

TCGA-BH-A0BZ-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

doxorubicin

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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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