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: BOP1

Gene summary for BOP1

Gene summary.

Gene information	Species	Human
	Gene symbol	BOP1
	Gene ID	23246
	Gene name	BOP1 ribosomal biogenesis factor
	Gene Alias	BOP1
	Cytomap	8q24.3
	Gene Type	protein-coding
	GO ID	GO:0000027
	UniProtAcc	Q14137

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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
23246	BOP1	HTA11_1391_2000001011	Human	Colorectum	AD	9.37e-08	3.24e-01	-0.059
23246	BOP1	HTA11_866_3004761011	Human	Colorectum	AD	1.62e-05	2.89e-01	0.096
23246	BOP1	HTA11_7696_3000711011	Human	Colorectum	AD	2.98e-08	2.81e-01	0.0674
23246	BOP1	HTA11_6818_2000001021	Human	Colorectum	AD	1.23e-02	3.02e-01	0.0588
23246	BOP1	HTA11_99999971662_82457	Human	Colorectum	MSS	1.64e-37	8.95e-01	0.3859
23246	BOP1	HTA11_99999974143_84620	Human	Colorectum	MSS	1.27e-15	4.71e-01	0.3005
23246	BOP1	CRC-3-11773	Human	Colorectum	CRC	2.12e-14	5.85e-01	0.2564
23246	BOP1	LZE20T	Human	Esophagus	ESCC	2.13e-04	2.29e-01	0.0662
23246	BOP1	LZE22T	Human	Esophagus	ESCC	1.57e-06	4.58e-01	0.068
23246	BOP1	LZE24T	Human	Esophagus	ESCC	7.15e-21	5.66e-01	0.0596
23246	BOP1	LZE21T	Human	Esophagus	ESCC	9.05e-05	4.96e-01	0.0655
23246	BOP1	P1T-E	Human	Esophagus	ESCC	8.48e-05	2.99e-01	0.0875
23246	BOP1	P2T-E	Human	Esophagus	ESCC	3.48e-27	5.64e-01	0.1177
23246	BOP1	P4T-E	Human	Esophagus	ESCC	6.35e-23	5.97e-01	0.1323
23246	BOP1	P5T-E	Human	Esophagus	ESCC	7.53e-37	7.40e-01	0.1327
23246	BOP1	P8T-E	Human	Esophagus	ESCC	7.24e-10	2.25e-01	0.0889
23246	BOP1	P9T-E	Human	Esophagus	ESCC	4.34e-24	6.70e-01	0.1131
23246	BOP1	P10T-E	Human	Esophagus	ESCC	1.53e-22	4.07e-01	0.116
23246	BOP1	P11T-E	Human	Esophagus	ESCC	3.55e-09	5.06e-01	0.1426
23246	BOP1	P12T-E	Human	Esophagus	ESCC	1.47e-43	9.53e-01	0.1122

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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
Oral Cavity		EOLP: Erosive Oral lichen planus
		LP: leukoplakia
		NEOLP: Non-erosive oral lichen planus
		OSCC: Oral squamous cell carcinoma
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:00004665	Thyroid	PTC	maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	15/5968	24/18723	1.95e-03	1.05e-02	15
GO:00903055	Thyroid	PTC	nucleic acid phosphodiester bond hydrolysis	105/5968	261/18723	2.53e-03	1.31e-02	105
GO:002261334	Thyroid	ATC	ribonucleoprotein complex biogenesis	292/6293	463/18723	3.05e-39	9.63e-36	292
GO:004225434	Thyroid	ATC	ribosome biogenesis	203/6293	299/18723	3.63e-34	4.59e-31	203
GO:000636432	Thyroid	ATC	rRNA processing	157/6293	225/18723	9.02e-29	5.70e-26	157
GO:001607232	Thyroid	ATC	rRNA metabolic process	161/6293	236/18723	1.02e-27	5.89e-25	161
GO:003447021	Thyroid	ATC	ncRNA processing	216/6293	395/18723	3.14e-18	3.98e-16	216
GO:004227335	Thyroid	ATC	ribosomal large subunit biogenesis	57/6293	72/18723	2.56e-15	1.82e-13	57
GO:007182635	Thyroid	ATC	ribonucleoprotein complex subunit organization	133/6293	227/18723	8.32e-15	5.01e-13	133
GO:002261835	Thyroid	ATC	ribonucleoprotein complex assembly	129/6293	220/18723	1.93e-14	1.10e-12	129
GO:007233135	Thyroid	ATC	signal transduction by p53 class mediator	102/6293	163/18723	3.16e-14	1.75e-12	102
GO:190179635	Thyroid	ATC	regulation of signal transduction by p53 class mediator	66/6293	93/18723	1.86e-13	9.20e-12	66
GO:003466021	Thyroid	ATC	ncRNA metabolic process	240/6293	485/18723	2.03e-13	9.91e-12	240
GO:004225535	Thyroid	ATC	ribosome assembly	43/6293	61/18723	4.24e-09	9.57e-08	43
GO:000047018	Thyroid	ATC	maturation of LSU-rRNA	23/6293	28/18723	1.78e-07	2.82e-06	23
GO:000046911	Thyroid	ATC	cleavage involved in rRNA processing	21/6293	27/18723	3.28e-06	3.69e-05	21
GO:000002735	Thyroid	ATC	ribosomal large subunit assembly	20/6293	27/18723	2.01e-05	1.81e-04	20
GO:009050112	Thyroid	ATC	RNA phosphodiester bond hydrolysis	76/6293	152/18723	2.07e-05	1.86e-04	76
GO:000046012	Thyroid	ATC	maturation of 5.8S rRNA	24/6293	35/18723	2.49e-05	2.16e-04	24
GO:000046312	Thyroid	ATC	maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	12/6293	15/18723	3.10e-04	1.94e-03	12

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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

BOP1

SNV

Missense_Mutation

novel

c.2015N>C

p.His672Pro

p.H672P

Q14137

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-A2-A1FW-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

cytoxan

BOP1

SNV

Missense_Mutation

rs782512248

c.226N>A

p.Glu76Lys

p.E76K

Q14137

protein_coding

tolerated(0.33)

benign(0.019)

TCGA-AR-A0TZ-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unspecific

Doxorubicin

BOP1

SNV

Missense_Mutation

novel

c.2015N>C

p.His672Pro

p.H672P

Q14137

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-AR-A1AT-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

anastrozole

BOP1

SNV

Missense_Mutation

novel

c.760N>A

p.Glu254Lys

p.E254K

Q14137

protein_coding

tolerated(0.75)

benign(0.012)

TCGA-D8-A73U-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

tamoxiphen

BOP1

insertion

Frame_Shift_Ins

novel

c.445_446insC

p.His149ProfsTer20

p.H149Pfs*20

Q14137

protein_coding

TCGA-BH-A0HA-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

BOP1

insertion

In_Frame_Ins

novel

c.146_147insAGATTATGGACAACTACGTTACCCCTTCTTGAGTTT

p.Asp49delinsGluAspTyrGlyGlnLeuArgTyrProPheLeuSerPhe

p.D49delinsEDYGQLRYPFLSF

Q14137

protein_coding

TCGA-BH-A0HB-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

docetaxel

BOP1

SNV

Missense_Mutation

novel

c.473N>A

p.Arg158His

p.R158H

Q14137

protein_coding

deleterious(0)

probably_damaging(0.939)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

BOP1

SNV

Missense_Mutation

novel

c.811N>T

p.Arg271Cys

p.R271C

Q14137

protein_coding

deleterious(0)

probably_damaging(0.971)

TCGA-C5-A1BJ-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

BOP1

SNV

Missense_Mutation

novel

c.1733G>T

p.Ser578Ile

p.S578I

Q14137

protein_coding

deleterious(0.03)

benign(0.325)

TCGA-MA-AA42-01

Cervix

cervical & endocervical cancer

Female

>=65

I/II

Unknown

BOP1

SNV

Missense_Mutation

novel

c.1399G>A

p.Ala467Thr

p.A467T

Q14137

protein_coding

tolerated(0.51)

benign(0.003)

TCGA-MA-AA42-01

Cervix

cervical & endocervical cancer

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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