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: RRP1B

Gene summary for RRP1B

Gene summary.

Gene information	Species	Human
	Gene symbol	RRP1B
	Gene ID	23076
	Gene name	ribosomal RNA processing 1B
	Gene Alias	KIAA0179
	Cytomap	21q22.3
	Gene Type	protein-coding
	GO ID	GO:0006139
	UniProtAcc	Q14684

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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
23076	RRP1B	LZE4T	Human	Esophagus	ESCC	4.60e-09	7.57e-02	0.0811
23076	RRP1B	LZE24T	Human	Esophagus	ESCC	9.18e-10	3.96e-01	0.0596
23076	RRP1B	LZE21T	Human	Esophagus	ESCC	7.20e-03	7.95e-02	0.0655
23076	RRP1B	P1T-E	Human	Esophagus	ESCC	5.59e-04	2.04e-01	0.0875
23076	RRP1B	P2T-E	Human	Esophagus	ESCC	8.32e-32	6.36e-01	0.1177
23076	RRP1B	P4T-E	Human	Esophagus	ESCC	4.72e-19	6.50e-01	0.1323
23076	RRP1B	P5T-E	Human	Esophagus	ESCC	4.04e-22	6.24e-01	0.1327
23076	RRP1B	P8T-E	Human	Esophagus	ESCC	8.38e-09	1.20e-01	0.0889
23076	RRP1B	P9T-E	Human	Esophagus	ESCC	1.69e-07	1.69e-01	0.1131
23076	RRP1B	P10T-E	Human	Esophagus	ESCC	2.12e-24	4.83e-01	0.116
23076	RRP1B	P11T-E	Human	Esophagus	ESCC	1.67e-05	4.23e-01	0.1426
23076	RRP1B	P12T-E	Human	Esophagus	ESCC	5.99e-26	3.35e-01	0.1122
23076	RRP1B	P15T-E	Human	Esophagus	ESCC	5.53e-09	2.78e-01	0.1149
23076	RRP1B	P16T-E	Human	Esophagus	ESCC	3.27e-26	5.44e-01	0.1153
23076	RRP1B	P17T-E	Human	Esophagus	ESCC	1.35e-09	3.43e-01	0.1278
23076	RRP1B	P20T-E	Human	Esophagus	ESCC	1.11e-15	4.01e-01	0.1124
23076	RRP1B	P21T-E	Human	Esophagus	ESCC	5.61e-20	5.44e-01	0.1617
23076	RRP1B	P22T-E	Human	Esophagus	ESCC	1.46e-12	3.64e-01	0.1236
23076	RRP1B	P23T-E	Human	Esophagus	ESCC	2.20e-15	5.30e-01	0.108
23076	RRP1B	P24T-E	Human	Esophagus	ESCC	1.15e-16	5.15e-01	0.1287

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
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
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:0022613111	Esophagus	ESCC	ribonucleoprotein complex biogenesis	365/8552	463/18723	1.74e-49	1.11e-45	365
GO:0042254111	Esophagus	ESCC	ribosome biogenesis	252/8552	299/18723	3.27e-44	1.04e-40	252
GO:0008380111	Esophagus	ESCC	RNA splicing	336/8552	434/18723	1.74e-42	3.67e-39	336
GO:003447015	Esophagus	ESCC	ncRNA processing	300/8552	395/18723	3.09e-35	3.26e-32	300
GO:0016072110	Esophagus	ESCC	rRNA metabolic process	197/8552	236/18723	1.31e-33	1.18e-30	197
GO:0006364110	Esophagus	ESCC	rRNA processing	189/8552	225/18723	4.88e-33	3.87e-30	189
GO:003466012	Esophagus	ESCC	ncRNA metabolic process	346/8552	485/18723	4.35e-31	2.51e-28	346
GO:0016032111	Esophagus	ESCC	viral process	301/8552	415/18723	3.34e-29	1.32e-26	301
GO:0043484111	Esophagus	ESCC	regulation of RNA splicing	116/8552	148/18723	3.18e-16	2.38e-14	116
GO:001908017	Esophagus	ESCC	viral gene expression	80/8552	94/18723	2.04e-15	1.28e-13	80
GO:000961518	Esophagus	ESCC	response to virus	238/8552	367/18723	6.65e-14	3.32e-12	238
GO:0044403111	Esophagus	ESCC	biological process involved in symbiotic interaction	186/8552	290/18723	1.43e-10	4.16e-09	186
GO:001908312	Esophagus	ESCC	viral transcription	41/8552	50/18723	1.35e-07	2.17e-06	41
GO:005185115	Esophagus	ESCC	modulation by host of symbiont process	43/8552	60/18723	4.00e-05	3.22e-04	43
GO:009858613	Esophagus	ESCC	cellular response to virus	56/8552	84/18723	8.20e-05	6.01e-04	56
GO:005181714	Esophagus	ESCC	modulation of process of other organism involved in symbiotic interaction	54/8552	81/18723	1.09e-04	7.64e-04	54
GO:0051346110	Esophagus	ESCC	negative regulation of hydrolase activity	208/8552	379/18723	1.76e-04	1.14e-03	208
GO:00439233	Esophagus	ESCC	positive regulation by host of viral transcription	14/8552	16/18723	6.78e-04	3.56e-03	14
GO:003582114	Esophagus	ESCC	modulation of process of other organism	64/8552	106/18723	1.61e-03	7.50e-03	64
GO:005170214	Esophagus	ESCC	biological process involved in interaction with symbiont	57/8552	94/18723	2.46e-03	1.07e-02	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

RRP1B

SNV

Missense_Mutation

c.257A>G

p.Asn86Ser

p.N86S

Q14684

protein_coding

tolerated(0.09)

possibly_damaging(0.752)

TCGA-A1-A0SP-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

RRP1B

SNV

Missense_Mutation

c.542N>A

p.Gly181Glu

p.G181E

Q14684

protein_coding

deleterious(0)

probably_damaging(0.973)

TCGA-A7-A6VV-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cyclophosphamide

RRP1B

insertion

Frame_Shift_Ins

novel

c.1501_1502insAAGGCGGTTTTCCAAGTGTTGTGCTGTTTTTGGTGGA

p.Gly501GlufsTer23

p.G501Efs*23

Q14684

protein_coding

TCGA-A2-A0EX-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

tamoxiphen

RRP1B

insertion

Nonsense_Mutation

novel

c.1647_1648insGTCATAAAGCATTAGCAGAG

p.Pro550ValfsTer5

p.P550Vfs*5

Q14684

protein_coding

TCGA-A8-A09E-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Hormone Therapy

anastrozole

RRP1B

insertion

Frame_Shift_Ins

novel

c.1649_1650insCAAAGCTTCAGTCT

p.Pro551LysfsTer48

p.P551Kfs*48

Q14684

protein_coding

TCGA-A8-A09E-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Hormone Therapy

anastrozole

RRP1B

insertion

Frame_Shift_Ins

novel

c.2258_2259insCCTGGGACCTGTTAAGAGAAGCTACCTGGTGAGACGTGATCCAAAAA

p.Arg753SerfsTer30

p.R753Sfs*30

Q14684

protein_coding

TCGA-AN-A0FF-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

RRP1B

insertion

In_Frame_Ins

novel

c.1529_1530insGTGTCAGCAGCGCTCAGGTTTGGGTGGGAGAAACGG

p.Pro510_Arg511insCysGlnGlnArgSerGlyLeuGlyGlyArgAsnGly

p.P510_R511insCQQRSGLGGRNG

Q14684

protein_coding

TCGA-AO-A0JJ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cyclophospamide

RRP1B

SNV

Missense_Mutation

novel

c.1348N>A

p.Ala450Thr

p.A450T

Q14684

protein_coding

tolerated(0.25)

possibly_damaging(0.511)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

RRP1B

SNV

Missense_Mutation

c.860G>T

p.Gly287Val

p.G287V

Q14684

protein_coding

tolerated(0.06)

benign(0.255)

TCGA-IR-A3LK-01

Cervix

cervical & endocervical cancer

Female

>=65

I/II

Chemotherapy

cisplatin

RRP1B

SNV

Missense_Mutation

c.450N>C

p.Met150Ile

p.M150I

Q14684

protein_coding

deleterious(0.03)

possibly_damaging(0.542)

TCGA-Q1-A73O-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

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
23076	RRP1B	NA		atenolol	ATENOLOL	31327267

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