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: RPLP0

Gene summary for RPLP0

Gene summary.

Gene information	Species	Human
	Gene symbol	RPLP0
	Gene ID	6175
	Gene name	ribosomal protein lateral stalk subunit P0
	Gene Alias	L10E
	Cytomap	12q24.23
	Gene Type	protein-coding
	GO ID	GO:0000027
	UniProtAcc	A0A024RBS2

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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
6175	RPLP0	CA_HPV_1	Human	Cervix	CC	2.69e-04	-2.75e-01	0.0264
6175	RPLP0	CA_HPV_2	Human	Cervix	CC	1.82e-13	-2.92e-01	0.0391
6175	RPLP0	CA_HPV_3	Human	Cervix	CC	1.41e-06	1.79e-01	0.0414
6175	RPLP0	CCI_1	Human	Cervix	CC	2.25e-42	-1.52e+00	0.528
6175	RPLP0	CCI_2	Human	Cervix	CC	1.16e-19	-9.81e-01	0.5249
6175	RPLP0	CCI_3	Human	Cervix	CC	8.40e-52	-1.58e+00	0.516
6175	RPLP0	CCII_1	Human	Cervix	CC	7.61e-71	-1.63e+00	0.3249
6175	RPLP0	sample3	Human	Cervix	CC	4.01e-18	-1.79e-01	0.1387
6175	RPLP0	H2	Human	Cervix	HSIL_HPV	4.68e-09	-2.95e-01	0.0632
6175	RPLP0	L1	Human	Cervix	CC	4.85e-07	-3.94e-01	0.0802
6175	RPLP0	T3	Human	Cervix	CC	3.96e-15	-1.50e-01	0.1389
6175	RPLP0	HTA11_3410_2000001011	Human	Colorectum	AD	3.40e-74	1.90e+00	0.0155
6175	RPLP0	HTA11_2487_2000001011	Human	Colorectum	SER	8.55e-43	2.69e+00	-0.1808
6175	RPLP0	HTA11_2951_2000001011	Human	Colorectum	AD	1.41e-33	3.03e+00	0.0216
6175	RPLP0	HTA11_1938_2000001011	Human	Colorectum	AD	1.35e-40	2.55e+00	-0.0811
6175	RPLP0	HTA11_78_2000001011	Human	Colorectum	AD	5.28e-41	2.29e+00	-0.1088
6175	RPLP0	HTA11_347_2000001011	Human	Colorectum	AD	4.97e-53	2.72e+00	-0.1954
6175	RPLP0	HTA11_411_2000001011	Human	Colorectum	SER	6.83e-24	2.83e+00	-0.2602
6175	RPLP0	HTA11_2112_2000001011	Human	Colorectum	SER	7.00e-10	2.68e+00	-0.2196
6175	RPLP0	HTA11_3361_2000001011	Human	Colorectum	AD	1.18e-38	2.76e+00	-0.1207

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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
GC		CAG: Chronic atrophic gastritis
		CAG with IM: Chronic atrophic gastritis with intestinal metaplasia
		CSG: Chronic superficial gastritis
		GC: Gastric cancer
		SIM: Severe intestinal metaplasia
		WIM: Wild intestinal metaplasia
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:000218110	Cervix	CC	cytoplasmic translation	96/2311	148/18723	4.87e-51	2.91e-47	96
GO:004225510	Cervix	CC	ribosome assembly	25/2311	61/18723	1.70e-08	1.27e-06	25
GO:004227310	Cervix	CC	ribosomal large subunit biogenesis	26/2311	72/18723	1.87e-07	8.48e-06	26
GO:002261310	Cervix	CC	ribonucleoprotein complex biogenesis	88/2311	463/18723	2.11e-05	3.82e-04	88
GO:004225410	Cervix	CC	ribosome biogenesis	62/2311	299/18723	2.48e-05	4.27e-04	62
GO:002261810	Cervix	CC	ribonucleoprotein complex assembly	49/2311	220/18723	2.52e-05	4.29e-04	49
GO:000002710	Cervix	CC	ribosomal large subunit assembly	12/2311	27/18723	3.52e-05	5.65e-04	12
GO:007182610	Cervix	CC	ribonucleoprotein complex subunit organization	49/2311	227/18723	5.91e-05	8.54e-04	49
GO:000218115	Cervix	HSIL_HPV	cytoplasmic translation	86/737	148/18723	3.97e-82	1.91e-78	86
GO:004225515	Cervix	HSIL_HPV	ribosome assembly	20/737	61/18723	8.44e-14	2.03e-10	20
GO:002261315	Cervix	HSIL_HPV	ribonucleoprotein complex biogenesis	52/737	463/18723	9.85e-12	6.81e-09	52
GO:004225415	Cervix	HSIL_HPV	ribosome biogenesis	40/737	299/18723	1.25e-11	6.81e-09	40
GO:004227315	Cervix	HSIL_HPV	ribosomal large subunit biogenesis	17/737	72/18723	1.94e-09	3.23e-07	17
GO:002261815	Cervix	HSIL_HPV	ribonucleoprotein complex assembly	29/737	220/18723	1.19e-08	1.30e-06	29
GO:007182615	Cervix	HSIL_HPV	ribonucleoprotein complex subunit organization	29/737	227/18723	2.42e-08	2.18e-06	29
GO:000002715	Cervix	HSIL_HPV	ribosomal large subunit assembly	9/737	27/18723	5.35e-07	2.77e-05	9
GO:00713533	Cervix	HSIL_HPV	cellular response to interleukin-4	7/737	33/18723	2.48e-04	4.30e-03	7
GO:00706703	Cervix	HSIL_HPV	response to interleukin-4	7/737	36/18723	4.38e-04	6.51e-03	7
GO:0002181	Colorectum	AD	cytoplasmic translation	109/3918	148/18723	3.40e-43	2.13e-39	109
GO:0022618	Colorectum	AD	ribonucleoprotein complex assembly	92/3918	220/18723	1.49e-12	2.60e-10	92

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0517120	Cervix	CC	Coronavirus disease - COVID-19	111/1267	232/8465	1.82e-33	5.90e-31	3.49e-31	111
hsa0301020	Cervix	CC	Ribosome	85/1267	167/8465	3.17e-28	5.14e-26	3.04e-26	85
hsa05171110	Cervix	CC	Coronavirus disease - COVID-19	111/1267	232/8465	1.82e-33	5.90e-31	3.49e-31	111
hsa03010110	Cervix	CC	Ribosome	85/1267	167/8465	3.17e-28	5.14e-26	3.04e-26	85
hsa0301025	Cervix	HSIL_HPV	Ribosome	80/459	167/8465	9.61e-58	2.82e-55	2.28e-55	80
hsa0517125	Cervix	HSIL_HPV	Coronavirus disease - COVID-19	91/459	232/8465	2.14e-56	3.13e-54	2.53e-54	91
hsa0301035	Cervix	HSIL_HPV	Ribosome	80/459	167/8465	9.61e-58	2.82e-55	2.28e-55	80
hsa0517135	Cervix	HSIL_HPV	Coronavirus disease - COVID-19	91/459	232/8465	2.14e-56	3.13e-54	2.53e-54	91
hsa03010	Colorectum	AD	Ribosome	96/2092	167/8465	8.28e-20	5.54e-18	3.54e-18	96
hsa05171	Colorectum	AD	Coronavirus disease - COVID-19	113/2092	232/8465	9.90e-16	2.55e-14	1.63e-14	113
hsa030101	Colorectum	AD	Ribosome	96/2092	167/8465	8.28e-20	5.54e-18	3.54e-18	96
hsa051711	Colorectum	AD	Coronavirus disease - COVID-19	113/2092	232/8465	9.90e-16	2.55e-14	1.63e-14	113
hsa030102	Colorectum	SER	Ribosome	92/1580	167/8465	2.21e-26	3.66e-24	2.66e-24	92
hsa051712	Colorectum	SER	Coronavirus disease - COVID-19	98/1580	232/8465	3.33e-17	8.50e-16	6.17e-16	98
hsa030103	Colorectum	SER	Ribosome	92/1580	167/8465	2.21e-26	3.66e-24	2.66e-24	92
hsa051713	Colorectum	SER	Coronavirus disease - COVID-19	98/1580	232/8465	3.33e-17	8.50e-16	6.17e-16	98
hsa030104	Colorectum	MSS	Ribosome	96/1875	167/8465	1.82e-23	2.03e-21	1.24e-21	96
hsa051714	Colorectum	MSS	Coronavirus disease - COVID-19	108/1875	232/8465	6.50e-17	1.67e-15	1.03e-15	108
hsa030105	Colorectum	MSS	Ribosome	96/1875	167/8465	1.82e-23	2.03e-21	1.24e-21	96
hsa051715	Colorectum	MSS	Coronavirus disease - COVID-19	108/1875	232/8465	6.50e-17	1.67e-15	1.03e-15	108

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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

RPLP0

SNV

Missense_Mutation

c.784N>A

p.Ala262Thr

p.A262T

P05388

protein_coding

tolerated(0.05)

possibly_damaging(0.817)

TCGA-BH-A1FG-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

RPLP0

insertion

In_Frame_Ins

novel

c.211_212insCTC

p.Asn71delinsThrHis

p.N71delinsTH

P05388

protein_coding

TCGA-BH-A0AW-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

carboplatin

RPLP0

insertion

Frame_Shift_Ins

novel

c.210_211insCATTTTTCGTTCATGGA

p.Asn71HisfsTer77

p.N71Hfs*77

P05388

protein_coding

TCGA-BH-A0AW-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

carboplatin

RPLP0

SNV

Missense_Mutation

rs563131457

c.662A>G

p.Asn221Ser

p.N221S

P05388

protein_coding

tolerated(0.08)

benign(0.022)

TCGA-EK-A2R9-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

RPLP0

SNV

Missense_Mutation

novel

c.818N>G

p.Ser273Cys

p.S273C

P05388

protein_coding

deleterious(0)

possibly_damaging(0.56)

TCGA-VS-A958-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

RPLP0

SNV

Missense_Mutation

novel

c.511G>A

p.Glu171Lys

p.E171K

P05388

protein_coding

deleterious(0.03)

benign(0.048)

TCGA-AA-3514-01

Colorectum

colon adenocarcinoma

Female

>=65

I/II

Unknown

RPLP0

SNV

Missense_Mutation

novel

c.518N>T

p.Thr173Met

p.T173M

P05388

protein_coding

deleterious(0.02)

benign(0.186)

TCGA-A5-A0G1-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

RPLP0

SNV

Missense_Mutation

c.409N>C

p.Phe137Leu

p.F137L

P05388

protein_coding

deleterious(0.01)

benign(0.196)

TCGA-A5-A0GA-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

III/IV

Chemotherapy

taxol

RPLP0

SNV

Missense_Mutation

rs766132340

c.86N>C

p.Ile29Thr

p.I29T

P05388

protein_coding

deleterious(0.01)

possibly_damaging(0.457)

TCGA-A5-A0R7-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

RPLP0

SNV

Missense_Mutation

c.25T>C

p.Trp9Arg

p.W9R

P05388

protein_coding

tolerated(0.41)

benign(0.02)

TCGA-A5-A0VP-01

Endometrium

uterine corpus endometrioid carcinoma

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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