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: RPLP1

Gene summary for RPLP1

Gene summary.

Gene information	Species	Human
	Gene symbol	RPLP1
	Gene ID	6176
	Gene name	ribosomal protein lateral stalk subunit P1
	Gene Alias	LP1
	Cytomap	15q23
	Gene Type	protein-coding
	GO ID	GO:0001932
	UniProtAcc	A0A024R608

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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
6176	RPLP1	GSM5353216_PA_PB1A_Pool_1_3_S50_L002	Human	Prostate	Tumor	2.25e-46	-5.46e-01	0.159
6176	RPLP1	GSM5353217_PA_PB1A_Pool_2_S107_L004	Human	Prostate	Tumor	4.37e-44	-6.68e-01	0.156
6176	RPLP1	GSM5353218_PA_PB1B_Pool_1_2_S74_L003	Human	Prostate	Tumor	1.21e-43	-6.08e-01	0.1479
6176	RPLP1	GSM5353220_PA_PB1B_Pool_3_S51_L002	Human	Prostate	Tumor	6.86e-54	-1.08e+00	0.1531
6176	RPLP1	GSM5353221_PA_PB2A_Pool_1_3_S25_L001	Human	Prostate	Tumor	1.05e-101	-5.75e-01	0.1633
6176	RPLP1	GSM5353222_PA_PB2B_Pool_1_3_S52_L002	Human	Prostate	Tumor	1.08e-125	-7.66e-01	0.1608
6176	RPLP1	GSM5353223_PA_PB2B_Pool_2_S26_L001	Human	Prostate	Tumor	1.35e-93	-6.16e-01	0.1604
6176	RPLP1	GSM5353224_PA_PR5186_Pool_1_2_3_S27_L001	Human	Prostate	Tumor	1.10e-95	-5.48e-01	0.1621
6176	RPLP1	GSM5353225_PA_PR5196-1_Pool_1_2_3_S53_L002	Human	Prostate	Tumor	1.66e-86	-7.57e-01	0.1619
6176	RPLP1	GSM5353226_PA_PR5196-2_Pool_1_2_3_S54_L002	Human	Prostate	Tumor	7.86e-71	-8.32e-01	0.159
6176	RPLP1	GSM5353227_PA_PR5199-193K_Pool_1_2_3_S55_L002	Human	Prostate	Tumor	1.05e-111	-8.30e-01	0.1602
6176	RPLP1	GSM5353228_PA_PR5199-640K_Pool_1_3_S108_L004	Human	Prostate	Tumor	1.79e-39	-8.49e-01	0.1537
6176	RPLP1	GSM5353232_PA_PR5249_T1_S3_L001	Human	Prostate	Tumor	8.88e-41	-1.12e+00	0.1439
6176	RPLP1	GSM5353236_PA_PR5251_T1_S7_L001	Human	Prostate	Tumor	8.13e-83	-7.25e-01	0.1608
6176	RPLP1	GSM5353237_PA_PR5251_T2_S8_L001	Human	Prostate	Tumor	2.13e-72	-7.95e-01	0.1622
6176	RPLP1	GSM5353240_PA_PR5254_T1_S15_L001	Human	Prostate	Tumor	4.88e-134	-6.54e-01	0.1575
6176	RPLP1	GSM5353243_PA_PR5261_T1_S23_L002	Human	Prostate	Tumor	1.07e-133	-1.02e+00	0.1545
6176	RPLP1	GSM5353244_PA_PR5261_T2_S24_L002	Human	Prostate	Tumor	8.10e-122	-9.45e-01	0.1569
6176	RPLP1	GSM5353247_PA_PR5269_3_S27_L002	Human	Prostate	Tumor	3.74e-37	-1.01e+00	0.1532
6176	RPLP1	GSM5353248_PA_PR5269_4_S28_L002	Human	Prostate	Tumor	5.89e-44	-8.97e-01	0.1541

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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
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:003367410	Cervix	CC	positive regulation of kinase activity	101/2311	467/18723	8.66e-09	7.22e-07	101
GO:00458608	Cervix	CC	positive regulation of protein kinase activity	85/2311	386/18723	5.61e-08	3.29e-06	85
GO:000218115	Cervix	HSIL_HPV	cytoplasmic translation	86/737	148/18723	3.97e-82	1.91e-78	86
GO:003367413	Cervix	HSIL_HPV	positive regulation of kinase activity	34/737	467/18723	4.49e-04	6.63e-03	34
GO:004586013	Cervix	HSIL_HPV	positive regulation of protein kinase activity	27/737	386/18723	2.93e-03	2.74e-02	27
GO:00064148	Cervix	HSIL_HPV	translational elongation	7/737	55/18723	5.59e-03	4.47e-02	7
GO:0002181	Colorectum	AD	cytoplasmic translation	109/3918	148/18723	3.40e-43	2.13e-39	109
GO:0033674	Colorectum	AD	positive regulation of kinase activity	131/3918	467/18723	1.28e-04	1.85e-03	131
GO:0045860	Colorectum	AD	positive regulation of protein kinase activity	107/3918	386/18723	8.01e-04	7.92e-03	107
GO:0006414	Colorectum	AD	translational elongation	21/3918	55/18723	2.53e-03	1.93e-02	21
GO:00021811	Colorectum	SER	cytoplasmic translation	102/2897	148/18723	1.38e-48	8.49e-45	102
GO:00336741	Colorectum	SER	positive regulation of kinase activity	95/2897	467/18723	2.62e-03	2.41e-02	95
GO:00064141	Colorectum	SER	translational elongation	17/2897	55/18723	3.00e-03	2.65e-02	17
GO:00458601	Colorectum	SER	positive regulation of protein kinase activity	79/2897	386/18723	4.85e-03	3.79e-02	79
GO:00021812	Colorectum	MSS	cytoplasmic translation	108/3467	148/18723	1.78e-47	1.11e-43	108
GO:00336742	Colorectum	MSS	positive regulation of kinase activity	122/3467	467/18723	2.50e-05	5.21e-04	122
GO:00458602	Colorectum	MSS	positive regulation of protein kinase activity	102/3467	386/18723	6.93e-05	1.20e-03	102
GO:00064142	Colorectum	MSS	translational elongation	19/3467	55/18723	3.47e-03	2.59e-02	19
GO:00021813	Colorectum	MSI-H	cytoplasmic translation	100/1319	148/18723	1.50e-79	8.31e-76	100

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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

RPLP1

deletion

Frame_Shift_Del

c.339delT

p.Phe113LeufsTer7

p.F113Lfs*7

P05386

protein_coding

TCGA-CK-5912-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

RPLP1

SNV

Missense_Mutation

novel

c.64N>T

p.Thr22Ser

p.T22S

P05386

protein_coding

tolerated(0.07)

benign(0.006)

TCGA-AX-A3G9-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

carboplatin

RPLP1

SNV

Missense_Mutation

novel

c.200G>T

p.Gly67Val

p.G67V

P05386

protein_coding

deleterious(0.02)

possibly_damaging(0.903)

TCGA-95-7043-01

Lung

lung adenocarcinoma

Female

<65

I/II

Unknown

RPLP1

SNV

Missense_Mutation

rs766033183

c.149N>T

p.Ala50Val

p.A50V

P05386

protein_coding

tolerated(0.06)

possibly_damaging(0.764)

TCGA-XK-AAIW-01

Prostate

prostate adenocarcinoma

Male

>=65

Unknown

RPLP1

SNV

Missense_Mutation

c.299N>G

p.Glu100Gly

p.E100G

P05386

protein_coding

deleterious(0)

possibly_damaging(0.864)

TCGA-BR-6452-01

Stomach

stomach adenocarcinoma

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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