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: RPS6KA5

Gene summary for RPS6KA5

Gene summary.

Gene information	Species	Human
	Gene symbol	RPS6KA5
	Gene ID	9252
	Gene name	ribosomal protein S6 kinase A5
	Gene Alias	MSK1
	Cytomap	14q32.11
	Gene Type	protein-coding
	GO ID	GO:0000902
	UniProtAcc	O75582

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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
9252	RPS6KA5	HTA11_3410_2000001011	Human	Colorectum	AD	3.18e-19	-6.55e-01	0.0155
9252	RPS6KA5	HTA11_2487_2000001011	Human	Colorectum	SER	9.42e-09	-5.33e-01	-0.1808
9252	RPS6KA5	HTA11_3361_2000001011	Human	Colorectum	AD	3.54e-04	-4.59e-01	-0.1207
9252	RPS6KA5	HTA11_696_2000001011	Human	Colorectum	AD	5.03e-10	-4.50e-01	-0.1464
9252	RPS6KA5	HTA11_5212_2000001011	Human	Colorectum	AD	5.29e-03	-6.79e-01	-0.2061
9252	RPS6KA5	HTA11_7862_2000001011	Human	Colorectum	AD	4.57e-02	-5.79e-01	-0.0179
9252	RPS6KA5	HTA11_866_3004761011	Human	Colorectum	AD	9.06e-07	-4.98e-01	0.096
9252	RPS6KA5	HTA11_8622_2000001021	Human	Colorectum	SER	5.67e-03	-6.65e-01	0.0528
9252	RPS6KA5	HTA11_6818_2000001021	Human	Colorectum	AD	1.51e-04	-5.27e-01	0.0588
9252	RPS6KA5	HTA11_99999970781_79442	Human	Colorectum	MSS	1.04e-04	-3.40e-01	0.294
9252	RPS6KA5	HTA11_99999971662_82457	Human	Colorectum	MSS	1.04e-24	-7.06e-01	0.3859
9252	RPS6KA5	HTA11_99999973899_84307	Human	Colorectum	MSS	6.43e-04	-6.08e-01	0.2585
9252	RPS6KA5	HTA11_99999974143_84620	Human	Colorectum	MSS	1.50e-28	-7.61e-01	0.3005
9252	RPS6KA5	F007	Human	Colorectum	FAP	3.83e-04	-3.91e-01	0.1176
9252	RPS6KA5	A002-C-010	Human	Colorectum	FAP	2.21e-03	-3.07e-01	0.242
9252	RPS6KA5	A001-C-207	Human	Colorectum	FAP	1.28e-11	-5.57e-01	0.1278
9252	RPS6KA5	A015-C-203	Human	Colorectum	FAP	7.54e-23	-4.31e-01	-0.1294
9252	RPS6KA5	A015-C-204	Human	Colorectum	FAP	2.01e-06	-4.04e-01	-0.0228
9252	RPS6KA5	A014-C-040	Human	Colorectum	FAP	4.72e-03	-3.44e-01	-0.1184
9252	RPS6KA5	A002-C-201	Human	Colorectum	FAP	1.04e-14	-3.89e-01	0.0324

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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
Endometrium		AEH: Atypical endometrial hyperplasia
		EEC: Endometrioid Cancer
Esophagus		ESCC: Esophageal squamous cell carcinoma
		HGIN: High-grade intraepithelial neoplasias
		LGIN: Low-grade intraepithelial neoplasias
Lung		AAH: Atypical adenomatous hyperplasia
		AIS: Adenocarcinoma in situ
		IAC: Invasive lung adenocarcinoma
		MIA: Minimally invasive adenocarcinoma

∗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:0038127	Colorectum	AD	ERBB signaling pathway	55/3918	121/18723	1.19e-09	8.85e-08	55
GO:0007173	Colorectum	AD	epidermal growth factor receptor signaling pathway	50/3918	108/18723	3.08e-09	2.07e-07	50
GO:0007409	Colorectum	AD	axonogenesis	122/3918	418/18723	3.36e-05	6.15e-04	122
GO:0061564	Colorectum	AD	axon development	132/3918	467/18723	8.40e-05	1.31e-03	132
GO:0018105	Colorectum	AD	peptidyl-serine phosphorylation	88/3918	315/18723	1.73e-03	1.43e-02	88
GO:0018209	Colorectum	AD	peptidyl-serine modification	92/3918	338/18723	3.19e-03	2.36e-02	92
GO:0051091	Colorectum	AD	positive regulation of DNA-binding transcription factor activity	73/3918	260/18723	3.52e-03	2.54e-02	73
GO:0007411	Colorectum	AD	axon guidance	64/3918	227/18723	5.41e-03	3.55e-02	64
GO:0097485	Colorectum	AD	neuron projection guidance	64/3918	228/18723	6.02e-03	3.78e-02	64
GO:0031056	Colorectum	AD	regulation of histone modification	45/3918	152/18723	7.05e-03	4.31e-02	45
GO:00381271	Colorectum	SER	ERBB signaling pathway	35/2897	121/18723	1.21e-04	2.49e-03	35
GO:00071731	Colorectum	SER	epidermal growth factor receptor signaling pathway	32/2897	108/18723	1.42e-04	2.82e-03	32
GO:00310561	Colorectum	SER	regulation of histone modification	37/2897	152/18723	2.80e-03	2.50e-02	37
GO:00074111	Colorectum	SER	axon guidance	51/2897	227/18723	3.29e-03	2.82e-02	51
GO:00974851	Colorectum	SER	neuron projection guidance	51/2897	228/18723	3.61e-03	3.03e-02	51
GO:00615641	Colorectum	SER	axon development	94/2897	467/18723	3.78e-03	3.13e-02	94
GO:00181051	Colorectum	SER	peptidyl-serine phosphorylation	66/2897	315/18723	5.47e-03	4.06e-02	66
GO:00510911	Colorectum	SER	positive regulation of DNA-binding transcription factor activity	56/2897	260/18723	5.55e-03	4.09e-02	56
GO:00074091	Colorectum	SER	axonogenesis	84/2897	418/18723	6.20e-03	4.49e-02	84
GO:00071732	Colorectum	MSS	epidermal growth factor receptor signaling pathway	43/3467	108/18723	1.92e-07	8.31e-06	43

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa05131	Colorectum	AD	Shigellosis	109/2092	247/8465	1.09e-11	2.44e-10	1.55e-10	109
hsa04722	Colorectum	AD	Neurotrophin signaling pathway	50/2092	119/8465	2.28e-05	2.24e-04	1.43e-04	50
hsa051311	Colorectum	AD	Shigellosis	109/2092	247/8465	1.09e-11	2.44e-10	1.55e-10	109
hsa047221	Colorectum	AD	Neurotrophin signaling pathway	50/2092	119/8465	2.28e-05	2.24e-04	1.43e-04	50
hsa051312	Colorectum	SER	Shigellosis	87/1580	247/8465	3.07e-10	7.27e-09	5.28e-09	87
hsa047222	Colorectum	SER	Neurotrophin signaling pathway	35/1580	119/8465	2.80e-03	2.02e-02	1.47e-02	35
hsa051313	Colorectum	SER	Shigellosis	87/1580	247/8465	3.07e-10	7.27e-09	5.28e-09	87
hsa047223	Colorectum	SER	Neurotrophin signaling pathway	35/1580	119/8465	2.80e-03	2.02e-02	1.47e-02	35
hsa051314	Colorectum	MSS	Shigellosis	94/1875	247/8465	6.82e-09	1.34e-07	8.23e-08	94
hsa047224	Colorectum	MSS	Neurotrophin signaling pathway	45/1875	119/8465	7.04e-05	6.55e-04	4.02e-04	45
hsa04713	Colorectum	MSS	Circadian entrainment	32/1875	97/8465	8.84e-03	3.25e-02	1.99e-02	32
hsa051315	Colorectum	MSS	Shigellosis	94/1875	247/8465	6.82e-09	1.34e-07	8.23e-08	94
hsa047225	Colorectum	MSS	Neurotrophin signaling pathway	45/1875	119/8465	7.04e-05	6.55e-04	4.02e-04	45
hsa047131	Colorectum	MSS	Circadian entrainment	32/1875	97/8465	8.84e-03	3.25e-02	1.99e-02	32
hsa051318	Colorectum	FAP	Shigellosis	76/1404	247/8465	1.57e-08	5.84e-07	3.55e-07	76
hsa047226	Colorectum	FAP	Neurotrophin signaling pathway	38/1404	119/8465	2.49e-05	2.78e-04	1.69e-04	38
hsa04010	Colorectum	FAP	MAPK signaling pathway	68/1404	302/8465	4.00e-03	1.67e-02	1.02e-02	68
hsa04261	Colorectum	FAP	Adrenergic signaling in cardiomyocytes	38/1404	154/8465	6.16e-03	2.34e-02	1.42e-02	38
hsa051319	Colorectum	FAP	Shigellosis	76/1404	247/8465	1.57e-08	5.84e-07	3.55e-07	76
hsa047227	Colorectum	FAP	Neurotrophin signaling pathway	38/1404	119/8465	2.49e-05	2.78e-04	1.69e-04	38

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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

TF	Cell Type	Tissue	Disease Stage	Target Gene	RSS	Regulon Activity
RPS6KA5	M1MAC	Cervix	ADJ	CASK,LIN7B,IKZF2, etc.	1.29e-01
RPS6KA5	M1MAC	Cervix	CC	CASK,LIN7B,IKZF2, etc.	4.63e-02
RPS6KA5	PLA	Cervix	Healthy	CASK,LIN7B,IKZF2, etc.	1.07e-02
RPS6KA5	CD8TEXINT	Cervix	Healthy	CASK,LIN7B,IKZF2, etc.	2.59e-03
RPS6KA5	M1MAC	Cervix	HSIL_HPV	CASK,LIN7B,IKZF2, etc.	1.88e-02
RPS6KA5	MON	Cervix	HSIL_HPV	CASK,LIN7B,IKZF2, etc.	1.43e-02
RPS6KA5	DC	Cervix	HSIL_HPV	CASK,LIN7B,IKZF2, etc.	2.33e-02
RPS6KA5	BMEM	Cervix	HSIL_HPV	CASK,LIN7B,IKZF2, etc.	0.00e+00
RPS6KA5	DC	Cervix	N_HPV	CASK,LIN7B,IKZF2, etc.	1.17e-02
RPS6KA5	TFH	Cervix	N_HPV	CASK,LIN7B,IKZF2, etc.	7.43e-03

∗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

RPS6KA5

SNV

Missense_Mutation

novel

c.1642N>A

p.Glu548Lys

p.E548K

O75582

protein_coding

deleterious(0.01)

probably_damaging(0.998)

TCGA-3C-AALI-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unspecific

Poly E

Complete Response

RPS6KA5

SNV

Missense_Mutation

novel

c.885N>A

p.Met295Ile

p.M295I

O75582

protein_coding

tolerated(0.39)

benign(0)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

RPS6KA5

SNV

Missense_Mutation

rs369503281

c.1322N>A

p.Arg441Gln

p.R441Q

O75582

protein_coding

deleterious(0.01)

probably_damaging(0.942)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

RPS6KA5

SNV

Missense_Mutation

c.1575G>T

p.Met525Ile

p.M525I

O75582

protein_coding

tolerated(0.17)

possibly_damaging(0.519)

TCGA-AR-A250-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

RPS6KA5

SNV

Missense_Mutation

novel

c.560N>T

p.Ser187Phe

p.S187F

O75582

protein_coding

deleterious(0.01)

probably_damaging(0.95)

TCGA-BH-A0H5-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

RPS6KA5

SNV

Missense_Mutation

c.888A>C

p.Lys296Asn

p.K296N

O75582

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-BH-A18G-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

RPS6KA5

SNV

Missense_Mutation

c.1718C>T

p.Pro573Leu

p.P573L

O75582

protein_coding

deleterious(0.02)

possibly_damaging(0.761)

TCGA-BH-A1FM-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

RPS6KA5

SNV

Missense_Mutation

c.1898G>A

p.Ser633Asn

p.S633N

O75582

protein_coding

tolerated(0.21)

benign(0.031)

TCGA-C8-A12U-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

RPS6KA5

SNV

Missense_Mutation

c.2303N>G

p.Ser768Cys

p.S768C

O75582

protein_coding

deleterious(0.01)

probably_damaging(0.981)

TCGA-E9-A1NC-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

RPS6KA5

insertion

In_Frame_Ins

novel

c.1103_1104insAAGACCAGC

p.Ser368_Glu369insArgProAla

p.S368_E369insRPA

O75582

protein_coding

TCGA-A2-A0CM-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

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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
9252	RPS6KA5	DRUGGABLE GENOME, ENZYME, KINASE, TRANSCRIPTION FACTOR, SERINE THREONINE KINASE		PHA-767491	CHEMBL225519
9252	RPS6KA5	DRUGGABLE GENOME, ENZYME, KINASE, TRANSCRIPTION FACTOR, SERINE THREONINE KINASE	inhibitor	249565811
9252	RPS6KA5	DRUGGABLE GENOME, ENZYME, KINASE, TRANSCRIPTION FACTOR, SERINE THREONINE KINASE		GSK-269962A	GSK-269962A
9252	RPS6KA5	DRUGGABLE GENOME, ENZYME, KINASE, TRANSCRIPTION FACTOR, SERINE THREONINE KINASE		GW843682X	GW843682X
9252	RPS6KA5	DRUGGABLE GENOME, ENZYME, KINASE, TRANSCRIPTION FACTOR, SERINE THREONINE KINASE		US9365572, 5
9252	RPS6KA5	DRUGGABLE GENOME, ENZYME, KINASE, TRANSCRIPTION FACTOR, SERINE THREONINE KINASE	inhibitor	HESPERADIN	HESPERADIN	19035792
9252	RPS6KA5	DRUGGABLE GENOME, ENZYME, KINASE, TRANSCRIPTION FACTOR, SERINE THREONINE KINASE	inhibitor	249565810	CHEMBL188434
9252	RPS6KA5	DRUGGABLE GENOME, ENZYME, KINASE, TRANSCRIPTION FACTOR, SERINE THREONINE KINASE		ILORASERTIB	ILORASERTIB
9252	RPS6KA5	DRUGGABLE GENOME, ENZYME, KINASE, TRANSCRIPTION FACTOR, SERINE THREONINE KINASE		LINIFANIB	LINIFANIB
9252	RPS6KA5	DRUGGABLE GENOME, ENZYME, KINASE, TRANSCRIPTION FACTOR, SERINE THREONINE KINASE		DOVITINIB	DOVITINIB

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