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: RIPK1

Gene summary for RIPK1

Gene summary.

Gene information	Species	Human
	Gene symbol	RIPK1
	Gene ID	8737
	Gene name	receptor interacting serine/threonine kinase 1
	Gene Alias	AIEFL
	Cytomap	6p25.2
	Gene Type	protein-coding
	GO ID	GO:0000165
	UniProtAcc	A0A024QZU0

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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
8737	RIPK1	AEH-subject1	Human	Endometrium	AEH	2.98e-26	7.30e-01	-0.3059
8737	RIPK1	AEH-subject2	Human	Endometrium	AEH	1.11e-14	5.70e-01	-0.2525
8737	RIPK1	AEH-subject3	Human	Endometrium	AEH	1.10e-19	6.30e-01	-0.2576
8737	RIPK1	EEC-subject1	Human	Endometrium	EEC	2.16e-04	3.11e-01	-0.2682
8737	RIPK1	EEC-subject2	Human	Endometrium	EEC	1.24e-04	3.34e-01	-0.2607
8737	RIPK1	EEC-subject4	Human	Endometrium	EEC	1.59e-02	1.86e-01	-0.2571
8737	RIPK1	LZE4T	Human	Esophagus	ESCC	1.45e-05	8.73e-02	0.0811
8737	RIPK1	LZE7T	Human	Esophagus	ESCC	3.35e-02	1.61e-01	0.0667
8737	RIPK1	LZE20T	Human	Esophagus	ESCC	4.60e-03	5.91e-02	0.0662
8737	RIPK1	LZE24T	Human	Esophagus	ESCC	5.27e-10	1.27e-01	0.0596
8737	RIPK1	P1T-E	Human	Esophagus	ESCC	2.87e-11	3.10e-01	0.0875
8737	RIPK1	P2T-E	Human	Esophagus	ESCC	5.07e-19	3.07e-01	0.1177
8737	RIPK1	P4T-E	Human	Esophagus	ESCC	2.77e-12	1.43e-01	0.1323
8737	RIPK1	P5T-E	Human	Esophagus	ESCC	1.12e-12	1.48e-02	0.1327
8737	RIPK1	P8T-E	Human	Esophagus	ESCC	2.98e-13	1.74e-01	0.0889
8737	RIPK1	P9T-E	Human	Esophagus	ESCC	1.14e-06	2.03e-01	0.1131
8737	RIPK1	P10T-E	Human	Esophagus	ESCC	3.54e-03	2.44e-02	0.116
8737	RIPK1	P11T-E	Human	Esophagus	ESCC	3.79e-12	4.09e-01	0.1426
8737	RIPK1	P12T-E	Human	Esophagus	ESCC	5.43e-08	1.56e-01	0.1122
8737	RIPK1	P15T-E	Human	Esophagus	ESCC	2.10e-08	1.42e-01	0.1149

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
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
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:200123316	Endometrium	AEH	regulation of apoptotic signaling pathway	86/2100	356/18723	2.97e-12	4.95e-10	86
GO:000697916	Endometrium	AEH	response to oxidative stress	93/2100	446/18723	1.94e-09	1.64e-07	93
GO:000030216	Endometrium	AEH	response to reactive oxygen species	54/2100	222/18723	2.54e-08	1.49e-06	54
GO:20012358	Endometrium	AEH	positive regulation of apoptotic signaling pathway	36/2100	126/18723	7.56e-08	3.92e-06	36
GO:006219716	Endometrium	AEH	cellular response to chemical stress	71/2100	337/18723	1.03e-07	5.05e-06	71
GO:004254215	Endometrium	AEH	response to hydrogen peroxide	38/2100	146/18723	4.70e-07	1.92e-05	38
GO:009719116	Endometrium	AEH	extrinsic apoptotic signaling pathway	49/2100	219/18723	1.58e-06	4.94e-05	49
GO:200123416	Endometrium	AEH	negative regulation of apoptotic signaling pathway	49/2100	224/18723	3.12e-06	8.58e-05	49
GO:200123616	Endometrium	AEH	regulation of extrinsic apoptotic signaling pathway	37/2100	151/18723	3.17e-06	8.69e-05	37
GO:003459916	Endometrium	AEH	cellular response to oxidative stress	58/2100	288/18723	6.49e-06	1.58e-04	58
GO:00431229	Endometrium	AEH	regulation of I-kappaB kinase/NF-kappaB signaling	52/2100	249/18723	6.58e-06	1.59e-04	52
GO:00514039	Endometrium	AEH	stress-activated MAPK cascade	50/2100	239/18723	9.33e-06	2.18e-04	50
GO:00310989	Endometrium	AEH	stress-activated protein kinase signaling cascade	51/2100	247/18723	1.12e-05	2.52e-04	51
GO:00328728	Endometrium	AEH	regulation of stress-activated MAPK cascade	42/2100	192/18723	1.53e-05	3.23e-04	42
GO:00431238	Endometrium	AEH	positive regulation of I-kappaB kinase/NF-kappaB signaling	41/2100	186/18723	1.59e-05	3.32e-04	41
GO:00434105	Endometrium	AEH	positive regulation of MAPK cascade	84/2100	480/18723	2.19e-05	4.25e-04	84
GO:00703028	Endometrium	AEH	regulation of stress-activated protein kinase signaling cascade	42/2100	195/18723	2.27e-05	4.35e-04	42
GO:00072498	Endometrium	AEH	I-kappaB kinase/NF-kappaB signaling	55/2100	281/18723	2.60e-05	4.88e-04	55
GO:003461415	Endometrium	AEH	cellular response to reactive oxygen species	34/2100	155/18723	9.00e-05	1.30e-03	34
GO:00159319	Endometrium	AEH	nucleobase-containing compound transport	44/2100	222/18723	1.19e-04	1.66e-03	44

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0513013	Stomach	GC	Pathogenic Escherichia coli infection	43/708	197/8465	2.99e-09	6.39e-08	4.50e-08	43
hsa0513213	Stomach	GC	Salmonella infection	42/708	249/8465	7.57e-06	1.05e-04	7.41e-05	42
hsa0516913	Stomach	GC	Epstein-Barr virus infection	33/708	202/8465	1.35e-04	1.31e-03	9.22e-04	33
hsa0513113	Stomach	GC	Shigellosis	36/708	247/8465	6.74e-04	5.42e-03	3.82e-03	36
hsa0516311	Stomach	GC	Human cytomegalovirus infection	33/708	225/8465	9.98e-04	7.42e-03	5.23e-03	33
hsa0517011	Stomach	GC	Human immunodeficiency virus 1 infection	30/708	212/8465	2.91e-03	1.76e-02	1.24e-02	30
hsa0513021	Stomach	CAG with IM	Pathogenic Escherichia coli infection	41/640	197/8465	1.58e-09	3.13e-08	2.20e-08	41
hsa0513221	Stomach	CAG with IM	Salmonella infection	42/640	249/8465	5.52e-07	9.75e-06	6.84e-06	42
hsa051692	Stomach	CAG with IM	Epstein-Barr virus infection	32/640	202/8465	4.57e-05	4.69e-04	3.29e-04	32
hsa0516321	Stomach	CAG with IM	Human cytomegalovirus infection	31/640	225/8465	7.66e-04	5.94e-03	4.17e-03	31
hsa0513121	Stomach	CAG with IM	Shigellosis	33/640	247/8465	9.05e-04	6.85e-03	4.81e-03	33
hsa0517021	Stomach	CAG with IM	Human immunodeficiency virus 1 infection	29/640	212/8465	1.26e-03	8.93e-03	6.27e-03	29
hsa051604	Stomach	CAG with IM	Hepatitis C	21/640	157/8465	7.26e-03	4.05e-02	2.84e-02	21
hsa0421710	Stomach	CAG with IM	Necroptosis	21/640	159/8465	8.37e-03	4.59e-02	3.22e-02	21
hsa0513031	Stomach	CAG with IM	Pathogenic Escherichia coli infection	41/640	197/8465	1.58e-09	3.13e-08	2.20e-08	41
hsa0513231	Stomach	CAG with IM	Salmonella infection	42/640	249/8465	5.52e-07	9.75e-06	6.84e-06	42
hsa051693	Stomach	CAG with IM	Epstein-Barr virus infection	32/640	202/8465	4.57e-05	4.69e-04	3.29e-04	32
hsa0516331	Stomach	CAG with IM	Human cytomegalovirus infection	31/640	225/8465	7.66e-04	5.94e-03	4.17e-03	31
hsa0513131	Stomach	CAG with IM	Shigellosis	33/640	247/8465	9.05e-04	6.85e-03	4.81e-03	33
hsa0517031	Stomach	CAG with IM	Human immunodeficiency virus 1 infection	29/640	212/8465	1.26e-03	8.93e-03	6.27e-03	29

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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

RIPK1

SNV

Missense_Mutation

c.1237N>T

p.Arg413Cys

p.R413C

Q13546

protein_coding

deleterious(0)

probably_damaging(0.925)

TCGA-A8-A09Z-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

RIPK1

SNV

Missense_Mutation

c.919G>C

p.Glu307Gln

p.E307Q

Q13546

protein_coding

tolerated(0.52)

benign(0.003)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

RIPK1

SNV

Missense_Mutation

c.808N>T

p.Ala270Ser

p.A270S

Q13546

protein_coding

tolerated(0.38)

benign(0.173)

TCGA-BH-A0HP-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Chemotherapy

doxorubicin

RIPK1

SNV

Missense_Mutation

novel

c.1281N>C

p.Glu427Asp

p.E427D

Q13546

protein_coding

tolerated(0.41)

benign(0)

TCGA-C8-A132-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

RIPK1

SNV

Missense_Mutation

c.439N>A

p.Asp147Asn

p.D147N

Q13546

protein_coding

deleterious(0.03)

probably_damaging(0.987)

TCGA-E2-A152-01

Breast

breast invasive carcinoma

Female

<65

I/II

Targeted Molecular therapy

trastuzumab

RIPK1

insertion

Frame_Shift_Ins

novel

c.1407_1408insGGTCCTGTGGAGGAGTCCTGGTTTGCTCCTTCCCTGG

p.Ser470GlyfsTer42

p.S470Gfs*42

Q13546

protein_coding

TCGA-A8-A092-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

paclitaxel

RIPK1

SNV

Missense_Mutation

c.324N>C

p.Met108Ile

p.M108I

Q13546

protein_coding

tolerated(0.62)

benign(0)

TCGA-JW-A5VL-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

RIPK1

SNV

Missense_Mutation

c.1297G>A

p.Glu433Lys

p.E433K

Q13546

protein_coding

tolerated(0.79)

benign(0.021)

TCGA-Q1-A73O-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

RIPK1

SNV

Missense_Mutation

rs748885856

c.1571N>T

p.Pro524Leu

p.P524L

Q13546

protein_coding

tolerated(0.12)

benign(0)

TCGA-VS-A953-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

RIPK1

deletion

Frame_Shift_Del

novel

c.1302delN

p.Gly436AlafsTer76

p.G436Afs*76

Q13546

protein_coding

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
8737	RIPK1	KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME, ENZYME	inhibitor	340590273
8737	RIPK1	KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME, ENZYME	inhibitor	249565867
8737	RIPK1	KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME, ENZYME	inhibitor	178102513	PONATINIB
8737	RIPK1	KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME, ENZYME	inhibitor	384403680
8737	RIPK1	KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME, ENZYME		RESVERATROL	RESVERATROL	16116226
8737	RIPK1	KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME, ENZYME	inhibitor	336446940
8737	RIPK1	KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME, ENZYME	inhibitor	354702223	NECROSTATIN
8737	RIPK1	KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME, ENZYME		GSK2982772
8737	RIPK1	KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME, ENZYME	inhibitor	354702224
8737	RIPK1	KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME, ENZYME	inhibitor	354702222

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