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: RNF144B

Gene summary for RNF144B

Gene summary.

Gene information	Species	Human
	Gene symbol	RNF144B
	Gene ID	255488
	Gene name	ring finger protein 144B
	Gene Alias	IBRDC2
	Cytomap	6p22.3
	Gene Type	protein-coding
	GO ID	GO:0000209
	UniProtAcc	Q7Z419

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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
255488	RNF144B	N_HPV_2	Human	Cervix	N_HPV	2.69e-02	1.75e-01	-0.0131
255488	RNF144B	CCI_1	Human	Cervix	CC	9.44e-08	9.86e-01	0.528
255488	RNF144B	CCI_2	Human	Cervix	CC	1.94e-05	9.09e-01	0.5249
255488	RNF144B	sample3	Human	Cervix	CC	9.10e-05	1.95e-01	0.1387
255488	RNF144B	T3	Human	Cervix	CC	7.95e-04	2.14e-01	0.1389
255488	RNF144B	LZE5T	Human	Esophagus	ESCC	6.39e-07	5.10e-01	0.0514
255488	RNF144B	LZE7T	Human	Esophagus	ESCC	5.21e-04	2.72e-01	0.0667
255488	RNF144B	LZE20T	Human	Esophagus	ESCC	3.58e-05	1.79e-01	0.0662
255488	RNF144B	LZE22T	Human	Esophagus	ESCC	1.05e-02	4.12e-01	0.068
255488	RNF144B	LZE24T	Human	Esophagus	ESCC	1.88e-04	2.30e-01	0.0596
255488	RNF144B	LZE6T	Human	Esophagus	ESCC	1.30e-03	1.91e-01	0.0845
255488	RNF144B	P1T-E	Human	Esophagus	ESCC	1.23e-05	3.53e-01	0.0875
255488	RNF144B	P2T-E	Human	Esophagus	ESCC	1.61e-29	5.99e-01	0.1177
255488	RNF144B	P5T-E	Human	Esophagus	ESCC	1.19e-03	1.37e-01	0.1327
255488	RNF144B	P8T-E	Human	Esophagus	ESCC	3.86e-25	4.96e-01	0.0889
255488	RNF144B	P9T-E	Human	Esophagus	ESCC	6.87e-07	1.80e-01	0.1131
255488	RNF144B	P10T-E	Human	Esophagus	ESCC	2.32e-24	4.13e-01	0.116
255488	RNF144B	P11T-E	Human	Esophagus	ESCC	1.79e-08	4.49e-01	0.1426
255488	RNF144B	P12T-E	Human	Esophagus	ESCC	9.14e-09	1.84e-01	0.1122
255488	RNF144B	P15T-E	Human	Esophagus	ESCC	1.47e-02	1.12e-01	0.1149

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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
Esophagus		ESCC: Esophageal squamous cell carcinoma
		HGIN: High-grade intraepithelial neoplasias
		LGIN: Low-grade intraepithelial neoplasias
Oral Cavity		EOLP: Erosive Oral lichen planus
		LP: leukoplakia
		NEOLP: Non-erosive oral lichen planus
		OSCC: Oral squamous cell carcinoma
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:004217610	Cervix	CC	regulation of protein catabolic process	104/2311	391/18723	9.39e-15	9.36e-12	104
GO:004586210	Cervix	CC	positive regulation of proteolysis	95/2311	372/18723	1.84e-12	6.86e-10	95
GO:190336210	Cervix	CC	regulation of cellular protein catabolic process	72/2311	255/18723	5.98e-12	2.10e-09	72
GO:004573210	Cervix	CC	positive regulation of protein catabolic process	65/2311	231/18723	7.44e-11	1.39e-08	65
GO:001049810	Cervix	CC	proteasomal protein catabolic process	111/2311	490/18723	8.98e-11	1.58e-08	111
GO:000989610	Cervix	CC	positive regulation of catabolic process	109/2311	492/18723	5.26e-10	6.99e-08	109
GO:190305010	Cervix	CC	regulation of proteolysis involved in cellular protein catabolic process	60/2311	221/18723	1.82e-09	1.98e-07	60
GO:200005810	Cervix	CC	regulation of ubiquitin-dependent protein catabolic process	47/2311	164/18723	1.63e-08	1.25e-06	47
GO:004316110	Cervix	CC	proteasome-mediated ubiquitin-dependent protein catabolic process	91/2311	412/18723	1.65e-08	1.25e-06	91
GO:003133110	Cervix	CC	positive regulation of cellular catabolic process	91/2311	427/18723	9.64e-08	5.25e-06	91
GO:00002097	Cervix	CC	protein polyubiquitination	58/2311	236/18723	1.57e-07	7.41e-06	58
GO:190336410	Cervix	CC	positive regulation of cellular protein catabolic process	43/2311	155/18723	1.80e-07	8.28e-06	43
GO:006113610	Cervix	CC	regulation of proteasomal protein catabolic process	48/2311	187/18723	4.63e-07	1.77e-05	48
GO:003243410	Cervix	CC	regulation of proteasomal ubiquitin-dependent protein catabolic process	38/2311	134/18723	4.99e-07	1.88e-05	38
GO:19030528	Cervix	CC	positive regulation of proteolysis involved in cellular protein catabolic process	34/2311	133/18723	2.28e-05	4.01e-04	34
GO:200006010	Cervix	CC	positive regulation of ubiquitin-dependent protein catabolic process	29/2311	107/18723	2.77e-05	4.62e-04	29
GO:00324369	Cervix	CC	positive regulation of proteasomal ubiquitin-dependent protein catabolic process	25/2311	90/18723	6.22e-05	8.90e-04	25
GO:19018008	Cervix	CC	positive regulation of proteasomal protein catabolic process	29/2311	114/18723	9.71e-05	1.27e-03	29
GO:004586225	Cervix	N_HPV	positive regulation of proteolysis	29/534	372/18723	1.08e-06	5.80e-05	29
GO:190336225	Cervix	N_HPV	regulation of cellular protein catabolic process	22/534	255/18723	4.31e-06	1.66e-04	22

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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

RNF144B

SNV

Missense_Mutation

c.730N>G

p.Leu244Val

p.L244V

Q7Z419

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-A7-A0DA-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

RNF144B

SNV

Missense_Mutation

c.461N>G

p.Ser154Trp

p.S154W

Q7Z419

protein_coding

deleterious(0)

probably_damaging(0.984)

TCGA-AR-A250-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

RNF144B

deletion

Frame_Shift_Del

c.44delN

p.Asn16IlefsTer27

p.N16Ifs*27

Q7Z419

protein_coding

TCGA-A8-A09Z-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

RNF144B

deletion

Frame_Shift_Del

c.74delN

p.Leu27SerfsTer16

p.L27Sfs*16

Q7Z419

protein_coding

TCGA-D8-A27V-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

tamoxiphen

RNF144B

SNV

Missense_Mutation

novel

c.901T>C

p.Ser301Pro

p.S301P

Q7Z419

protein_coding

tolerated_low_confidence(0.43)

benign(0)

TCGA-EA-A410-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

RNF144B

SNV

Missense_Mutation

novel

c.236N>A

p.Val79Glu

p.V79E

Q7Z419

protein_coding

tolerated(0.44)

benign(0.065)

TCGA-VS-A9UB-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

RNF144B

SNV

Missense_Mutation

rs767789668

c.233N>C

p.Met78Thr

p.M78T

Q7Z419

protein_coding

tolerated(0.17)

benign(0.003)

TCGA-A6-A565-01

Colorectum

colon adenocarcinoma

Female

<65

III/IV

Unspecific

5FU

RNF144B

SNV

Missense_Mutation

novel

c.17N>T

p.Arg6Met

p.R6M

Q7Z419

protein_coding

deleterious_low_confidence(0.05)

benign(0.133)

TCGA-AG-A00Y-01

Colorectum

rectum adenocarcinoma

Male

>=65

I/II

Unknown

RNF144B

SNV

Missense_Mutation

novel

c.775N>A

p.Val259Met

p.V259M

Q7Z419

protein_coding

deleterious(0.01)

probably_damaging(0.985)

TCGA-A5-A0G2-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Unknown

RNF144B

SNV

Missense_Mutation

rs755843328

c.31G>A

p.Ala11Thr

p.A11T

Q7Z419

protein_coding

tolerated(1)

benign(0)

TCGA-AJ-A8CT-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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