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: RBM6

Gene summary for RBM6

Gene summary.

Gene information	Species	Human
	Gene symbol	RBM6
	Gene ID	10180
	Gene name	RNA binding motif protein 6
	Gene Alias	3G2
	Cytomap	3p21.31
	Gene Type	protein-coding
	GO ID	GO:0000375
	UniProtAcc	A8K6Q4

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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
10180	RBM6	GSM5276937	Human	Endometrium	EEC	6.86e-03	-2.58e-01	-0.0897
10180	RBM6	GSM6177620_NYU_UCEC1_lib1_lib1	Human	Endometrium	EEC	3.77e-17	-7.67e-03	-0.1869
10180	RBM6	GSM6177620_NYU_UCEC1_lib2_lib2	Human	Endometrium	EEC	3.65e-19	-1.71e-01	-0.1875
10180	RBM6	GSM6177620_NYU_UCEC1_lib3_lib3	Human	Endometrium	EEC	2.54e-24	-1.22e-01	-0.1883
10180	RBM6	GSM6177621_NYU_UCEC2_lib1_lib1	Human	Endometrium	EEC	2.12e-16	4.42e-02	-0.1934
10180	RBM6	GSM6177622_NYU_UCEC3_lib1_lib1	Human	Endometrium	EEC	6.92e-35	-2.55e-01	-0.1917
10180	RBM6	GSM6177622_NYU_UCEC3_lib2_lib2	Human	Endometrium	EEC	3.70e-32	-2.81e-01	-0.1916
10180	RBM6	GSM6177623_NYU_UCEC3_Vis	Human	Endometrium	EEC	1.99e-09	2.31e-01	-0.1269
10180	RBM6	LZE2T	Human	Esophagus	ESCC	7.51e-03	5.86e-01	0.082
10180	RBM6	LZE3D	Human	Esophagus	HGIN	4.21e-03	5.69e-01	0.0668
10180	RBM6	LZE4T	Human	Esophagus	ESCC	2.70e-15	3.82e-01	0.0811
10180	RBM6	LZE5T	Human	Esophagus	ESCC	5.01e-03	3.32e-01	0.0514
10180	RBM6	LZE7T	Human	Esophagus	ESCC	1.57e-08	3.83e-01	0.0667
10180	RBM6	LZE8T	Human	Esophagus	ESCC	5.53e-05	5.84e-02	0.067
10180	RBM6	LZE20T	Human	Esophagus	ESCC	4.33e-02	1.06e-02	0.0662
10180	RBM6	LZE21D1	Human	Esophagus	HGIN	2.85e-03	3.47e-01	0.0632
10180	RBM6	LZE22T	Human	Esophagus	ESCC	6.62e-08	4.53e-01	0.068
10180	RBM6	LZE24T	Human	Esophagus	ESCC	2.31e-14	3.12e-01	0.0596
10180	RBM6	LZE21T	Human	Esophagus	ESCC	1.22e-05	3.61e-01	0.0655
10180	RBM6	LZE6T	Human	Esophagus	ESCC	4.41e-02	2.17e-01	0.0845

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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
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
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:0008380	Colorectum	AD	RNA splicing	169/3918	434/18723	3.59e-18	2.04e-15	169
GO:0000377	Colorectum	AD	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	130/3918	320/18723	5.88e-16	2.16e-13	130
GO:0000398	Colorectum	AD	mRNA splicing, via spliceosome	130/3918	320/18723	5.88e-16	2.16e-13	130
GO:0000375	Colorectum	AD	RNA splicing, via transesterification reactions	131/3918	324/18723	7.11e-16	2.22e-13	131
GO:00083802	Colorectum	MSS	RNA splicing	159/3467	434/18723	1.75e-19	1.22e-16	159
GO:00003772	Colorectum	MSS	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	121/3467	320/18723	2.52e-16	8.27e-14	121
GO:00003982	Colorectum	MSS	mRNA splicing, via spliceosome	121/3467	320/18723	2.52e-16	8.27e-14	121
GO:00003752	Colorectum	MSS	RNA splicing, via transesterification reactions	122/3467	324/18723	2.75e-16	8.58e-14	122
GO:00083803	Colorectum	MSI-H	RNA splicing	82/1319	434/18723	1.22e-16	4.53e-14	82
GO:00003753	Colorectum	MSI-H	RNA splicing, via transesterification reactions	67/1319	324/18723	7.99e-16	2.61e-13	67
GO:00003773	Colorectum	MSI-H	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	66/1319	320/18723	1.51e-15	4.41e-13	66
GO:00003983	Colorectum	MSI-H	mRNA splicing, via spliceosome	66/1319	320/18723	1.51e-15	4.41e-13	66
GO:00083804	Colorectum	FAP	RNA splicing	108/2622	434/18723	7.90e-10	1.86e-07	108
GO:00003754	Colorectum	FAP	RNA splicing, via transesterification reactions	84/2622	324/18723	8.06e-09	1.10e-06	84
GO:00003774	Colorectum	FAP	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	83/2622	320/18723	9.66e-09	1.23e-06	83
GO:00003984	Colorectum	FAP	mRNA splicing, via spliceosome	83/2622	320/18723	9.66e-09	1.23e-06	83
GO:00083805	Colorectum	CRC	RNA splicing	90/2078	434/18723	2.80e-09	7.97e-07	90
GO:00003775	Colorectum	CRC	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	66/2078	320/18723	4.39e-07	3.37e-05	66
GO:00003985	Colorectum	CRC	mRNA splicing, via spliceosome	66/2078	320/18723	4.39e-07	3.37e-05	66
GO:00003755	Colorectum	CRC	RNA splicing, via transesterification reactions	66/2078	324/18723	7.00e-07	4.61e-05	66

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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

RBM6

SNV

Missense_Mutation

c.1528N>C

p.Asp510His

p.D510H

P78332

protein_coding

deleterious(0)

possibly_damaging(0.823)

TCGA-A1-A0SI-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

RBM6

SNV

Missense_Mutation

novel

c.2317N>C

p.Asp773His

p.D773H

P78332

protein_coding

tolerated(0.13)

possibly_damaging(0.781)

TCGA-A7-A56D-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

RBM6

SNV

Missense_Mutation

c.2036N>G

p.Tyr679Cys

p.Y679C

P78332

protein_coding

deleterious(0)

benign(0.011)

TCGA-AR-A1AS-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

RBM6

SNV

Missense_Mutation

novel

c.3182N>T

p.Ala1061Val

p.A1061V

P78332

protein_coding

tolerated(0.06)

benign(0.119)

TCGA-BH-A0HF-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

RBM6

SNV

Missense_Mutation

rs748990943

c.1674C>G

p.Phe558Leu

p.F558L

P78332

protein_coding

tolerated(0.29)

benign(0)

TCGA-BH-A0W7-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

taxotere

RBM6

SNV

Missense_Mutation

rs746775897

c.182N>T

p.Ser61Leu

p.S61L

P78332

protein_coding

tolerated_low_confidence(0.11)

benign(0.041)

TCGA-D8-A147-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicine

RBM6

SNV

Missense_Mutation

c.1644N>G

p.Asn548Lys

p.N548K

P78332

protein_coding

tolerated(0.91)

benign(0.006)

TCGA-D8-A1JC-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

adriamycin

RBM6

SNV

Missense_Mutation

c.2773N>G

p.Pro925Ala

p.P925A

P78332

protein_coding

tolerated(0.11)

benign(0.138)

TCGA-D8-A27G-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

RBM6

SNV

Missense_Mutation

c.799C>A

p.Gln267Lys

p.Q267K

P78332

protein_coding

tolerated(0.41)

probably_damaging(0.952)

TCGA-E2-A14Z-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

arimidex

RBM6

SNV

Missense_Mutation

novel

c.280N>A

p.Asp94Asn

p.D94N

P78332

protein_coding

deleterious_low_confidence(0.01)

benign(0.023)

TCGA-GM-A2DO-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

tamoxiphen

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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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