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: RSRC1

Gene summary for RSRC1

Gene summary.

Gene information	Species	Human
	Gene symbol	RSRC1
	Gene ID	51319
	Gene name	arginine and serine rich coiled-coil 1
	Gene Alias	BM-011
	Cytomap	3q25.32
	Gene Type	protein-coding
	GO ID	GO:0000375
	UniProtAcc	Q96IZ7

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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
51319	RSRC1	Pt14.d	Human	Liver	HCC	7.52e-07	3.38e-01	0.0143
51319	RSRC1	S014	Human	Liver	HCC	1.96e-09	4.92e-01	0.2254
51319	RSRC1	S015	Human	Liver	HCC	4.31e-08	5.70e-01	0.2375
51319	RSRC1	S016	Human	Liver	HCC	7.60e-15	6.17e-01	0.2243
51319	RSRC1	S027	Human	Liver	HCC	1.20e-02	5.69e-01	0.2446
51319	RSRC1	S028	Human	Liver	HCC	5.50e-19	7.90e-01	0.2503
51319	RSRC1	S029	Human	Liver	HCC	5.70e-09	6.01e-01	0.2581
51319	RSRC1	C04	Human	Oral cavity	OSCC	8.75e-07	7.61e-01	0.2633
51319	RSRC1	C21	Human	Oral cavity	OSCC	1.40e-45	1.44e+00	0.2678
51319	RSRC1	C30	Human	Oral cavity	OSCC	8.76e-35	1.59e+00	0.3055
51319	RSRC1	C38	Human	Oral cavity	OSCC	1.21e-16	1.75e+00	0.172
51319	RSRC1	C43	Human	Oral cavity	OSCC	3.44e-09	3.61e-01	0.1704
51319	RSRC1	C46	Human	Oral cavity	OSCC	3.42e-18	6.50e-01	0.1673
51319	RSRC1	C51	Human	Oral cavity	OSCC	2.72e-09	8.30e-01	0.2674
51319	RSRC1	C57	Human	Oral cavity	OSCC	1.09e-08	6.65e-01	0.1679
51319	RSRC1	C06	Human	Oral cavity	OSCC	1.36e-10	1.74e+00	0.2699
51319	RSRC1	C08	Human	Oral cavity	OSCC	2.74e-40	1.06e+00	0.1919
51319	RSRC1	LN22	Human	Oral cavity	OSCC	1.22e-07	1.19e+00	0.1733
51319	RSRC1	LN38	Human	Oral cavity	OSCC	1.20e-12	1.68e+00	0.168
51319	RSRC1	LN46	Human	Oral cavity	OSCC	1.92e-11	7.52e-01	0.1666

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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
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
Oral Cavity		EOLP: Erosive Oral lichen planus
		LP: leukoplakia
		NEOLP: Non-erosive oral lichen planus
		OSCC: Oral squamous cell carcinoma
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:00069139	Cervix	CC	nucleocytoplasmic transport	71/2311	301/18723	4.04e-08	2.54e-06	71
GO:00511699	Cervix	CC	nuclear transport	71/2311	301/18723	4.04e-08	2.54e-06	71
GO:000838010	Cervix	CC	RNA splicing	76/2311	434/18723	9.79e-04	8.19e-03	76
GO:000037710	Cervix	CC	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	55/2311	320/18723	6.71e-03	3.70e-02	55
GO:000039810	Cervix	CC	mRNA splicing, via spliceosome	55/2311	320/18723	6.71e-03	3.70e-02	55
GO:000037510	Cervix	CC	RNA splicing, via transesterification reactions	55/2311	324/18723	8.61e-03	4.44e-02	55
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:0006913	Colorectum	AD	nucleocytoplasmic transport	102/3918	301/18723	1.00e-07	4.85e-06	102
GO:0051169	Colorectum	AD	nuclear transport	102/3918	301/18723	1.00e-07	4.85e-06	102
GO:0000380	Colorectum	AD	alternative mRNA splicing, via spliceosome	33/3918	77/18723	1.13e-05	2.55e-04	33
GO:00083801	Colorectum	SER	RNA splicing	123/2897	434/18723	3.84e-12	8.41e-10	123
GO:00003751	Colorectum	SER	RNA splicing, via transesterification reactions	90/2897	324/18723	8.68e-09	7.50e-07	90
GO:00003771	Colorectum	SER	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	89/2897	320/18723	9.82e-09	8.14e-07	89
GO:00003981	Colorectum	SER	mRNA splicing, via spliceosome	89/2897	320/18723	9.82e-09	8.14e-07	89
GO:00069131	Colorectum	SER	nucleocytoplasmic transport	77/2897	301/18723	3.39e-06	1.32e-04	77
GO:00511691	Colorectum	SER	nuclear transport	77/2897	301/18723	3.39e-06	1.32e-04	77
GO:00003801	Colorectum	SER	alternative mRNA splicing, via spliceosome	24/2897	77/18723	4.08e-04	6.09e-03	24

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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

RSRC1

SNV

Missense_Mutation

novel

c.329N>T

p.Ser110Leu

p.S110L

Q96IZ7

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.978)

TCGA-C5-A902-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

RSRC1

SNV

Missense_Mutation

c.518N>A

p.Gly173Glu

p.G173E

Q96IZ7

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.993)

TCGA-DS-A0VM-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

RSRC1

SNV

Missense_Mutation

rs773344897

c.337N>T

p.Arg113Cys

p.R113C

Q96IZ7

protein_coding

tolerated_low_confidence(0.12)

possibly_damaging(0.656)

TCGA-VS-A9U6-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

RSRC1

SNV

Missense_Mutation

novel

c.974N>G

p.Gln325Arg

p.Q325R

Q96IZ7

protein_coding

tolerated_low_confidence(0.07)

benign(0.202)

TCGA-A6-2672-01

Colorectum

colon adenocarcinoma

Female

>=65

III/IV

Unknown

RSRC1

SNV

Missense_Mutation

rs557840086

c.7N>T

p.Arg3Cys

p.R3C

Q96IZ7

protein_coding

tolerated_low_confidence(0.09)

probably_damaging(0.994)

TCGA-AA-A022-01

Colorectum

colon adenocarcinoma

Female

>=65

I/II

Unknown

RSRC1

SNV

Missense_Mutation

c.101C>A

p.Thr34Lys

p.T34K

Q96IZ7

protein_coding

deleterious_low_confidence(0)

benign(0.342)

TCGA-AZ-4308-01

Colorectum

colon adenocarcinoma

Female

<65

III/IV

Targeted Molecular therapy

avastin

RSRC1

SNV

Missense_Mutation

novel

c.695N>C

p.Ile232Thr

p.I232T

Q96IZ7

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.91)

TCGA-CA-6717-01

Colorectum

colon adenocarcinoma

Male

<65

I/II

Chemotherapy

oxaliplatin

RSRC1

SNV

Missense_Mutation

c.96N>A

p.Ser32Arg

p.S32R

Q96IZ7

protein_coding

deleterious_low_confidence(0)

benign(0.112)

TCGA-AF-6672-01

Colorectum

rectum adenocarcinoma

Male

<65

III/IV

Ancillary

leucovorin

RSRC1

SNV

Missense_Mutation

novel

c.471N>T

p.Lys157Asn

p.K157N

Q96IZ7

protein_coding

deleterious_low_confidence(0.01)

benign(0.011)

TCGA-AG-A002-01

Colorectum

rectum adenocarcinoma

Male

<65

I/II

Unknown

RSRC1

SNV

Missense_Mutation

novel

c.217N>C

p.Ser73Arg

p.S73R

Q96IZ7

protein_coding

deleterious_low_confidence(0)

possibly_damaging(0.587)

TCGA-A5-A0G2-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

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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