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: SRRM1

Gene summary for SRRM1

Gene summary.

Gene information	Species	Human
	Gene symbol	SRRM1
	Gene ID	10250
	Gene name	serine and arginine repetitive matrix 1
	Gene Alias	160-KD
	Cytomap	1p36.11
	Gene Type	protein-coding
	GO ID	GO:0000375
	UniProtAcc	B7Z7U0

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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
10250	SRRM1	HTA11_3410_2000001011	Human	Colorectum	AD	1.85e-05	-3.33e-01	0.0155
10250	SRRM1	A015-C-203	Human	Colorectum	FAP	8.96e-20	2.88e-01	-0.1294
10250	SRRM1	A015-C-204	Human	Colorectum	FAP	2.40e-04	3.24e-01	-0.0228
10250	SRRM1	A002-C-201	Human	Colorectum	FAP	8.81e-08	4.31e-02	0.0324
10250	SRRM1	A001-C-119	Human	Colorectum	FAP	8.90e-08	4.48e-01	-0.1557
10250	SRRM1	A001-C-108	Human	Colorectum	FAP	1.01e-16	4.55e-01	-0.0272
10250	SRRM1	A002-C-205	Human	Colorectum	FAP	1.26e-25	5.00e-01	-0.1236
10250	SRRM1	A014-C-108	Human	Colorectum	FAP	1.97e-05	5.17e-01	-0.124
10250	SRRM1	A001-C-104	Human	Colorectum	FAP	8.99e-06	3.43e-01	0.0184
10250	SRRM1	A015-C-006	Human	Colorectum	FAP	6.91e-24	6.32e-01	-0.0994
10250	SRRM1	A015-C-106	Human	Colorectum	FAP	6.97e-09	3.03e-01	-0.0511
10250	SRRM1	A002-C-114	Human	Colorectum	FAP	1.76e-16	4.22e-01	-0.1561
10250	SRRM1	A015-C-104	Human	Colorectum	FAP	1.80e-29	4.10e-01	-0.1899
10250	SRRM1	A001-C-014	Human	Colorectum	FAP	6.77e-12	3.51e-01	0.0135
10250	SRRM1	A002-C-016	Human	Colorectum	FAP	5.22e-14	2.29e-01	0.0521
10250	SRRM1	A015-C-002	Human	Colorectum	FAP	2.02e-13	5.05e-01	-0.0763
10250	SRRM1	A001-C-007	Human	Colorectum	CRC	4.45e-03	5.07e-01	0.1899
10250	SRRM1	A001-C-203	Human	Colorectum	FAP	5.48e-11	3.76e-01	-0.0481
10250	SRRM1	A002-C-116	Human	Colorectum	FAP	4.40e-21	-1.25e-02	-0.0452
10250	SRRM1	A014-C-008	Human	Colorectum	FAP	2.27e-17	5.58e-01	-0.191

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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
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
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
Prostate		BPH: Benign Prostatic Hyperplasia
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: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: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
GO:000838016	Endometrium	AEH	RNA splicing	111/2100	434/18723	2.42e-17	1.12e-14	111
GO:000037515	Endometrium	AEH	RNA splicing, via transesterification reactions	88/2100	324/18723	1.11e-15	3.91e-13	88
GO:000037715	Endometrium	AEH	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	87/2100	320/18723	1.51e-15	4.78e-13	87
GO:000039815	Endometrium	AEH	mRNA splicing, via spliceosome	87/2100	320/18723	1.51e-15	4.78e-13	87
GO:000838017	Endometrium	EEC	RNA splicing	111/2168	434/18723	2.45e-16	1.13e-13	111
GO:000037516	Endometrium	EEC	RNA splicing, via transesterification reactions	88/2168	324/18723	7.46e-15	2.63e-12	88
GO:000037716	Endometrium	EEC	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	87/2168	320/18723	9.97e-15	3.15e-12	87
GO:000039816	Endometrium	EEC	mRNA splicing, via spliceosome	87/2168	320/18723	9.97e-15	3.15e-12	87

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa03015	Colorectum	AD	mRNA surveillance pathway	35/2092	97/8465	7.95e-03	3.13e-02	2.00e-02	35
hsa030151	Colorectum	AD	mRNA surveillance pathway	35/2092	97/8465	7.95e-03	3.13e-02	2.00e-02	35
hsa030152	Colorectum	FAP	mRNA surveillance pathway	26/1404	97/8465	7.11e-03	2.64e-02	1.60e-02	26
hsa030153	Colorectum	FAP	mRNA surveillance pathway	26/1404	97/8465	7.11e-03	2.64e-02	1.60e-02	26
hsa0301321	Esophagus	ESCC	Nucleocytoplasmic transport	89/4205	108/8465	1.20e-12	2.37e-11	1.21e-11	89
hsa0301524	Esophagus	ESCC	mRNA surveillance pathway	72/4205	97/8465	6.12e-07	4.10e-06	2.10e-06	72
hsa0301331	Esophagus	ESCC	Nucleocytoplasmic transport	89/4205	108/8465	1.20e-12	2.37e-11	1.21e-11	89
hsa0301534	Esophagus	ESCC	mRNA surveillance pathway	72/4205	97/8465	6.12e-07	4.10e-06	2.10e-06	72
hsa030154	Liver	Cirrhotic	mRNA surveillance pathway	46/2530	97/8465	1.92e-04	1.30e-03	8.03e-04	46
hsa0301511	Liver	Cirrhotic	mRNA surveillance pathway	46/2530	97/8465	1.92e-04	1.30e-03	8.03e-04	46
hsa03013	Liver	HCC	Nucleocytoplasmic transport	81/4020	108/8465	4.28e-09	6.83e-08	3.80e-08	81
hsa0301521	Liver	HCC	mRNA surveillance pathway	66/4020	97/8465	3.16e-05	1.88e-04	1.04e-04	66
hsa030131	Liver	HCC	Nucleocytoplasmic transport	81/4020	108/8465	4.28e-09	6.83e-08	3.80e-08	81
hsa0301531	Liver	HCC	mRNA surveillance pathway	66/4020	97/8465	3.16e-05	1.88e-04	1.04e-04	66
hsa030136	Oral cavity	OSCC	Nucleocytoplasmic transport	82/3704	108/8465	7.93e-12	1.33e-10	6.77e-11	82
hsa030158	Oral cavity	OSCC	mRNA surveillance pathway	75/3704	97/8465	1.30e-11	2.01e-10	1.02e-10	75
hsa0301311	Oral cavity	OSCC	Nucleocytoplasmic transport	82/3704	108/8465	7.93e-12	1.33e-10	6.77e-11	82
hsa0301513	Oral cavity	OSCC	mRNA surveillance pathway	75/3704	97/8465	1.30e-11	2.01e-10	1.02e-10	75
hsa0301523	Oral cavity	LP	mRNA surveillance pathway	50/2418	97/8465	1.39e-06	1.50e-05	9.66e-06	50
hsa030132	Oral cavity	LP	Nucleocytoplasmic transport	53/2418	108/8465	4.68e-06	4.10e-05	2.64e-05	53

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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

SRRM1

SNV

Missense_Mutation

c.94G>A

p.Glu32Lys

p.E32K

Q8IYB3

protein_coding

tolerated_low_confidence(0.07)

probably_damaging(0.932)

TCGA-A2-A25D-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Hormone Therapy

tamoxiphen

SRRM1

SNV

Missense_Mutation

rs377349401

c.730N>G

p.Ile244Val

p.I244V

Q8IYB3

protein_coding

tolerated_low_confidence(0.15)

benign(0)

TCGA-AN-A0AK-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SRRM1

SNV

Missense_Mutation

novel

c.599N>G

p.Ser200Cys

p.S200C

Q8IYB3

protein_coding

deleterious_low_confidence(0.01)

probably_damaging(0.984)

TCGA-BH-A0B6-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

SRRM1

SNV

Missense_Mutation

novel

c.763N>A

p.Glu255Lys

p.E255K

Q8IYB3

protein_coding

tolerated_low_confidence(0.07)

benign(0.052)

TCGA-C8-A12Q-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Unknown

SRRM1

SNV

Missense_Mutation

rs150723178

c.2327C>T

p.Pro776Leu

p.P776L

Q8IYB3

protein_coding

deleterious_low_confidence(0)

benign(0.086)

TCGA-E2-A1B1-01

Breast

breast invasive carcinoma

Female

<65

I/II

Other, specify in notesbiphosphonate

zoledronic

SRRM1

SNV

Missense_Mutation

novel

c.958C>T

p.Arg320Trp

p.R320W

Q8IYB3

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.985)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

SRRM1

SNV

Missense_Mutation

rs760382573

c.1049G>A

p.Arg350His

p.R350H

Q8IYB3

protein_coding

deleterious_low_confidence(0)

benign(0.001)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

SRRM1

SNV

Missense_Mutation

novel

c.2399N>A

p.Arg800Lys

p.R800K

Q8IYB3

protein_coding

tolerated_low_confidence(0.31)

benign(0.009)

TCGA-DG-A2KM-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

SRRM1

SNV

Missense_Mutation

novel

c.835C>T

p.Arg279Trp

p.R279W

Q8IYB3

protein_coding

tolerated_low_confidence(0.07)

possibly_damaging(0.545)

TCGA-DS-A1OC-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

gemcitabine

SRRM1

insertion

Frame_Shift_Ins

novel

c.836_837insATTT

p.Ser280PhefsTer21

p.S280Ffs*21

Q8IYB3

protein_coding

TCGA-DS-A1OC-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

gemcitabine

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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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