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: PRPF40A

Gene summary for PRPF40A

Gene summary.

Gene information	Species	Human
	Gene symbol	PRPF40A
	Gene ID	55660
	Gene name	pre-mRNA processing factor 40 homolog A
	Gene Alias	FBP-11
	Cytomap	2q23.3
	Gene Type	protein-coding
	GO ID	GO:0000375
	UniProtAcc	O75400

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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
55660	PRPF40A	GSM5353221_PA_PB2A_Pool_1_3_S25_L001	Human	Prostate	Tumor	1.27e-03	4.54e-01	0.1633
55660	PRPF40A	GSM5353222_PA_PB2B_Pool_1_3_S52_L002	Human	Prostate	Tumor	4.08e-06	4.14e-01	0.1608
55660	PRPF40A	GSM5353223_PA_PB2B_Pool_2_S26_L001	Human	Prostate	Tumor	5.78e-05	4.83e-01	0.1604
55660	PRPF40A	GSM5353227_PA_PR5199-193K_Pool_1_2_3_S55_L002	Human	Prostate	Tumor	2.23e-06	3.77e-01	0.1602
55660	PRPF40A	GSM5353232_PA_PR5249_T1_S3_L001	Human	Prostate	Tumor	2.83e-03	2.52e-01	0.1439
55660	PRPF40A	GSM5353236_PA_PR5251_T1_S7_L001	Human	Prostate	Tumor	1.06e-02	3.62e-01	0.1608
55660	PRPF40A	GSM5353240_PA_PR5254_T1_S15_L001	Human	Prostate	Tumor	1.58e-07	2.93e-01	0.1575
55660	PRPF40A	GSM5353243_PA_PR5261_T1_S23_L002	Human	Prostate	Tumor	1.36e-18	2.84e-01	0.1545
55660	PRPF40A	GSM5353244_PA_PR5261_T2_S24_L002	Human	Prostate	Tumor	1.95e-12	2.39e-01	0.1569
55660	PRPF40A	P1_S1_AK	Human	Skin	AK	2.53e-09	4.43e-01	-0.3399
55660	PRPF40A	P2_S3_AK	Human	Skin	AK	1.13e-06	3.11e-01	-0.3287
55660	PRPF40A	P3_S6_AK	Human	Skin	AK	2.28e-03	2.99e-01	-0.3256
55660	PRPF40A	P4_S8_cSCC	Human	Skin	cSCC	1.42e-19	4.01e-01	-0.3095
55660	PRPF40A	P5_S10_cSCC	Human	Skin	cSCC	3.96e-13	2.71e-01	-0.299
55660	PRPF40A	P1_cSCC	Human	Skin	cSCC	1.29e-48	1.53e+00	0.0292
55660	PRPF40A	P2_cSCC	Human	Skin	cSCC	2.27e-34	9.71e-01	-0.024
55660	PRPF40A	P4_cSCC	Human	Skin	cSCC	1.42e-51	1.25e+00	-0.00290000000000005
55660	PRPF40A	P10_cSCC	Human	Skin	cSCC	1.54e-43	1.30e+00	0.1017
55660	PRPF40A	cSCC_p7	Human	Skin	cSCC	1.86e-05	-1.09e-01	-0.2332
55660	PRPF40A	cSCC_p8	Human	Skin	cSCC	1.13e-06	1.66e-01	-0.1971

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Breast		IDC: Invasive ductal carcinoma
		DCIS: Ductal carcinoma in situ
		Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers
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
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:00083809	Breast	Precancer	RNA splicing	65/1080	434/18723	1.27e-12	2.53e-10	65
GO:00003759	Breast	Precancer	RNA splicing, via transesterification reactions	52/1080	324/18723	1.74e-11	2.22e-09	52
GO:00003779	Breast	Precancer	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	51/1080	320/18723	3.55e-11	4.04e-09	51
GO:00003989	Breast	Precancer	mRNA splicing, via spliceosome	51/1080	320/18723	3.55e-11	4.04e-09	51
GO:00226049	Breast	Precancer	regulation of cell morphogenesis	29/1080	309/18723	6.88e-03	4.67e-02	29
GO:000838014	Breast	IDC	RNA splicing	73/1434	434/18723	1.27e-10	1.57e-08	73
GO:000037514	Breast	IDC	RNA splicing, via transesterification reactions	58/1434	324/18723	9.44e-10	9.58e-08	58
GO:000037714	Breast	IDC	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	57/1434	320/18723	1.60e-09	1.49e-07	57
GO:000039814	Breast	IDC	mRNA splicing, via spliceosome	57/1434	320/18723	1.60e-09	1.49e-07	57
GO:000838024	Breast	DCIS	RNA splicing	73/1390	434/18723	3.05e-11	5.08e-09	73
GO:000037524	Breast	DCIS	RNA splicing, via transesterification reactions	58/1390	324/18723	2.89e-10	3.34e-08	58
GO:000037724	Breast	DCIS	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	57/1390	320/18723	5.01e-10	5.35e-08	57
GO:000039824	Breast	DCIS	mRNA splicing, via spliceosome	57/1390	320/18723	5.01e-10	5.35e-08	57
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:0022604	Colorectum	AD	regulation of cell morphogenesis	109/3918	309/18723	3.08e-09	2.07e-07	109
GO:0008360	Colorectum	AD	regulation of cell shape	56/3918	154/18723	7.01e-06	1.73e-04	56
GO:0000910	Colorectum	AD	cytokinesis	59/3918	173/18723	3.74e-05	6.75e-04	59

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa030408	Breast	Precancer	Spliceosome	39/684	217/8465	1.44e-06	2.27e-05	1.74e-05	39
hsa0304013	Breast	Precancer	Spliceosome	39/684	217/8465	1.44e-06	2.27e-05	1.74e-05	39
hsa0304023	Breast	IDC	Spliceosome	40/867	217/8465	1.53e-04	1.42e-03	1.06e-03	40
hsa0304033	Breast	IDC	Spliceosome	40/867	217/8465	1.53e-04	1.42e-03	1.06e-03	40
hsa0304043	Breast	DCIS	Spliceosome	40/846	217/8465	8.97e-05	8.52e-04	6.28e-04	40
hsa0304053	Breast	DCIS	Spliceosome	40/846	217/8465	8.97e-05	8.52e-04	6.28e-04	40
hsa03040	Colorectum	AD	Spliceosome	73/2092	217/8465	1.73e-03	9.68e-03	6.18e-03	73
hsa030401	Colorectum	AD	Spliceosome	73/2092	217/8465	1.73e-03	9.68e-03	6.18e-03	73
hsa030409	Endometrium	AEH	Spliceosome	54/1197	217/8465	1.47e-05	1.65e-04	1.21e-04	54
hsa0304014	Endometrium	AEH	Spliceosome	54/1197	217/8465	1.47e-05	1.65e-04	1.21e-04	54
hsa0304024	Endometrium	EEC	Spliceosome	54/1237	217/8465	3.78e-05	3.88e-04	2.89e-04	54
hsa0304034	Endometrium	EEC	Spliceosome	54/1237	217/8465	3.78e-05	3.88e-04	2.89e-04	54
hsa0304018	Esophagus	HGIN	Spliceosome	79/1383	217/8465	3.22e-13	7.00e-12	5.56e-12	79
hsa0304019	Esophagus	HGIN	Spliceosome	79/1383	217/8465	3.22e-13	7.00e-12	5.56e-12	79
hsa0304027	Esophagus	ESCC	Spliceosome	128/4205	217/8465	3.31e-03	8.79e-03	4.50e-03	128
hsa0304037	Esophagus	ESCC	Spliceosome	128/4205	217/8465	3.31e-03	8.79e-03	4.50e-03	128
hsa030407	Liver	Cirrhotic	Spliceosome	102/2530	217/8465	5.69e-08	9.47e-07	5.84e-07	102
hsa0304012	Liver	Cirrhotic	Spliceosome	102/2530	217/8465	5.69e-08	9.47e-07	5.84e-07	102
hsa0304022	Liver	HCC	Spliceosome	122/4020	217/8465	5.55e-03	1.60e-02	8.91e-03	122
hsa0304032	Liver	HCC	Spliceosome	122/4020	217/8465	5.55e-03	1.60e-02	8.91e-03	122

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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

PRPF40A

SNV

Missense_Mutation

novel

c.722N>G

p.Met241Arg

p.M241R

O75400

protein_coding

tolerated(0.65)

benign(0.184)

TCGA-A7-A26H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

anastrozole

PRPF40A

SNV

Missense_Mutation

c.2510G>T

p.Arg837Ile

p.R837I

O75400

protein_coding

deleterious(0.02)

possibly_damaging(0.503)

TCGA-D8-A1JG-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

PRPF40A

SNV

Missense_Mutation

rs765112518

c.742G>A

p.Glu248Lys

p.E248K

O75400

protein_coding

tolerated(0.78)

benign(0)

TCGA-D8-A27G-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

PRPF40A

SNV

Missense_Mutation

c.1098G>C

p.Lys366Asn

p.K366N

O75400

protein_coding

deleterious(0)

possibly_damaging(0.835)

TCGA-E9-A1N9-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

PRPF40A

SNV

Missense_Mutation

c.2414N>T

p.Ser805Leu

p.S805L

O75400

protein_coding

deleterious(0)

probably_damaging(0.916)

TCGA-EW-A1OZ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Targeted Molecular therapy

trastuzumab

PRPF40A

SNV

Missense_Mutation

novel

c.1499G>A

p.Arg500Gln

p.R500Q

O75400

protein_coding

deleterious(0.03)

probably_damaging(0.992)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

PRPF40A

SNV

Missense_Mutation

c.2422N>A

p.Asp808Asn

p.D808N

O75400

protein_coding

tolerated(0.07)

benign(0.202)

TCGA-C5-A1BJ-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

PRPF40A

SNV

Missense_Mutation

c.1618N>A

p.Glu540Lys

p.E540K

O75400

protein_coding

tolerated(0.46)

possibly_damaging(0.81)

TCGA-EK-A2RN-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

PRPF40A

SNV

Missense_Mutation

novel

c.2203N>A

p.Glu735Lys

p.E735K

O75400

protein_coding

deleterious(0.01)

probably_damaging(0.981)

TCGA-LP-A4AU-01

Cervix

cervical & endocervical cancer

Female

<65

III/IV

Chemotherapy

cisplatin

PRPF40A

SNV

Missense_Mutation

c.1205G>C

p.Ser402Thr

p.S402T

O75400

protein_coding

tolerated(0.12)

probably_damaging(0.964)

TCGA-A6-A567-01

Colorectum

colon adenocarcinoma

Male

<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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