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: SECISBP2

Gene summary for SECISBP2

Gene summary.

Gene information	Species	Human
	Gene symbol	SECISBP2
	Gene ID	79048
	Gene name	SECIS binding protein 2
	Gene Alias	SBP2
	Cytomap	9q22.2
	Gene Type	protein-coding
	GO ID	GO:0000184
	UniProtAcc	B4DZC7

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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
79048	SECISBP2	HTA11_347_2000001011	Human	Colorectum	AD	1.59e-02	2.86e-01	-0.1954
79048	SECISBP2	HTA11_99999965104_69814	Human	Colorectum	MSS	1.12e-10	8.22e-01	0.281
79048	SECISBP2	HTA11_99999974143_84620	Human	Colorectum	MSS	7.38e-03	-2.26e-01	0.3005
79048	SECISBP2	A015-C-203	Human	Colorectum	FAP	3.07e-25	-1.87e-01	-0.1294
79048	SECISBP2	A015-C-204	Human	Colorectum	FAP	1.28e-02	1.05e-02	-0.0228
79048	SECISBP2	A014-C-040	Human	Colorectum	FAP	5.00e-03	-9.28e-02	-0.1184
79048	SECISBP2	A002-C-201	Human	Colorectum	FAP	8.96e-10	-1.27e-01	0.0324
79048	SECISBP2	A002-C-203	Human	Colorectum	FAP	2.33e-02	-1.42e-02	0.2786
79048	SECISBP2	A001-C-108	Human	Colorectum	FAP	7.03e-12	-1.33e-02	-0.0272
79048	SECISBP2	A002-C-205	Human	Colorectum	FAP	1.01e-15	-1.80e-01	-0.1236
79048	SECISBP2	A015-C-006	Human	Colorectum	FAP	4.17e-11	-1.47e-01	-0.0994
79048	SECISBP2	A015-C-106	Human	Colorectum	FAP	4.01e-07	1.66e-02	-0.0511
79048	SECISBP2	A002-C-114	Human	Colorectum	FAP	1.41e-13	-1.58e-01	-0.1561
79048	SECISBP2	A015-C-104	Human	Colorectum	FAP	7.27e-27	-4.41e-02	-0.1899
79048	SECISBP2	A001-C-014	Human	Colorectum	FAP	2.48e-12	1.32e-02	0.0135
79048	SECISBP2	A002-C-016	Human	Colorectum	FAP	4.29e-17	-1.05e-01	0.0521
79048	SECISBP2	A015-C-002	Human	Colorectum	FAP	5.09e-09	7.23e-03	-0.0763
79048	SECISBP2	A001-C-203	Human	Colorectum	FAP	3.40e-08	5.24e-02	-0.0481
79048	SECISBP2	A002-C-116	Human	Colorectum	FAP	2.34e-29	-2.38e-01	-0.0452
79048	SECISBP2	A014-C-008	Human	Colorectum	FAP	5.23e-10	-9.63e-02	-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
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:1903311	Colorectum	AD	regulation of mRNA metabolic process	117/3918	288/18723	1.69e-14	4.23e-12	117
GO:0009895	Colorectum	AD	negative regulation of catabolic process	124/3918	320/18723	1.66e-13	3.35e-11	124
GO:0031330	Colorectum	AD	negative regulation of cellular catabolic process	104/3918	262/18723	2.66e-12	3.96e-10	104
GO:0006401	Colorectum	AD	RNA catabolic process	102/3918	278/18723	8.64e-10	6.76e-08	102
GO:0044270	Colorectum	AD	cellular nitrogen compound catabolic process	147/3918	451/18723	3.35e-09	2.23e-07	147
GO:0046700	Colorectum	AD	heterocycle catabolic process	145/3918	445/18723	4.37e-09	2.84e-07	145
GO:0006402	Colorectum	AD	mRNA catabolic process	87/3918	232/18723	4.40e-09	2.84e-07	87
GO:0034655	Colorectum	AD	nucleobase-containing compound catabolic process	133/3918	407/18723	1.56e-08	9.12e-07	133
GO:0019439	Colorectum	AD	aromatic compound catabolic process	146/3918	467/18723	7.48e-08	3.84e-06	146
GO:1901361	Colorectum	AD	organic cyclic compound catabolic process	153/3918	495/18723	8.23e-08	4.18e-06	153
GO:0061013	Colorectum	AD	regulation of mRNA catabolic process	64/3918	166/18723	1.44e-07	6.59e-06	64
GO:0006417	Colorectum	AD	regulation of translation	141/3918	468/18723	1.32e-06	4.22e-05	141
GO:1903312	Colorectum	AD	negative regulation of mRNA metabolic process	37/3918	92/18723	1.95e-05	4.01e-04	37
GO:1902369	Colorectum	AD	negative regulation of RNA catabolic process	30/3918	75/18723	1.30e-04	1.87e-03	30
GO:0000956	Colorectum	AD	nuclear-transcribed mRNA catabolic process	40/3918	112/18723	2.11e-04	2.79e-03	40
GO:1902373	Colorectum	AD	negative regulation of mRNA catabolic process	24/3918	63/18723	1.34e-03	1.17e-02	24
GO:0006414	Colorectum	AD	translational elongation	21/3918	55/18723	2.53e-03	1.93e-02	21
GO:19033112	Colorectum	MSS	regulation of mRNA metabolic process	115/3467	288/18723	1.23e-17	6.41e-15	115
GO:00064012	Colorectum	MSS	RNA catabolic process	102/3467	278/18723	5.07e-13	1.02e-10	102
GO:00064022	Colorectum	MSS	mRNA catabolic process	89/3467	232/18723	8.70e-13	1.60e-10	89

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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

SECISBP2

SNV

Missense_Mutation

rs147681365

c.1720N>A

p.Glu574Lys

p.E574K

Q96T21

protein_coding

tolerated(0.7)

benign(0.01)

TCGA-BH-A18G-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SECISBP2

SNV

Missense_Mutation

c.92N>G

p.Asn31Ser

p.N31S

Q96T21

protein_coding

tolerated(0.44)

benign(0.007)

TCGA-E9-A1RE-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Hormone Therapy

tamoxiphen

SECISBP2

SNV

Missense_Mutation

novel

c.2057N>C

p.Leu686Pro

p.L686P

Q96T21

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-GM-A3NY-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

SECISBP2

insertion

Nonsense_Mutation

novel

c.572_573insTAGCTCCGGAAATTAACAGAAACATTTGCTGGAAGGAGG

p.Ser191_Asp192insSerSerGlyAsnTerGlnLysHisLeuLeuGluGlyGly

p.S191_D192insSSGN*QKHLLEGG

Q96T21

protein_coding

TCGA-A8-A09C-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SECISBP2

SNV

Missense_Mutation

novel

c.158N>C

p.Phe53Ser

p.F53S

Q96T21

protein_coding

tolerated(0.06)

benign(0.348)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

SECISBP2

SNV

Missense_Mutation

novel

c.2011N>T

p.Arg671Cys

p.R671C

Q96T21

protein_coding

deleterious(0)

possibly_damaging(0.906)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

SECISBP2

SNV

Missense_Mutation

c.2464N>A

p.Glu822Lys

p.E822K

Q96T21

protein_coding

tolerated(1)

benign(0.02)

TCGA-DG-A2KK-01

Cervix

cervical & endocervical cancer

Female

<65

III/IV

Chemotherapy

cisplatin

SECISBP2

SNV

Missense_Mutation

c.1863N>G

p.Phe621Leu

p.F621L

Q96T21

protein_coding

tolerated(1)

benign(0)

TCGA-EX-A69M-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

SECISBP2

SNV

Missense_Mutation

c.2146G>A

p.Asp716Asn

p.D716N

Q96T21

protein_coding

tolerated(0.05)

probably_damaging(0.999)

TCGA-MY-A5BD-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

SECISBP2

insertion

In_Frame_Ins

novel

c.1619_1633dupGGCAAGAGAGAAAGC

p.Arg540_Lys544dup

p.R540_K544dup

Q96T21

protein_coding

TCGA-JW-AAVH-01

Cervix

cervical & endocervical cancer

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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