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: FBLN1

Gene summary for FBLN1

Gene summary.

Gene information	Species	Human
	Gene symbol	FBLN1
	Gene ID	2192
	Gene name	fibulin 1
	Gene Alias	FBLN
	Cytomap	22q13.31
	Gene Type	protein-coding
	GO ID	GO:0000003
	UniProtAcc	P23142

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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
2192	FBLN1	GSM6177620_NYU_UCEC1_lib3_lib3	Human	Endometrium	EEC	1.22e-54	-1.14e+00	-0.1883
2192	FBLN1	GSM6177621_NYU_UCEC2_lib1_lib1	Human	Endometrium	EEC	1.10e-59	3.36e-01	-0.1934
2192	FBLN1	GSM6177622_NYU_UCEC3_lib1_lib1	Human	Endometrium	EEC	1.18e-99	-1.27e+00	-0.1917
2192	FBLN1	GSM6177622_NYU_UCEC3_lib2_lib2	Human	Endometrium	EEC	1.05e-82	-1.29e+00	-0.1916
2192	FBLN1	GSM6177623_NYU_UCEC3_Vis	Human	Endometrium	EEC	2.09e-34	-7.58e-01	-0.1269
2192	FBLN1	LZE4T	Human	Esophagus	ESCC	2.65e-06	-4.72e-01	0.0811
2192	FBLN1	LZE5T	Human	Esophagus	ESCC	1.01e-02	-3.79e-01	0.0514
2192	FBLN1	LZE8T	Human	Esophagus	ESCC	3.14e-02	-4.15e-01	0.067
2192	FBLN1	LZE20T	Human	Esophagus	ESCC	1.31e-04	-2.59e-01	0.0662
2192	FBLN1	LZE22D1	Human	Esophagus	HGIN	1.66e-02	-4.28e-01	0.0595
2192	FBLN1	LZE22T	Human	Esophagus	ESCC	2.55e-05	-5.66e-02	0.068
2192	FBLN1	LZE24T	Human	Esophagus	ESCC	1.82e-07	-4.72e-01	0.0596
2192	FBLN1	LZE6T	Human	Esophagus	ESCC	1.21e-03	-4.32e-01	0.0845
2192	FBLN1	P2T-E	Human	Esophagus	ESCC	3.73e-50	1.33e+00	0.1177
2192	FBLN1	P4T-E	Human	Esophagus	ESCC	1.41e-12	1.17e+00	0.1323
2192	FBLN1	P8T-E	Human	Esophagus	ESCC	1.81e-47	1.69e+00	0.0889
2192	FBLN1	P9T-E	Human	Esophagus	ESCC	5.04e-12	1.35e+00	0.1131
2192	FBLN1	P10T-E	Human	Esophagus	ESCC	4.09e-07	3.45e-01	0.116
2192	FBLN1	P11T-E	Human	Esophagus	ESCC	4.62e-07	1.35e+00	0.1426
2192	FBLN1	P12T-E	Human	Esophagus	ESCC	1.07e-46	1.55e+00	0.1122

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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
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:004206010	Cervix	CC	wound healing	109/2311	422/18723	1.84e-14	1.57e-11	109
GO:001081010	Cervix	CC	regulation of cell-substrate adhesion	69/2311	221/18723	8.57e-14	5.69e-11	69
GO:00315898	Cervix	CC	cell-substrate adhesion	96/2311	363/18723	1.48e-13	8.85e-11	96
GO:005254710	Cervix	CC	regulation of peptidase activity	112/2311	461/18723	6.70e-13	3.08e-10	112
GO:002260410	Cervix	CC	regulation of cell morphogenesis	84/2311	309/18723	1.00e-12	4.29e-10	84
GO:004586210	Cervix	CC	positive regulation of proteolysis	95/2311	372/18723	1.84e-12	6.86e-10	95
GO:001095210	Cervix	CC	positive regulation of peptidase activity	54/2311	197/18723	8.06e-09	6.99e-07	54
GO:00071626	Cervix	CC	negative regulation of cell adhesion	72/2311	303/18723	2.36e-08	1.70e-06	72
GO:19000249	Cervix	CC	regulation of substrate adhesion-dependent cell spreading	23/2311	57/18723	8.94e-08	5.04e-06	23
GO:00107699	Cervix	CC	regulation of cell morphogenesis involved in differentiation	31/2311	96/18723	2.43e-07	1.05e-05	31
GO:00344469	Cervix	CC	substrate adhesion-dependent cell spreading	32/2311	108/18723	1.36e-06	4.55e-05	32
GO:004593610	Cervix	CC	negative regulation of phosphate metabolic process	88/2311	441/18723	2.92e-06	8.27e-05	88
GO:005087810	Cervix	CC	regulation of body fluid levels	78/2311	379/18723	3.20e-06	8.77e-05	78
GO:001056310	Cervix	CC	negative regulation of phosphorus metabolic process	88/2311	442/18723	3.21e-06	8.77e-05	88
GO:004232610	Cervix	CC	negative regulation of phosphorylation	77/2311	385/18723	1.09e-05	2.38e-04	77
GO:00512713	Cervix	CC	negative regulation of cellular component movement	73/2311	367/18723	2.22e-05	3.95e-04	73
GO:000193310	Cervix	CC	negative regulation of protein phosphorylation	69/2311	342/18723	2.29e-05	4.01e-04	69
GO:00400133	Cervix	CC	negative regulation of locomotion	76/2311	391/18723	3.47e-05	5.60e-04	76
GO:20001463	Cervix	CC	negative regulation of cell motility	71/2311	359/18723	3.47e-05	5.60e-04	71
GO:00108122	Cervix	CC	negative regulation of cell-substrate adhesion	21/2311	68/18723	4.35e-05	6.66e-04	21

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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

FBLN1

SNV

Missense_Mutation

rs752324735

c.1679A>C

p.Tyr560Ser

p.Y560S

P23142

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-A2-A1FX-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

taxotere

FBLN1

SNV

Missense_Mutation

c.1905C>A

p.Asp635Glu

p.D635E

P23142

protein_coding

tolerated(0.17)

benign(0.081)

TCGA-D8-A147-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicine

FBLN1

SNV

Missense_Mutation

c.1679A>G

p.Tyr560Cys

p.Y560C

P23142

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-D8-A1XK-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicine+cyclophosphamide

FBLN1

SNV

Missense_Mutation

rs749073587

c.482N>T

p.Thr161Met

p.T161M

P23142

protein_coding

tolerated(0.13)

benign(0.003)

TCGA-E9-A22A-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

tamoxiphen

FBLN1

insertion

Nonsense_Mutation

novel

c.751_752insCCAGATGTTAGATGTTTTATCTCTCCGTCTTTTATCT

p.Gly251AlafsTer4

p.G251Afs*4

P23142

protein_coding

TCGA-BH-A0AY-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

FBLN1

SNV

Missense_Mutation

novel

c.1027N>T

p.Arg343Cys

p.R343C

P23142

protein_coding

deleterious(0)

probably_damaging(0.992)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

FBLN1

SNV

Missense_Mutation

novel

c.1512N>A

p.Ser504Arg

p.S504R

P23142

protein_coding

deleterious(0)

probably_damaging(0.997)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

FBLN1

SNV

Missense_Mutation

c.1788N>G

p.Ile596Met

p.I596M

P23142

protein_coding

deleterious(0.02)

possibly_damaging(0.572)

TCGA-JW-A5VL-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

FBLN1

SNV

Missense_Mutation

rs200901023

c.1721C>T

p.Thr574Met

p.T574M

P23142

protein_coding

tolerated(0.06)

probably_damaging(0.993)

TCGA-AA-3678-01

Colorectum

colon adenocarcinoma

Female

<65

III/IV

Chemotherapy

folinic

FBLN1

SNV

Missense_Mutation

rs759317468

c.826N>A

p.Asp276Asn

p.D276N

P23142

protein_coding

tolerated(0.4)

benign(0.044)

TCGA-AA-A00N-01

Colorectum

colon adenocarcinoma

Male

>=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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