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: FSTL3

Gene summary for FSTL3

Gene summary.

Gene information	Species	Human
	Gene symbol	FSTL3
	Gene ID	10272
	Gene name	follistatin like 3
	Gene Alias	FLRG
	Cytomap	19p13.3
	Gene Type	protein-coding
	GO ID	GO:0000003
	UniProtAcc	A0A024R1Y8

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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
10272	FSTL3	LZE24T	Human	Esophagus	ESCC	1.11e-12	6.66e-01	0.0596
10272	FSTL3	P4T-E	Human	Esophagus	ESCC	4.08e-08	3.66e-01	0.1323
10272	FSTL3	P5T-E	Human	Esophagus	ESCC	1.27e-22	4.86e-01	0.1327
10272	FSTL3	P8T-E	Human	Esophagus	ESCC	4.14e-03	2.10e-01	0.0889
10272	FSTL3	P9T-E	Human	Esophagus	ESCC	7.10e-04	3.75e-01	0.1131
10272	FSTL3	P10T-E	Human	Esophagus	ESCC	1.35e-10	3.63e-01	0.116
10272	FSTL3	P11T-E	Human	Esophagus	ESCC	9.86e-49	2.27e+00	0.1426
10272	FSTL3	P12T-E	Human	Esophagus	ESCC	1.56e-02	2.51e-01	0.1122
10272	FSTL3	P16T-E	Human	Esophagus	ESCC	1.98e-02	2.20e-02	0.1153
10272	FSTL3	P17T-E	Human	Esophagus	ESCC	5.47e-16	1.12e+00	0.1278
10272	FSTL3	P19T-E	Human	Esophagus	ESCC	9.67e-20	2.07e+00	0.1662
10272	FSTL3	P20T-E	Human	Esophagus	ESCC	4.76e-03	3.04e-01	0.1124
10272	FSTL3	P21T-E	Human	Esophagus	ESCC	1.02e-20	7.16e-01	0.1617
10272	FSTL3	P22T-E	Human	Esophagus	ESCC	1.89e-06	1.41e-01	0.1236
10272	FSTL3	P23T-E	Human	Esophagus	ESCC	3.75e-02	2.17e-01	0.108
10272	FSTL3	P24T-E	Human	Esophagus	ESCC	4.41e-20	9.62e-01	0.1287
10272	FSTL3	P26T-E	Human	Esophagus	ESCC	5.25e-04	2.24e-01	0.1276
10272	FSTL3	P28T-E	Human	Esophagus	ESCC	1.30e-16	4.04e-01	0.1149
10272	FSTL3	P30T-E	Human	Esophagus	ESCC	1.57e-02	2.74e-01	0.137
10272	FSTL3	P31T-E	Human	Esophagus	ESCC	1.05e-03	2.07e-01	0.1251

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
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:0048732111	Esophagus	ESCC	gland development	269/8552	436/18723	7.81e-12	2.95e-10	269
GO:0030099111	Esophagus	ESCC	myeloid cell differentiation	232/8552	381/18723	1.22e-09	2.90e-08	232
GO:004578527	Esophagus	ESCC	positive regulation of cell adhesion	255/8552	437/18723	5.07e-08	9.11e-07	255
GO:0061458110	Esophagus	ESCC	reproductive system development	247/8552	427/18723	2.24e-07	3.42e-06	247
GO:004860818	Esophagus	ESCC	reproductive structure development	245/8552	424/18723	2.82e-07	4.14e-06	245
GO:000257317	Esophagus	ESCC	myeloid leukocyte differentiation	128/8552	208/18723	2.75e-06	3.15e-05	128
GO:000150317	Esophagus	ESCC	ossification	232/8552	408/18723	3.00e-06	3.40e-05	232
GO:00303239	Esophagus	ESCC	respiratory tube development	112/8552	181/18723	7.82e-06	7.69e-05	112
GO:00605417	Esophagus	ESCC	respiratory system development	123/8552	203/18723	1.26e-05	1.15e-04	123
GO:00303249	Esophagus	ESCC	lung development	109/8552	177/18723	1.40e-05	1.27e-04	109
GO:001003827	Esophagus	ESCC	response to metal ion	208/8552	373/18723	5.02e-05	3.90e-04	208
GO:000717810	Esophagus	ESCC	transmembrane receptor protein serine/threonine kinase signaling pathway	195/8552	355/18723	2.58e-04	1.58e-03	195
GO:1903706110	Esophagus	ESCC	regulation of hemopoiesis	201/8552	367/18723	2.60e-04	1.58e-03	201
GO:002240720	Esophagus	ESCC	regulation of cell-cell adhesion	239/8552	448/18723	5.88e-04	3.19e-03	239
GO:000268316	Esophagus	ESCC	negative regulation of immune system process	231/8552	434/18723	8.48e-04	4.36e-03	231
GO:0045637111	Esophagus	ESCC	regulation of myeloid cell differentiation	118/8552	210/18723	1.35e-03	6.43e-03	118
GO:002240919	Esophagus	ESCC	positive regulation of cell-cell adhesion	155/8552	284/18723	1.50e-03	7.06e-03	155
GO:190210510	Esophagus	ESCC	regulation of leukocyte differentiation	152/8552	279/18723	1.82e-03	8.35e-03	152
GO:007124117	Esophagus	ESCC	cellular response to inorganic substance	125/8552	226/18723	2.17e-03	9.67e-03	125
GO:00022446	Esophagus	ESCC	hematopoietic progenitor cell differentiation	66/8552	114/18723	5.74e-03	2.13e-02	66

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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

FSTL3

SNV

Missense_Mutation

rs769239267

c.593N>T

p.Ala198Val

p.A198V

O95633

protein_coding

tolerated(0.21)

benign(0.106)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

FSTL3

SNV

Missense_Mutation

c.780N>C

p.Glu260Asp

p.E260D

O95633

protein_coding

tolerated_low_confidence(0.14)

benign(0.001)

TCGA-IR-A3LK-01

Cervix

cervical & endocervical cancer

Female

>=65

I/II

Chemotherapy

cisplatin

FSTL3

SNV

Missense_Mutation

c.780G>T

p.Glu260Asp

p.E260D

O95633

protein_coding

tolerated_low_confidence(0.14)

benign(0.001)

TCGA-CA-6717-01

Colorectum

colon adenocarcinoma

Male

<65

I/II

Chemotherapy

oxaliplatin

FSTL3

SNV

Missense_Mutation

novel

c.578T>C

p.Val193Ala

p.V193A

O95633

protein_coding

tolerated(0.05)

benign(0.278)

TCGA-AP-A1DK-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

FSTL3

SNV

Missense_Mutation

rs761509739

c.712C>T

p.Arg238Cys

p.R238C

O95633

protein_coding

deleterious(0)

probably_damaging(0.985)

TCGA-AP-A1DK-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

FSTL3

SNV

Missense_Mutation

novel

c.673N>A

p.Arg225Ser

p.R225S

O95633

protein_coding

deleterious(0)

probably_damaging(0.949)

TCGA-AP-A1DV-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

FSTL3

SNV

Missense_Mutation

novel

c.704N>A

p.Ile235Asn

p.I235N

O95633

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-AP-A1E0-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

paclitaxel

FSTL3

SNV

Missense_Mutation

novel

c.625G>A

p.Glu209Lys

p.E209K

O95633

protein_coding

tolerated(0.25)

benign(0.139)

TCGA-EO-A22U-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

FSTL3

SNV

Missense_Mutation

rs769455629

c.173N>A

p.Arg58Gln

p.R58Q

O95633

protein_coding

tolerated(0.54)

benign(0)

TCGA-39-5034-01

Lung

lung squamous cell carcinoma

Female

>=65

I/II

Unknown

FSTL3

SNV

Missense_Mutation

c.786N>A

p.Phe262Leu

p.F262L

O95633

protein_coding

deleterious_low_confidence(0.02)

benign(0.084)

TCGA-46-3766-01

Lung

lung squamous cell carcinoma

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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