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

Home

Download

Statistics

Help

Contact

	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: ORMDL3

Gene summary for ORMDL3

Gene summary.

Gene information	Species	Human
	Gene symbol	ORMDL3
	Gene ID	94103
	Gene name	ORMDL sphingolipid biosynthesis regulator 3
	Gene Alias	ORMDL3
	Cytomap	17q21.1
	Gene Type	protein-coding
	GO ID	GO:0001783
	UniProtAcc	A0A024R1W6

Top

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
94103	ORMDL3	GSM4909282	Human	Breast	IDC	1.93e-02	-8.32e-02	-0.0288
94103	ORMDL3	GSM4909290	Human	Breast	IDC	7.80e-10	4.03e-01	0.2096
94103	ORMDL3	GSM4909291	Human	Breast	IDC	1.20e-50	1.07e+00	0.1753
94103	ORMDL3	GSM4909292	Human	Breast	IDC	8.53e-12	9.14e-01	0.1236
94103	ORMDL3	GSM4909294	Human	Breast	IDC	3.01e-10	4.55e-01	0.2022
94103	ORMDL3	GSM4909296	Human	Breast	IDC	2.80e-02	-1.03e-01	0.1524
94103	ORMDL3	GSM4909319	Human	Breast	IDC	3.47e-05	-5.03e-02	0.1563
94103	ORMDL3	NCCBC14	Human	Breast	DCIS	3.25e-36	1.00e+00	0.2021
94103	ORMDL3	NCCBC5	Human	Breast	DCIS	1.00e-09	4.30e-01	0.2046
94103	ORMDL3	P1	Human	Breast	IDC	6.70e-04	-1.11e-02	0.1527
94103	ORMDL3	DCIS2	Human	Breast	DCIS	7.52e-35	1.57e-01	0.0085
94103	ORMDL3	HTA11_3410_2000001011	Human	Colorectum	AD	2.93e-06	1.99e-01	0.0155
94103	ORMDL3	HTA11_2487_2000001011	Human	Colorectum	SER	3.20e-11	4.05e-01	-0.1808
94103	ORMDL3	HTA11_2951_2000001011	Human	Colorectum	AD	9.45e-03	3.08e-01	0.0216
94103	ORMDL3	HTA11_1938_2000001011	Human	Colorectum	AD	5.57e-09	3.74e-01	-0.0811
94103	ORMDL3	HTA11_347_2000001011	Human	Colorectum	AD	6.20e-18	3.98e-01	-0.1954
94103	ORMDL3	HTA11_411_2000001011	Human	Colorectum	SER	1.21e-07	7.18e-01	-0.2602
94103	ORMDL3	HTA11_3361_2000001011	Human	Colorectum	AD	4.61e-05	3.12e-01	-0.1207
94103	ORMDL3	HTA11_83_2000001011	Human	Colorectum	SER	3.74e-02	2.03e-01	-0.1526
94103	ORMDL3	HTA11_696_2000001011	Human	Colorectum	AD	5.62e-18	4.48e-01	-0.1464

Page: 1 2 3 4 5 6 7

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
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
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.

Top

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).

Page: 1 2 3 4 5 6 7 8 9

Enriched GO biological processes.

GO ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	Count
GO:000989614	Breast	IDC	positive regulation of catabolic process	62/1434	492/18723	7.06e-05	1.42e-03	62
GO:005134814	Breast	IDC	negative regulation of transferase activity	39/1434	268/18723	7.89e-05	1.56e-03	39
GO:001921612	Breast	IDC	regulation of lipid metabolic process	45/1434	331/18723	1.21e-04	2.24e-03	45
GO:003133114	Breast	IDC	positive regulation of cellular catabolic process	54/1434	427/18723	1.85e-04	3.07e-03	54
GO:00468904	Breast	IDC	regulation of lipid biosynthetic process	26/1434	171/18723	5.92e-04	7.50e-03	26
GO:190382914	Breast	IDC	positive regulation of cellular protein localization	36/1434	276/18723	1.19e-03	1.28e-02	36
GO:00030125	Breast	IDC	muscle system process	50/1434	452/18723	5.52e-03	4.05e-02	50
GO:0070229	Breast	IDC	negative regulation of lymphocyte apoptotic process	7/1434	30/18723	6.48e-03	4.56e-02	7
GO:005134824	Breast	DCIS	negative regulation of transferase activity	39/1390	268/18723	4.02e-05	8.60e-04	39
GO:000989624	Breast	DCIS	positive regulation of catabolic process	61/1390	492/18723	5.32e-05	1.09e-03	61
GO:003133124	Breast	DCIS	positive regulation of cellular catabolic process	54/1390	427/18723	8.34e-05	1.58e-03	54
GO:001921621	Breast	DCIS	regulation of lipid metabolic process	43/1390	331/18723	2.37e-04	3.71e-03	43
GO:190382924	Breast	DCIS	positive regulation of cellular protein localization	37/1390	276/18723	3.40e-04	4.87e-03	37
GO:004689012	Breast	DCIS	regulation of lipid biosynthetic process	24/1390	171/18723	1.89e-03	1.81e-02	24
GO:000301212	Breast	DCIS	muscle system process	50/1390	452/18723	3.02e-03	2.57e-02	50
GO:0009896	Colorectum	AD	positive regulation of catabolic process	180/3918	492/18723	4.33e-16	1.94e-13	180
GO:0031331	Colorectum	AD	positive regulation of cellular catabolic process	156/3918	427/18723	4.68e-14	1.05e-11	156
GO:1903829	Colorectum	AD	positive regulation of cellular protein localization	110/3918	276/18723	4.58e-13	8.44e-11	110
GO:0010506	Colorectum	AD	regulation of autophagy	111/3918	317/18723	3.57e-09	2.35e-07	111
GO:1900180	Colorectum	AD	regulation of protein localization to nucleus	55/3918	136/18723	1.70e-07	7.34e-06	55

Page: 1 2 3 4 5 6 7 8 9 10

Enriched KEGG pathways.

Pathway ID

Tissue

Disease Stage

Description

Gene Ratio

Bg Ratio

pvalue

p.adjust

qvalue

Count

Page: 1

Top

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

Page: 1

Top

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.

Page: 1

Top

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

ORMDL3

SNV

Missense_Mutation

c.221N>T

p.Thr74Ile

p.T74I

Q8N138

protein_coding

deleterious(0)

probably_damaging(0.998)

TCGA-A7-A0CD-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

ORMDL3

SNV

Missense_Mutation

novel

c.373N>A

p.Val125Met

p.V125M

Q8N138

protein_coding

tolerated(0.05)

benign(0.021)

TCGA-A7-A3J0-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

anastrazole

ORMDL3

SNV

Missense_Mutation

c.398G>A

p.Ser133Asn

p.S133N

Q8N138

protein_coding

deleterious(0.04)

benign(0.171)

TCGA-AP-A0LI-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

III/IV

Chemotherapy

paclitaxel

ORMDL3

SNV

Missense_Mutation

novel

c.79G>A

p.Val27Met

p.V27M

Q8N138

protein_coding

tolerated(0.07)

benign(0.214)

TCGA-AX-A2HG-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

ORMDL3

SNV

Missense_Mutation

rs759149603

c.142G>A

p.Val48Ile

p.V48I

Q8N138

protein_coding

tolerated(0.11)

benign(0.339)

TCGA-B5-A1MX-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Hormone Therapy

megace

ORMDL3

SNV

Missense_Mutation

novel

c.260A>C

p.Glu87Ala

p.E87A

Q8N138

protein_coding

deleterious(0)

possibly_damaging(0.779)

TCGA-B5-A3FA-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

ORMDL3

SNV

Missense_Mutation

novel

c.62N>A

p.Gly21Asp

p.G21D

Q8N138

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-SJ-A6ZI-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

ORMDL3

SNV

Missense_Mutation

novel

c.286A>T

p.Thr96Ser

p.T96S

Q8N138

protein_coding

tolerated(0.11)

probably_damaging(0.992)

TCGA-95-7043-01

Lung

lung adenocarcinoma

Female

<65

I/II

Unknown

ORMDL3

SNV

Missense_Mutation

novel

c.223N>A

p.Pro75Thr

p.P75T

Q8N138

protein_coding

tolerated(0.51)

probably_damaging(0.999)

TCGA-43-3920-01

Lung

lung squamous cell carcinoma

Male

>=65

I/II

Unknown

ORMDL3

SNV

Missense_Mutation

rs139204234

c.197N>T

p.Thr66Met

p.T66M

Q8N138

protein_coding

tolerated(0.24)

possibly_damaging(0.885)

TCGA-BA-6869-01

Oral cavity

head & neck squamous cell carcinoma

Male

<65

III/IV

Unknown

Page: 1 2

Top

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

Page: 1