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: LSM10

Gene summary for LSM10

Gene summary.

Gene information	Species	Human
	Gene symbol	LSM10
	Gene ID	84967
	Gene name	LSM10, U7 small nuclear RNA associated
	Gene Alias	MST074
	Cytomap	1p34.3
	Gene Type	protein-coding
	GO ID	GO:0000082
	UniProtAcc	Q969L4

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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
84967	LSM10	LZE4T	Human	Esophagus	ESCC	1.97e-14	3.22e-01	0.0811
84967	LSM10	LZE7T	Human	Esophagus	ESCC	2.02e-09	5.26e-01	0.0667
84967	LSM10	LZE8T	Human	Esophagus	ESCC	2.87e-02	2.44e-01	0.067
84967	LSM10	LZE20T	Human	Esophagus	ESCC	4.59e-13	2.97e-01	0.0662
84967	LSM10	LZE22D1	Human	Esophagus	HGIN	1.38e-02	1.99e-01	0.0595
84967	LSM10	LZE22T	Human	Esophagus	ESCC	2.61e-04	2.96e-01	0.068
84967	LSM10	LZE24T	Human	Esophagus	ESCC	1.30e-26	6.95e-01	0.0596
84967	LSM10	LZE6T	Human	Esophagus	ESCC	3.38e-03	4.61e-01	0.0845
84967	LSM10	P1T-E	Human	Esophagus	ESCC	6.35e-10	3.86e-01	0.0875
84967	LSM10	P2T-E	Human	Esophagus	ESCC	1.70e-25	5.35e-01	0.1177
84967	LSM10	P4T-E	Human	Esophagus	ESCC	3.12e-30	7.90e-01	0.1323
84967	LSM10	P5T-E	Human	Esophagus	ESCC	1.22e-28	6.40e-01	0.1327
84967	LSM10	P8T-E	Human	Esophagus	ESCC	1.75e-15	3.55e-01	0.0889
84967	LSM10	P9T-E	Human	Esophagus	ESCC	7.87e-17	4.23e-01	0.1131
84967	LSM10	P10T-E	Human	Esophagus	ESCC	5.57e-29	6.06e-01	0.116
84967	LSM10	P11T-E	Human	Esophagus	ESCC	9.28e-10	5.15e-01	0.1426
84967	LSM10	P12T-E	Human	Esophagus	ESCC	1.16e-27	5.13e-01	0.1122
84967	LSM10	P15T-E	Human	Esophagus	ESCC	5.00e-29	5.77e-01	0.1149
84967	LSM10	P16T-E	Human	Esophagus	ESCC	2.10e-16	3.00e-01	0.1153
84967	LSM10	P17T-E	Human	Esophagus	ESCC	6.41e-09	5.04e-01	0.1278

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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:000838026	Esophagus	HGIN	RNA splicing	160/2587	434/18723	3.74e-34	1.12e-30	160
GO:000734610	Esophagus	HGIN	regulation of mitotic cell cycle	98/2587	457/18723	4.39e-06	1.42e-04	98
GO:00447729	Esophagus	HGIN	mitotic cell cycle phase transition	89/2587	424/18723	2.80e-05	7.21e-04	89
GO:19019906	Esophagus	HGIN	regulation of mitotic cell cycle phase transition	65/2587	299/18723	1.12e-04	2.36e-03	65
GO:20000456	Esophagus	HGIN	regulation of G1/S transition of mitotic cell cycle	36/2587	142/18723	1.74e-04	3.35e-03	36
GO:00000827	Esophagus	HGIN	G1/S transition of mitotic cell cycle	48/2587	214/18723	3.97e-04	6.07e-03	48
GO:00448437	Esophagus	HGIN	cell cycle G1/S phase transition	52/2587	241/18723	6.19e-04	8.58e-03	52
GO:19028065	Esophagus	HGIN	regulation of cell cycle G1/S phase transition	39/2587	168/18723	6.60e-04	9.03e-03	39
GO:00311243	Esophagus	HGIN	mRNA 3'-end processing	18/2587	62/18723	1.37e-03	1.61e-02	18
GO:004593110	Esophagus	HGIN	positive regulation of mitotic cell cycle	28/2587	121/18723	3.72e-03	3.39e-02	28
GO:19019876	Esophagus	HGIN	regulation of cell cycle phase transition	72/2587	390/18723	5.78e-03	4.70e-02	72
GO:0008380111	Esophagus	ESCC	RNA splicing	336/8552	434/18723	1.74e-42	3.67e-39	336
GO:004477216	Esophagus	ESCC	mitotic cell cycle phase transition	281/8552	424/18723	4.63e-18	4.45e-16	281
GO:000734615	Esophagus	ESCC	regulation of mitotic cell cycle	293/8552	457/18723	8.00e-16	5.64e-14	293
GO:190198713	Esophagus	ESCC	regulation of cell cycle phase transition	242/8552	390/18723	3.86e-11	1.26e-09	242
GO:190199013	Esophagus	ESCC	regulation of mitotic cell cycle phase transition	191/8552	299/18723	1.35e-10	3.94e-09	191
GO:004578710	Esophagus	ESCC	positive regulation of cell cycle	196/8552	313/18723	9.27e-10	2.24e-08	196
GO:004593116	Esophagus	ESCC	positive regulation of mitotic cell cycle	83/8552	121/18723	2.78e-07	4.08e-06	83
GO:000008214	Esophagus	ESCC	G1/S transition of mitotic cell cycle	134/8552	214/18723	4.04e-07	5.55e-06	134
GO:004484314	Esophagus	ESCC	cell cycle G1/S phase transition	148/8552	241/18723	5.68e-07	7.48e-06	148

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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

LSM10

SNV

Missense_Mutation

rs750020323

c.124C>T

p.Arg42Cys

p.R42C

Q969L4

protein_coding

tolerated(0.07)

possibly_damaging(0.825)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

LSM10

insertion

In_Frame_Ins

novel

c.51_52insTCTCAAGTGCTC

p.Leu17_Ile18insSerGlnValLeu

p.L17_I18insSQVL

Q969L4

protein_coding

TCGA-AO-A03T-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cyclophosphamide

LSM10

SNV

Missense_Mutation

rs749640330

c.238N>T

p.Arg80Cys

p.R80C

Q969L4

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-AA-3492-01

Colorectum

colon adenocarcinoma

Female

>=65

I/II

Unknown

LSM10

SNV

Missense_Mutation

rs748038554

c.5C>T

p.Ala2Val

p.A2V

Q969L4

protein_coding

tolerated(0.23)

benign(0.072)

TCGA-AZ-4315-01

Colorectum

colon adenocarcinoma

Male

<65

I/II

Unknown

LSM10

SNV

Missense_Mutation

rs748038554

c.5N>T

p.Ala2Val

p.A2V

Q969L4

protein_coding

tolerated(0.23)

benign(0.072)

TCGA-A5-A0G1-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

LSM10

SNV

Missense_Mutation

rs752469850

c.340C>T

p.Arg114Trp

p.R114W

Q969L4

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-AP-A051-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

LSM10

SNV

Missense_Mutation

novel

c.139N>A

p.Asp47Asn

p.D47N

Q969L4

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-AP-A0LM-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

cisplatin

LSM10

SNV

Missense_Mutation

rs756588557

c.239G>A

p.Arg80His

p.R80H

Q969L4

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-B5-A11E-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

LSM10

SNV

Missense_Mutation

novel

c.263N>C

p.Val88Ala

p.V88A

Q969L4

protein_coding

deleterious(0)

benign(0.214)

TCGA-B5-A3FA-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

LSM10

SNV

Missense_Mutation

rs775621505

c.80G>A

p.Arg27Gln

p.R27Q

Q969L4

protein_coding

tolerated(0.83)

benign(0)

TCGA-BG-A2L7-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Chemotherapy

carboplatin

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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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