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: USH1C

Gene summary for USH1C

Gene summary.

Gene information	Species	Human
	Gene symbol	USH1C
	Gene ID	10083
	Gene name	USH1 protein network component harmonin
	Gene Alias	AIE-75
	Cytomap	11p15.1
	Gene Type	protein-coding
	GO ID	GO:0000086
	UniProtAcc	A0A0S2Z4V1

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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
10083	USH1C	Pat18-B	Human	Stomach	GC	5.19e-05	2.46e-01	-0.0432
10083	USH1C	Pat19-B	Human	Stomach	GC	7.70e-07	2.98e-01	0.0826
10083	USH1C	Pat22-B	Human	Stomach	GC	7.46e-17	3.42e-01	-0.1042
10083	USH1C	Pat25-A	Human	Stomach	CAG with IM	9.43e-15	3.15e-01	-0.1648
10083	USH1C	Pat26-A	Human	Stomach	CSG	8.37e-20	3.28e-01	-0.2402
10083	USH1C	Pat28-A	Human	Stomach	CSG	5.55e-05	2.08e-01	-0.2594
10083	USH1C	SIM_1	Human	Stomach	SIM	1.71e-04	2.40e-01	0.3573
10083	USH1C	SIM_2	Human	Stomach	SIM	1.33e-05	2.04e-01	0.3139

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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
GC		CAG: Chronic atrophic gastritis
		CAG with IM: Chronic atrophic gastritis with intestinal metaplasia
		CSG: Chronic superficial gastritis
		GC: Gastric cancer
		SIM: Severe intestinal metaplasia
		WIM: Wild intestinal metaplasia
Liver		HCC: Hepatocellular carcinoma
		NAFLD: Non-alcoholic fatty liver disease

∗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:0007015	Colorectum	AD	actin filament organization	167/3918	442/18723	1.65e-16	7.94e-14	167
GO:0032535	Colorectum	AD	regulation of cellular component size	142/3918	383/18723	1.74e-13	3.41e-11	142
GO:0061572	Colorectum	AD	actin filament bundle organization	60/3918	161/18723	1.33e-06	4.23e-05	60
GO:0051017	Colorectum	AD	actin filament bundle assembly	58/3918	157/18723	2.74e-06	7.89e-05	58
GO:0032530	Colorectum	AD	regulation of microvillus organization	10/3918	13/18723	2.43e-05	4.69e-04	10
GO:0032528	Colorectum	AD	microvillus organization	14/3918	24/18723	6.90e-05	1.11e-03	14
GO:0060249	Colorectum	AD	anatomical structure homeostasis	94/3918	314/18723	9.37e-05	1.42e-03	94
GO:0001894	Colorectum	AD	tissue homeostasis	81/3918	268/18723	1.96e-04	2.62e-03	81
GO:0035315	Colorectum	AD	hair cell differentiation	21/3918	47/18723	2.14e-04	2.82e-03	21
GO:0042491	Colorectum	AD	inner ear auditory receptor cell differentiation	17/3918	38/18723	8.26e-04	8.13e-03	17
GO:0042490	Colorectum	AD	mechanoreceptor differentiation	24/3918	67/18723	3.48e-03	2.52e-02	24
GO:0048568	Colorectum	AD	embryonic organ development	112/3918	427/18723	4.60e-03	3.14e-02	112
GO:0009913	Colorectum	AD	epidermal cell differentiation	58/3918	202/18723	5.16e-03	3.42e-02	58
GO:0008544	Colorectum	AD	epidermis development	87/3918	324/18723	5.99e-03	3.76e-02	87
GO:0060119	Colorectum	AD	inner ear receptor cell development	17/3918	45/18723	7.10e-03	4.33e-02	17
GO:00070151	Colorectum	SER	actin filament organization	134/2897	442/18723	1.39e-15	5.70e-13	134
GO:00325351	Colorectum	SER	regulation of cellular component size	115/2897	383/18723	3.04e-13	1.10e-10	115
GO:00325301	Colorectum	SER	regulation of microvillus organization	10/2897	13/18723	1.41e-06	6.46e-05	10
GO:00325281	Colorectum	SER	microvillus organization	14/2897	24/18723	1.83e-06	7.80e-05	14
GO:00615721	Colorectum	SER	actin filament bundle organization	48/2897	161/18723	2.97e-06	1.19e-04	48

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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

USH1C

SNV

Missense_Mutation

c.502N>A

p.Gly168Ser

p.G168S

Q9Y6N9

protein_coding

deleterious(0)

probably_damaging(0.971)

TCGA-A1-A0SH-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

USH1C

SNV

Missense_Mutation

novel

c.1149N>C

p.Gln383His

p.Q383H

Q9Y6N9

protein_coding

tolerated_low_confidence(0.13)

possibly_damaging(0.679)

TCGA-A8-A08H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

USH1C

SNV

Missense_Mutation

c.370G>A

p.Asp124Asn

p.D124N

Q9Y6N9

protein_coding

deleterious(0.02)

possibly_damaging(0.813)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

USH1C

SNV

Missense_Mutation

rs201644053

c.2500N>A

p.Asp834Asn

p.D834N

Q9Y6N9

protein_coding

deleterious_low_confidence(0)

possibly_damaging(0.514)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

USH1C

SNV

Missense_Mutation

novel

c.1455N>T

p.Lys485Asn

p.K485N

Q9Y6N9

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.994)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

USH1C

SNV

Missense_Mutation

rs774988386

c.1754N>T

p.Ser585Phe

p.S585F

Q9Y6N9

protein_coding

deleterious_low_confidence(0.01)

benign(0.084)

TCGA-AR-A0TX-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

USH1C

SNV

Missense_Mutation

c.1954N>T

p.His652Tyr

p.H652Y

Q9Y6N9

protein_coding

tolerated_low_confidence(0.38)

benign(0)

TCGA-BH-A0HF-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

USH1C

SNV

Missense_Mutation

rs397517883

c.587G>A

p.Arg196Gln

p.R196Q

Q9Y6N9

protein_coding

tolerated(0.11)

benign(0.32)

TCGA-E2-A56Z-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

USH1C

SNV

Missense_Mutation

c.2281N>C

p.Glu761Gln

p.E761Q

Q9Y6N9

protein_coding

deleterious_low_confidence(0.01)

probably_damaging(0.991)

TCGA-EW-A1J5-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

USH1C

SNV

Missense_Mutation

c.2498N>G

p.Ile833Ser

p.I833S

Q9Y6N9

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.996)

TCGA-EW-A1P5-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

anastrozole

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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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