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: KDM5A

Gene summary for KDM5A

Gene summary.

Gene information	Species	Human
	Gene symbol	KDM5A
	Gene ID	5927
	Gene name	lysine demethylase 5A
	Gene Alias	RBBP-2
	Cytomap	12p13.33
	Gene Type	protein-coding
	GO ID	GO:0000003
	UniProtAcc	P29375

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
5927	KDM5A	CA_HPV_1	Human	Cervix	CC	6.57e-04	-4.03e-02	0.0264
5927	KDM5A	CCI_2	Human	Cervix	CC	1.05e-02	7.11e-01	0.5249
5927	KDM5A	CCI_3	Human	Cervix	CC	7.68e-10	1.00e+00	0.516
5927	KDM5A	L1	Human	Cervix	CC	1.60e-05	-3.24e-01	0.0802
5927	KDM5A	LZE2T	Human	Esophagus	ESCC	2.35e-07	7.27e-01	0.082
5927	KDM5A	LZE4T	Human	Esophagus	ESCC	3.15e-14	3.95e-01	0.0811
5927	KDM5A	LZE7T	Human	Esophagus	ESCC	2.61e-07	7.25e-01	0.0667
5927	KDM5A	LZE8T	Human	Esophagus	ESCC	3.38e-13	5.93e-01	0.067
5927	KDM5A	LZE20T	Human	Esophagus	ESCC	1.00e-04	3.68e-01	0.0662
5927	KDM5A	LZE22T	Human	Esophagus	ESCC	1.23e-02	2.99e-01	0.068
5927	KDM5A	LZE24T	Human	Esophagus	ESCC	3.92e-09	4.73e-01	0.0596
5927	KDM5A	LZE21T	Human	Esophagus	ESCC	3.23e-05	3.43e-01	0.0655
5927	KDM5A	P1T-E	Human	Esophagus	ESCC	7.68e-08	7.55e-01	0.0875
5927	KDM5A	P2T-E	Human	Esophagus	ESCC	1.53e-54	1.08e+00	0.1177
5927	KDM5A	P4T-E	Human	Esophagus	ESCC	3.96e-37	1.04e+00	0.1323
5927	KDM5A	P5T-E	Human	Esophagus	ESCC	1.70e-22	3.51e-01	0.1327
5927	KDM5A	P8T-E	Human	Esophagus	ESCC	5.30e-30	6.96e-01	0.0889
5927	KDM5A	P9T-E	Human	Esophagus	ESCC	2.44e-08	2.24e-01	0.1131
5927	KDM5A	P10T-E	Human	Esophagus	ESCC	6.36e-35	7.71e-01	0.116
5927	KDM5A	P11T-E	Human	Esophagus	ESCC	1.62e-12	5.50e-01	0.1426

Page: 1 2 3 4 5 6 7 8

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
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.

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:00513469	Cervix	CC	negative regulation of hydrolase activity	81/2311	379/18723	4.27e-07	1.67e-05	81
GO:00614588	Cervix	CC	reproductive system development	87/2311	427/18723	1.37e-06	4.55e-05	87
GO:00486088	Cervix	CC	reproductive structure development	86/2311	424/18723	1.90e-06	5.97e-05	86
GO:00485118	Cervix	CC	rhythmic process	65/2311	298/18723	2.79e-06	8.04e-05	65
GO:00510904	Cervix	CC	regulation of DNA-binding transcription factor activity	87/2311	440/18723	4.85e-06	1.22e-04	87
GO:00063257	Cervix	CC	chromatin organization	78/2311	409/18723	5.40e-05	8.02e-04	78
GO:00076238	Cervix	CC	circadian rhythm	46/2311	210/18723	6.76e-05	9.60e-04	46
GO:00165705	Cervix	CC	histone modification	84/2311	463/18723	1.70e-04	2.01e-03	84
GO:00310565	Cervix	CC	regulation of histone modification	33/2311	152/18723	7.97e-04	7.00e-03	33
GO:00329226	Cervix	CC	circadian regulation of gene expression	18/2311	68/18723	1.18e-03	9.56e-03	18
GO:00063381	Cervix	CC	chromatin remodeling	45/2311	255/18723	8.33e-03	4.30e-02	45
GO:001657015	Esophagus	ESCC	histone modification	323/8552	463/18723	2.61e-26	7.88e-24	323
GO:003105614	Esophagus	ESCC	regulation of histone modification	106/8552	152/18723	1.52e-09	3.55e-08	106
GO:000632517	Esophagus	ESCC	chromatin organization	240/8552	409/18723	6.52e-08	1.14e-06	240
GO:00356015	Esophagus	ESCC	protein deacylation	79/8552	112/18723	8.30e-08	1.42e-06	79
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:00987325	Esophagus	ESCC	macromolecule deacylation	80/8552	116/18723	3.19e-07	4.50e-06	80
GO:00165754	Esophagus	ESCC	histone deacetylation	60/8552	82/18723	3.85e-07	5.32e-06	60
GO:00510908	Esophagus	ESCC	regulation of DNA-binding transcription factor activity	252/8552	440/18723	5.22e-07	6.97e-06	252

Page: 1 2 3 4 5 6 7 8 9 10 11

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

TF	Cell Type	Tissue	Disease Stage	Target Gene	RSS	Regulon Activity
KDM5A	TREG	Esophagus	ESCC	AURKA,BCHE,RP13-516M14.4, etc.	1.66e-01
KDM5A	BAS	Skin	SCCIS	SLC12A8,ANO9,TSNARE1, etc.	1.84e-01
KDM5A	STM	Thyroid	HT	FAM118A,GPATCH2L,TMEM87B, etc.	6.93e-01

∗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

KDM5A

SNV

Missense_Mutation

c.3908N>T

p.Ala1303Val

p.A1303V

P29375

protein_coding

deleterious(0.04)

possibly_damaging(0.604)

TCGA-A8-A079-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Chemotherapy

5-fluorouracil

KDM5A

SNV

Missense_Mutation

rs776901877

c.3045N>G

p.Ser1015Arg

p.S1015R

P29375

protein_coding

deleterious(0.03)

benign(0.189)

TCGA-A8-A095-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

5-fluorouracil

KDM5A

SNV

Missense_Mutation

c.5042N>C

p.Leu1681Pro

p.L1681P

P29375

protein_coding

deleterious_low_confidence(0.01)

possibly_damaging(0.478)

TCGA-A8-A09Z-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

KDM5A

SNV

Missense_Mutation

c.4082C>G

p.Ala1361Gly

p.A1361G

P29375

protein_coding

tolerated(0.45)

benign(0)

TCGA-A8-A0AB-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

5-fluorouracil

KDM5A

SNV

Missense_Mutation

novel

c.791N>A

p.Arg264Gln

p.R264Q

P29375

protein_coding

tolerated(0.34)

benign(0.03)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

KDM5A

SNV

Missense_Mutation

c.349C>A

p.Leu117Met

p.L117M

P29375

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-AN-A0AR-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

KDM5A

SNV

Missense_Mutation

rs748024384

c.1570G>A

p.Glu524Lys

p.E524K

P29375

protein_coding

deleterious(0)

benign(0.327)

TCGA-AN-A0FK-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Unknown

KDM5A

SNV

Missense_Mutation

c.2815G>C

p.Glu939Gln

p.E939Q

P29375

protein_coding

deleterious(0)

benign(0.217)

TCGA-AN-A0FL-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

KDM5A

SNV

Missense_Mutation

c.769G>C

p.Asp257His

p.D257H

P29375

protein_coding

deleterious(0.02)

benign(0.011)

TCGA-D8-A1JA-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

adriamycin

KDM5A

SNV

Missense_Mutation

c.659N>A

p.Arg220His

p.R220H

P29375

protein_coding

deleterious(0.02)

possibly_damaging(0.886)

TCGA-D8-A27W-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

doxorubicine+cyclophosphamide

Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18

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
5927	KDM5A	CLINICALLY ACTIONABLE, ENZYME, NUCLEAR HORMONE RECEPTOR		BDBM50158803
5927	KDM5A	CLINICALLY ACTIONABLE, ENZYME, NUCLEAR HORMONE RECEPTOR		US9714230, 46
5927	KDM5A	CLINICALLY ACTIONABLE, ENZYME, NUCLEAR HORMONE RECEPTOR		1190312-92-5
5927	KDM5A	CLINICALLY ACTIONABLE, ENZYME, NUCLEAR HORMONE RECEPTOR		US10022354, Example 152
5927	KDM5A	CLINICALLY ACTIONABLE, ENZYME, NUCLEAR HORMONE RECEPTOR		AKOS020330481
5927	KDM5A	CLINICALLY ACTIONABLE, ENZYME, NUCLEAR HORMONE RECEPTOR		BDBM50158794
5927	KDM5A	CLINICALLY ACTIONABLE, ENZYME, NUCLEAR HORMONE RECEPTOR	inhibitor	178103606
5927	KDM5A	CLINICALLY ACTIONABLE, ENZYME, NUCLEAR HORMONE RECEPTOR		US10174026, Example 2
5927	KDM5A	CLINICALLY ACTIONABLE, ENZYME, NUCLEAR HORMONE RECEPTOR		US10022354, Example 151
5927	KDM5A	CLINICALLY ACTIONABLE, ENZYME, NUCLEAR HORMONE RECEPTOR		US10174026, Example 99

Page: 1 2 3